diff --git a/.gitignore b/.gitignore index 26d6373d..ab262161 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ dist dist-ssr *.local coverage +util/__pycache__/ diff --git a/public/catalog/haddock3.easy.yaml b/public/catalog/haddock3.easy.yaml index 831ea531..958997d9 100644 --- a/public/catalog/haddock3.easy.yaml +++ b/public/catalog/haddock3.easy.yaml @@ -14,18 +14,23 @@ global: schema: type: object properties: + run_dir: + title: Run directory + description: Folder to store the HADDOCK3 run + $comment: The new folder that will be created to save the HADDOCK3 run + type: string + format: uri-reference molecules: - title: Molecules + title: Input Molecules + description: The input molecules that will be used for docking. + $comment: Molecules must be provided in PDB format. These PDB files can be + single molecules or ensembles using the MODEL/ENDMDL statements. type: array minItems: 1 maxItems: 20 items: type: string format: uri-reference - run_dir: - title: Run directory - type: string - format: uri-reference cns_exec: title: Path to the CNS executable description: If not provided, HADDOCK3 will use the cns path configured during @@ -73,7 +78,6 @@ global: - slurm - torque queue: - default: '' title: Queue name description: Name of the batch queue to which jobs will be submitted $comment: Name of the batch queue to which jobs will be submitted. If not @@ -105,7 +109,6 @@ global: maximum: 9999 minimum: 1 required: - - molecules - run_dir additionalProperties: false uiSchema: @@ -129,6 +132,7 @@ global: ui:group: execution concat: ui:group: execution + tomlSchema: {} nodes: - id: clustfcc category: analysis @@ -165,6 +169,7 @@ nodes: uiSchema: executable: ui:widget: file + tomlSchema: {} - id: seletop category: analysis label: HADDOCK3 module to select a top cluster/model. @@ -180,6 +185,7 @@ nodes: required: [] additionalProperties: false uiSchema: {} + tomlSchema: {} - id: seletopclusts category: analysis label: HADDOCK3 module to select a top cluster/model. @@ -201,6 +207,7 @@ nodes: required: [] additionalProperties: false uiSchema: {} + tomlSchema: {} - id: caprieval category: analysis label: Calculate CAPRI metrics. @@ -209,79 +216,186 @@ nodes: type: object properties: reference_fname: + title: Reference structure + description: Structure to be used when calculating the CAPRI metrics. + $comment: Reference tructure to be used when calculating the CAPRI metrics. + If none is defined then the lowest scoring model is selected by default. type: string format: uri-reference irmsd: default: true + title: Calculate I-RMSD + description: Performs Interface RMSD calculations. + $comment: Calculates the Interface Root Mean Square Deviation. This calculate + the RMSD of interface backbone atoms after fitting on the interface backbone + atoms. The interface is idenfied based on intermolecular contacts shorter + than the defined irmsd_cutoff. type: boolean fnat: default: true + title: Calculate FNAT + description: Performs FNAT calculations. + $comment: Calculates the Fraction of Native Contacts. This evaluates how many + contacts observed in the reference are present in the model. The distance + cutoff used to define intermolecular contacts is defined by the fnat_cutoff + parameter. type: boolean lrmsd: default: true + title: Calculate L-RMSD + description: Performs Ligand RMSD calculations. + $comment: Calculates the Ligand Root Mean Square Deviation. This calculation + is done by superimposing the receptors (defined by the receptor_chain parameter) + and then evaluating the RMSD on the ligands (defined by the ligand_chain + parameter). Superposition and RMSD calculations are done on backbone heavy + atoms. type: boolean ilrmsd: default: true + title: Calculate I-L-RMSD + description: Performs Interface Ligand RMSD calculations. + $comment: Calculates the Interface Ligand Root Mean Square Deviation. This + calculation is done by superimposing the model and the target on the interface + backbone atoms of the receptor (defined by the receptor_chain parameter) + and calculating the RMSD on all heavy atoms of the ligand (defined by the + ligand_chain parameter). type: boolean dockq: default: true + title: Calculate DockQ + description: Evaluate DockQ. + $comment: Evaluate DockQ. A single continuous quality measure for protein + docked models based on the CAPRI criteria, a combination of i-RMSD, l-RMSD + and FNAT value. For details check the DockQ publication `DOI:10.1371/journal.pone.0161879` type: boolean irmsd_cutoff: default: 10.0 + title: "Distance cutoff (\xC5) used to define interface residues." + description: "Distance cutoff (\xC5) used to define interface residues based\ + \ on intermolecular contacts." + $comment: "Distance cutoff (\xC5) used to define interface residues based\ + \ on intermolecular contacts." type: number - maximum: 9999 - minimum: -9999 + maximum: 20.0 + minimum: 3.0 fnat_cutoff: default: 5.0 + title: "Distance cutoff (\xC5) used to define interface contacts." + description: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." + $comment: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." type: number - maximum: 9999 - minimum: -9999 - lrmsd_cutoff: - default: 10.0 - type: number - maximum: 9999 - minimum: -9999 + maximum: 20.0 + minimum: 3.0 receptor_chain: default: A + title: Receptor ChainID + description: Receptor ChainID to be considered for the RMSD calculations. + $comment: Receptor ChainID to be considered for the RMSD calculations. This + determines which chain will be treated as the receptor for the L-RMSD and + for I-L-RMSD. type: string - minLength: 0 - maxLength: 100 + minLength: 1 + maxLength: 1 ligand_chain: default: B + title: Ligand ChainID + description: Ligand ChainID to be considered for the RMSD calculations. + $comment: Ligand ChainID to be considered for the RMSD calculations. This + determines which chain will be treated as the ligand for the L-RMSD and + for I-L-RMSD. type: string - minLength: 0 - maxLength: 100 - rankby: - default: score - type: string - minLength: 0 - maxLength: 100 - rank_ascending: - default: true - type: boolean + minLength: 1 + maxLength: 1 sortby: default: score + title: Sort the structures/clusters in the output file by this value + description: Which value should be used to sort the output. + $comment: Which value should be used to sort the output, the output table + will be sorted accordingly. type: string minLength: 0 - maxLength: 100 + maxLength: 20 + enum: + - score + - irmsd + - lrmsd + - ilrmsd + - fnat + - dockq sort_ascending: default: true + title: Sort in ascending order + description: Sort in ascending order. + $comment: Sort in ascending order. type: boolean alignment_method: default: sequence + title: Alignment method used to match the numbering. + description: Which alignment method should be used to match the numbering. + $comment: Alignment method used to match the numbering. Sequence alignment + is haddock3-friendly but might not produce best results for structures that + are too different, for that use type: string minLength: 0 maxLength: 100 + enum: + - structure + - sequence lovoalign_exec: - default: '' + title: Location (path) of the LovoAlign executable + description: Location (path) of the LovoAlign executable. + $comment: Location (path) of the LovoAlign executable. type: string minLength: 0 - maxLength: 100 + maxLength: 200 + clt_threshold: + default: 4 + title: Threshold (n) used for the average evaluation in the cluster-based + output + description: Threshold (n) used for the average evaluation in the cluster-based + output. + $comment: Threshold (n) used for the average evaluation in the cluster-based + output. + type: number + maximum: 1000 + minimum: 1 required: [] additionalProperties: false uiSchema: reference_fname: ui:widget: file + ui:group: analysis + irmsd: + ui:group: analysis + fnat: + ui:group: analysis + lrmsd: + ui:group: analysis + ilrmsd: + ui:group: analysis + dockq: + ui:group: analysis + irmsd_cutoff: + ui:group: analysis + fnat_cutoff: + ui:group: analysis + receptor_chain: + ui:group: analysis + ligand_chain: + ui:group: analysis + sortby: + ui:group: analysis + sort_ascending: + ui:group: analysis + alignment_method: + ui:group: analysis + lovoalign_exec: + ui:group: analysis + clt_threshold: + ui:group: analysis + tomlSchema: {} - id: gdock category: sampling label: HADDOCK3 gdock integration module. @@ -297,6 +411,7 @@ nodes: uiSchema: ambig_fname: ui:widget: file + tomlSchema: {} - id: rigidbody category: sampling label: HADDOCK3 rigid-body docking module. @@ -304,126 +419,14 @@ nodes: schema: type: object properties: - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -469,45 +472,7 @@ nodes: required: [] additionalProperties: false uiSchema: - mol_shape_1: - ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: - ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: - ui:group: molecule - mol_shape_10: - ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file @@ -524,6 +489,9 @@ nodes: ui:group: sampling elecflag: ui:group: force field + tomlSchema: + mol_shape: + indexed: true - id: lightdock category: sampling label: Run Lightdock as a HADDOCK3 module. @@ -562,12 +530,10 @@ nodes: minLength: 0 maxLength: 100 receptor_active: - default: '' type: string minLength: 0 maxLength: 100 receptor_passive: - default: '' type: string minLength: 0 maxLength: 100 @@ -577,12 +543,10 @@ nodes: minLength: 0 maxLength: 100 ligand_active: - default: '' type: string minLength: 0 maxLength: 100 ligand_passive: - default: '' type: string minLength: 0 maxLength: 100 @@ -598,6 +562,7 @@ nodes: required: [] additionalProperties: false uiSchema: {} + tomlSchema: {} - id: topoaa category: topology label: Create and manage CNS all-atom topology. @@ -618,1271 +583,96 @@ nodes: limit: default: true type: boolean - mol1: - type: object - properties: - prot_segid: - default: A - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol2: - type: object - properties: - prot_segid: - default: B - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol3: - type: object - properties: - prot_segid: - default: C - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol4: - type: object - properties: - prot_segid: - default: D - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol5: - type: object - properties: - prot_segid: - default: E - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol6: - type: object - properties: - prot_segid: - default: F - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol7: - type: object - properties: - prot_segid: - default: G - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol8: - type: object - properties: - prot_segid: - default: H - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol9: - type: object - properties: - prot_segid: - default: I - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol10: - type: object - properties: - prot_segid: - default: J - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol11: - type: object - properties: - prot_segid: - default: K - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol12: - type: object - properties: - prot_segid: - default: L - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol13: - type: object - properties: - prot_segid: - default: M - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol14: - type: object - properties: - prot_segid: - default: N - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol15: - type: object - properties: - prot_segid: - default: O - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol16: - type: object - properties: - prot_segid: - default: P - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol17: - type: object - properties: - prot_segid: - default: Q - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol18: - type: object - properties: - prot_segid: - default: R - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol19: - type: object - properties: - prot_segid: - default: S - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol20: - type: object - properties: - prot_segid: - default: T - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false + mol: + title: Input molecule configuration + description: Specific molecule configuration + $comment: You can expand this parameter and associated sub-parameters to the + other input molecules. For example, if you input three molecules, you can + define mol1, mol2, and mol3 subparameters. Those not defined will be populated + with the defaults. + type: array + items: + type: object + properties: + prot_segid: + default: A + title: Segment ID + description: Segment ID assigned to this molecule + $comment: Segment ID assigned to this molecule in CNS. Used to distinguish + different molecules + type: string + minLength: 0 + maxLength: 4 + cyclicpept: + default: false + title: Cyclic peptide + description: Defines the molecule as a cyclic peptide + $comment: This option defines the molecule as a cyclic peptide and HADDOCK + will generate a peptide bond between the N- and C-ter provided those + are within 2A. This cutoff can be changed in the generate-topology.cns + script. + type: boolean + nhisd: + default: 0 + title: Number of HISD residue + description: Defines the number of HISD residues (neutral HIS with the + proton on the ND atom) residues when autohis=false + $comment: Defines the number of HISD residues (neutral HIS with the + proton on the ND atom) residues. The corresponding residue numbers + must be defined in the following parameter (hisd_1, hisd_2, ...). + Add as many as needed. Note that HIS is interpreted as a charged Histidine) + type: number + maximum: 9999 + minimum: 0 + hisd: + type: array + items: + title: HISD residue number + description: Residue number of the Histidine to be defined as HISD + $comment: Residue number of the Histidine to be defined as HISD + type: number + maximum: 9999 + minimum: -9999 + nhise: + default: 0 + title: Number of HISE residue + description: Defines the number of HISE residues (neutral HIS with the + proton on the NE atom) residues when autohis=false + $comment: Defines the number of HISE residues (neutral HIS with the + proton on the NE atom) residues. The corresponding residue numbers + must be defined in the following parameter (hise_1, hise_2, ...). + Add as many as needed. Note that HIS is interpreted as a charged Histidine) + type: number + maximum: 9999 + minimum: 0 + hise: + type: array + items: + title: HISE residue number + description: Residue number of the Histidine to be defined as HISE + $comment: Residue number of the Histidine to be defined as HISE + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false required: [] additionalProperties: false uiSchema: delenph: ui:group: molecule - mol1: - ui:field: collapsible - mol2: - ui:field: collapsible - mol3: - ui:field: collapsible - mol4: - ui:field: collapsible - mol5: - ui:field: collapsible - mol6: - ui:field: collapsible - mol7: - ui:field: collapsible - mol8: - ui:field: collapsible - mol9: - ui:field: collapsible - mol10: - ui:field: collapsible - mol11: - ui:field: collapsible - mol12: - ui:field: collapsible - mol13: - ui:field: collapsible - mol14: - ui:field: collapsible - mol15: - ui:field: collapsible - mol16: - ui:field: collapsible - mol17: - ui:field: collapsible - mol18: - ui:field: collapsible - mol19: - ui:field: collapsible - mol20: - ui:field: collapsible + mol: + ui:group: input molecules + tomlSchema: + mol: + indexed: true + items: + sectioned: true + properties: + hisd: + indexed: true + hise: + indexed: true - id: emscoring category: scoring label: HADDOCK3 scoring module. @@ -1890,203 +680,99 @@ nodes: schema: type: object properties: - tolerance: - default: 5 - type: number - maximum: 9999 - minimum: -9999 - log_level: - default: verbose - type: string - minLength: 0 - maxLength: 100 - ligand_param_fname: - type: string - format: uri-reference - ligand_top_fname: - type: string - format: uri-reference - individualize: - default: true - type: boolean - nemsteps: - default: 40 - type: number - maximum: 9999 - minimum: -9999 elecflag: default: true + title: Include electrostatics energy + description: Include electrostatics energy during the calculations. + $comment: Include electrostatics energy during the calculations. If set to + false electrostatics will not be considered. type: boolean - dielec: - default: cdie + required: [] + additionalProperties: false + uiSchema: + elecflag: + ui:group: force field + tomlSchema: {} +- id: mdscoring + category: scoring + label: HADDOCK3 scoring module. + description: HADDOCK3 module to perform energy minimization scoring. + schema: + type: object + properties: + ssdihed: + default: none + title: Define automatically backbone dihedral angle restraints + description: If turned on, this option will automatically defined backbone + dihedral angle restraints for the selected regions. + $comment: This option allows to utomatically defined backbone dihedral angle + restraints for the selected regions. The restraints will be defined for + the phi and psi backbone dihedral angles of amino acids, with the target + value taken from the measured angle in the input structure, and the error + bound defined by the error_dih parameter. Those restraints can be applied + to the entire structure (all), the alpha/beta secondary structure elements + (alphabeta) or only to the alpha helical regions (alpha). Those are automatically + detected based on the measured dihedral angle combinations. type: string minLength: 0 maxLength: 100 - epsilon: - default: 1.0 + enum: + - none + - all + - alpha + - alphabeta + error_dih: + default: 10 + title: Force constant for backbone dihedral angle restraints + description: Force constant for backbone dihedral angle restraints (ssdihed + option) + $comment: Force constant for backbone dihedral angle restraints (ssdihed option) type: number - maximum: 9999 - minimum: -9999 - dihedflag: + maximum: 1000 + minimum: 0 + dnarest_on: + default: false + title: Restrain the DNA conformation + description: Automatically creates restraints to maintain the conformation + of DNA/RNA + $comment: 'This option allows to restraint the conformation of nucleic acids + based on the values from the input structures. The following restraints + will be automatically defined: - single base planarity - sugar pucker - + phosphate backbone diherdral angle restraints - Watson-Crick base pairing' + type: boolean + elecflag: default: true + title: Include electrostatics energy + description: Include electrostatics energy during the calculations. + $comment: Include electrostatics energy during the calculations. If set to + false electrostatics will not be considered. type: boolean - par_nonbonded: - default: OPLSX + solvent: + default: water + title: Solvent + description: Solvent to use during the short MD refinement + $comment: Solvent to use during the short MD refinement. Water and DMSO are + supported. A solvent shelll is generated by shifting pre-equilibrated boxes + around the complex. For water an 8A water shell is generated and for DMSO + a 12.5A shell. For DMSO, type: string minLength: 0 maxLength: 100 - w_air: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_bsa: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_cdih: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_dani: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_deint: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_desolv: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - w_dist: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_elec: - default: 0.2 - type: number - maximum: 9999 - minimum: -9999 - w_lcc: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_rg: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_sani: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_sym: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_vdw: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - w_vean: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_xpcs: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_xrdc: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_zres: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - shape_1: - default: false - type: boolean - shape_2: - default: false - type: boolean - shape_3: - default: false - type: boolean - shape_4: - default: false - type: boolean - shape_5: - default: false - type: boolean - shape_6: - default: false - type: boolean - shape_7: - default: false - type: boolean - shape_8: - default: false - type: boolean - shape_9: - default: false - type: boolean - shape_10: - default: false - type: boolean - shape_11: - default: false - type: boolean - shape_12: - default: false - type: boolean - shape_13: - default: false - type: boolean - shape_14: - default: false - type: boolean - shape_15: - default: false - type: boolean - shape_16: - default: false - type: boolean - shape_17: - default: false - type: boolean - shape_18: - default: false - type: boolean - shape_19: - default: false - type: boolean - shape_20: - default: false - type: boolean + enum: + - water + - dmso required: [] additionalProperties: false uiSchema: - ligand_param_fname: - ui:widget: file - ligand_top_fname: - ui:widget: file + ssdihed: + ui:group: dihedral restraints + error_dih: + ui:group: dihedral restraints + dnarest_on: + ui:group: other restraints + elecflag: + ui:group: force field + tomlSchema: {} - id: flexref category: refinement label: HADDOCK3 module for flexible refinement. @@ -2094,126 +780,14 @@ nodes: schema: type: object properties: - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -2391,45 +965,7 @@ nodes: required: [] additionalProperties: false uiSchema: - mol_shape_1: - ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: - ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: - ui:group: molecule - mol_shape_10: - ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file @@ -2453,6 +989,9 @@ nodes: ui:group: other restraints elecflag: ui:group: force field + tomlSchema: + mol_shape: + indexed: true - id: mdref category: refinement label: HADDOCK3 module for water refinement. @@ -2460,126 +999,14 @@ nodes: schema: type: object properties: - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -2681,45 +1108,7 @@ nodes: required: [] additionalProperties: false uiSchema: - mol_shape_1: - ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: - ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: - ui:group: molecule - mol_shape_10: - ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file @@ -2743,6 +1132,9 @@ nodes: ui:group: other restraints elecflag: ui:group: force field + tomlSchema: + mol_shape: + indexed: true - id: emref category: refinement label: HADDOCK3 module for energy minimization refinement. @@ -2750,126 +1142,14 @@ nodes: schema: type: object properties: - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -2964,9 +1244,6 @@ nodes: $comment: Include electrostatics energy during the calculations. If set to false electrostatics will not be considered. type: boolean - dihedflag: - default: true - type: boolean sampling: default: 200 title: Number of models to generate @@ -2978,45 +1255,7 @@ nodes: required: [] additionalProperties: false uiSchema: - mol_shape_1: - ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: - ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: - ui:group: molecule - mol_shape_10: - ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file @@ -3044,5 +1283,8 @@ nodes: ui:group: force field sampling: ui:group: sampling + tomlSchema: + mol_shape: + indexed: true examples: docking-protein-ligand: /examples/docking-protein-ligand.zip diff --git a/public/catalog/haddock3.expert.yaml b/public/catalog/haddock3.expert.yaml index dab2cf74..bc87a707 100644 --- a/public/catalog/haddock3.expert.yaml +++ b/public/catalog/haddock3.expert.yaml @@ -14,18 +14,23 @@ global: schema: type: object properties: + run_dir: + title: Run directory + description: Folder to store the HADDOCK3 run + $comment: The new folder that will be created to save the HADDOCK3 run + type: string + format: uri-reference molecules: - title: Molecules + title: Input Molecules + description: The input molecules that will be used for docking. + $comment: Molecules must be provided in PDB format. These PDB files can be + single molecules or ensembles using the MODEL/ENDMDL statements. type: array minItems: 1 maxItems: 20 items: type: string format: uri-reference - run_dir: - title: Run directory - type: string - format: uri-reference cns_exec: title: Path to the CNS executable description: If not provided, HADDOCK3 will use the cns path configured during @@ -73,7 +78,6 @@ global: - slurm - torque queue: - default: '' title: Queue name description: Name of the batch queue to which jobs will be submitted $comment: Name of the batch queue to which jobs will be submitted. If not @@ -105,7 +109,6 @@ global: maximum: 9999 minimum: 1 required: - - molecules - run_dir additionalProperties: false uiSchema: @@ -129,6 +132,7 @@ global: ui:group: execution concat: ui:group: execution + tomlSchema: {} nodes: - id: clustfcc category: analysis @@ -165,6 +169,7 @@ nodes: uiSchema: executable: ui:widget: file + tomlSchema: {} - id: seletop category: analysis label: HADDOCK3 module to select a top cluster/model. @@ -180,6 +185,7 @@ nodes: required: [] additionalProperties: false uiSchema: {} + tomlSchema: {} - id: seletopclusts category: analysis label: HADDOCK3 module to select a top cluster/model. @@ -201,6 +207,7 @@ nodes: required: [] additionalProperties: false uiSchema: {} + tomlSchema: {} - id: caprieval category: analysis label: Calculate CAPRI metrics. @@ -209,79 +216,186 @@ nodes: type: object properties: reference_fname: + title: Reference structure + description: Structure to be used when calculating the CAPRI metrics. + $comment: Reference tructure to be used when calculating the CAPRI metrics. + If none is defined then the lowest scoring model is selected by default. type: string format: uri-reference irmsd: default: true + title: Calculate I-RMSD + description: Performs Interface RMSD calculations. + $comment: Calculates the Interface Root Mean Square Deviation. This calculate + the RMSD of interface backbone atoms after fitting on the interface backbone + atoms. The interface is idenfied based on intermolecular contacts shorter + than the defined irmsd_cutoff. type: boolean fnat: default: true + title: Calculate FNAT + description: Performs FNAT calculations. + $comment: Calculates the Fraction of Native Contacts. This evaluates how many + contacts observed in the reference are present in the model. The distance + cutoff used to define intermolecular contacts is defined by the fnat_cutoff + parameter. type: boolean lrmsd: default: true + title: Calculate L-RMSD + description: Performs Ligand RMSD calculations. + $comment: Calculates the Ligand Root Mean Square Deviation. This calculation + is done by superimposing the receptors (defined by the receptor_chain parameter) + and then evaluating the RMSD on the ligands (defined by the ligand_chain + parameter). Superposition and RMSD calculations are done on backbone heavy + atoms. type: boolean ilrmsd: default: true + title: Calculate I-L-RMSD + description: Performs Interface Ligand RMSD calculations. + $comment: Calculates the Interface Ligand Root Mean Square Deviation. This + calculation is done by superimposing the model and the target on the interface + backbone atoms of the receptor (defined by the receptor_chain parameter) + and calculating the RMSD on all heavy atoms of the ligand (defined by the + ligand_chain parameter). type: boolean dockq: default: true + title: Calculate DockQ + description: Evaluate DockQ. + $comment: Evaluate DockQ. A single continuous quality measure for protein + docked models based on the CAPRI criteria, a combination of i-RMSD, l-RMSD + and FNAT value. For details check the DockQ publication `DOI:10.1371/journal.pone.0161879` type: boolean irmsd_cutoff: default: 10.0 - type: number - maximum: 9999 - minimum: -9999 + title: "Distance cutoff (\xC5) used to define interface residues." + description: "Distance cutoff (\xC5) used to define interface residues based\ + \ on intermolecular contacts." + $comment: "Distance cutoff (\xC5) used to define interface residues based\ + \ on intermolecular contacts." + type: number + maximum: 20.0 + minimum: 3.0 fnat_cutoff: default: 5.0 - type: number - maximum: 9999 - minimum: -9999 - lrmsd_cutoff: - default: 10.0 - type: number - maximum: 9999 - minimum: -9999 + title: "Distance cutoff (\xC5) used to define interface contacts." + description: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." + $comment: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." + type: number + maximum: 20.0 + minimum: 3.0 receptor_chain: default: A - type: string - minLength: 0 - maxLength: 100 + title: Receptor ChainID + description: Receptor ChainID to be considered for the RMSD calculations. + $comment: Receptor ChainID to be considered for the RMSD calculations. This + determines which chain will be treated as the receptor for the L-RMSD and + for I-L-RMSD. + type: string + minLength: 1 + maxLength: 1 ligand_chain: default: B - type: string - minLength: 0 - maxLength: 100 - rankby: - default: score - type: string - minLength: 0 - maxLength: 100 - rank_ascending: - default: true - type: boolean + title: Ligand ChainID + description: Ligand ChainID to be considered for the RMSD calculations. + $comment: Ligand ChainID to be considered for the RMSD calculations. This + determines which chain will be treated as the ligand for the L-RMSD and + for I-L-RMSD. + type: string + minLength: 1 + maxLength: 1 sortby: default: score + title: Sort the structures/clusters in the output file by this value + description: Which value should be used to sort the output. + $comment: Which value should be used to sort the output, the output table + will be sorted accordingly. type: string minLength: 0 - maxLength: 100 + maxLength: 20 + enum: + - score + - irmsd + - lrmsd + - ilrmsd + - fnat + - dockq sort_ascending: default: true + title: Sort in ascending order + description: Sort in ascending order. + $comment: Sort in ascending order. type: boolean alignment_method: default: sequence + title: Alignment method used to match the numbering. + description: Which alignment method should be used to match the numbering. + $comment: Alignment method used to match the numbering. Sequence alignment + is haddock3-friendly but might not produce best results for structures that + are too different, for that use type: string minLength: 0 maxLength: 100 + enum: + - structure + - sequence lovoalign_exec: - default: '' + title: Location (path) of the LovoAlign executable + description: Location (path) of the LovoAlign executable. + $comment: Location (path) of the LovoAlign executable. type: string minLength: 0 - maxLength: 100 + maxLength: 200 + clt_threshold: + default: 4 + title: Threshold (n) used for the average evaluation in the cluster-based + output + description: Threshold (n) used for the average evaluation in the cluster-based + output. + $comment: Threshold (n) used for the average evaluation in the cluster-based + output. + type: number + maximum: 1000 + minimum: 1 required: [] additionalProperties: false uiSchema: reference_fname: ui:widget: file + ui:group: analysis + irmsd: + ui:group: analysis + fnat: + ui:group: analysis + lrmsd: + ui:group: analysis + ilrmsd: + ui:group: analysis + dockq: + ui:group: analysis + irmsd_cutoff: + ui:group: analysis + fnat_cutoff: + ui:group: analysis + receptor_chain: + ui:group: analysis + ligand_chain: + ui:group: analysis + sortby: + ui:group: analysis + sort_ascending: + ui:group: analysis + alignment_method: + ui:group: analysis + lovoalign_exec: + ui:group: analysis + clt_threshold: + ui:group: analysis + tomlSchema: {} - id: gdock category: sampling label: HADDOCK3 gdock integration module. @@ -297,6 +411,7 @@ nodes: uiSchema: ambig_fname: ui:widget: file + tomlSchema: {} - id: rigidbody category: sampling label: HADDOCK3 rigid-body docking module. @@ -304,246 +419,22 @@ nodes: schema: type: object properties: - mol_fix_origin_1: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_2: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_3: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_4: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_5: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_6: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_7: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_8: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_9: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_10: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_11: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_12: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_13: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_14: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_15: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_16: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_17: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_18: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_19: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_20: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + mol_fix_origin: + type: array + items: + default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. + type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -673,1531 +564,994 @@ nodes: sampled, but it is possible to define per molecule segments from which the random restraints will be defined (see the nrair_X parameter). type: boolean - nrair_1: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + nrair: + type: array + items: + default: 0 + title: Number of segments from which to pick random restraints + description: Defines the number of segments for this molecule from which + to randomly define random interaction restraints. + $comment: Defines the number of segments for this molecule from which to + randomly define random interaction restraints. Only solvent accessible + residues will be considered. See also the ranair parameter. + type: number + maximum: 100 + minimum: 0 + rair: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Starting residue number for segment from which to define + random interaction restraints + $comment: Starting residue number for segment from which to define + random interaction restraints + type: number + maximum: 9999 + minimum: -9999 + end: + title: Ending residue number + description: Ending residue number for segment from which to define + random interaction restraints + $comment: Ending residue number for segment from which to define random + interaction restraints + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false + surfrest: + default: false + title: Surface contact restraints + description: Surface contact restraints between molecules + $comment: Surface contact restraints between molecules. These are defined + as an ambiguous distance restraint between all CA,BB or N1 atoms of two + molecules (for small ligands all atoms are considered). The upper limit + is set to 7A (or 4.5A in case of small ligands). Note that this option is + computationally more expensive than the center of mass restraints (see cmrest). + type: boolean + ksurf: + default: 1.0 + title: Surface contact restraints force constant + description: Force constant applied to the surface contact restraints. + $comment: Force constant applied to the surface contact restraints. type: number - maximum: 100 + maximum: 1000 minimum: 0 - rair_sta_1_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_1_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + sampling: + default: 1000 + title: Number of models to generate + description: Number of rigidbody docking models to generate + $comment: Number of rigidbody docking models to generate type: number - maximum: 9999 - minimum: -9999 - nrair_2: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + maximum: 50000 + minimum: 1 + crossdock: + default: true + title: Cross docking of starting ensembles + description: In case ensembles of starting structures are provided, if set + to true, takes all possible combinations for the docking. + $comment: This variable controls on starting models are combined in case ensembles + of starting structures are provided. If set to true, all possible combinations + of starting models will be used for the docking. If set to false, the first + model from molecule1 will be combined with the first model from molecule2 + and so on. + type: boolean + ntrials: + default: 5 + title: Number of internal docking trials + description: Number of internal docking trials. Only the best model will be + written to disk. + $comment: Number of internal docking trials. HADDOCK will repeat the docking + internally multiple times, ranking them internally and only writing the + best model to disk. type: number maximum: 100 - minimum: 0 - rair_sta_2_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_2_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_3: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + minimum: 1 + rotate180: + default: true + title: Sample 180-rotated solutions + description: If true, HADDOCK will rotate the molecule by 180 degree around + an axis perpendicular to the interface. + $comment: This parameter controls the sampling of 180 degree rotated solutions. + If set to true, HADDOCK will rotate the molecule by 180 degree around an + axis perpendicular to the interface. + type: boolean + randorien: + default: true + type: boolean + inter_rigid: + default: 1.0 + title: Scaling of intermolecular interactions + description: Scaling of intermolecular interactions + $comment: Scaling of intermolecular interactions. This allows in particular + to scale down intermolecular interactions to reach buried sites (recommended + value for this is 0.01). If scaled-down do note that the van der Waals intermolecular + energy might be bad because of clashes. In that case it is best to also + set the weight of the van der Waals energy term to 0 (w_vdw). type: number - maximum: 100 + maximum: 1 minimum: 0 - rair_sta_3_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_3_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_4: + tolerance: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Failure tolerance percentage + description: Percentage of allowed failures for a module to successfully complete + $comment: Percentage of allowed failures for a module to successfully complete type: number - maximum: 100 + maximum: 99 minimum: 0 - rair_sta_4_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_4_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + sym_on: + default: false + title: Symmetry restraints + description: Enables symmetry restraints + $comment: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 + supported) and the segments to which those apply must be defined. In addition + a custom symmetry restraint file can be supplied (symrest_fname). + type: boolean + ksym: + default: 10.0 + title: Force constant for symmetry restraints + description: Force constant for symmetry restraints + $comment: Force constant for symmetry restraints type: number - maximum: 9999 - minimum: -9999 - nrair_5: + maximum: 1000 + minimum: 0 + symtbl_fname: + title: Custom symmetry restraints filename + description: Filename of the custom symmetry restraints file + $comment: Filename of the custom symmetry restraints file. + type: string + format: uri-reference + numc2sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of C2 symmetry restraints + description: Defines the number of C2 symmetry restraints. + $comment: Defines the number of C2 symmetry restraints. For each, a pair of + segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. type: number - maximum: 100 + maximum: 40 minimum: 0 - rair_sta_5_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_5_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_6: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 - minimum: 0 - rair_sta_6_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_6_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_7: + c2sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C2 symmetry + segment + $comment: Residue number of first residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C2 symmetry + segment + $comment: Residue number of last residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C2 segment + description: Segment ID of first C2 segment + $comment: Segment ID of first C2 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C2 symmetry + segment + $comment: Residue number of first residue in the second C2 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C2 symmetry + segment + $comment: Residue number of last residue in the second C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C2 segment + description: Segment ID of second C2 segment + $comment: Segment ID of second C2 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc3sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of C3 symmetry restraints + description: Defines the number of C3 symmetry restraints. + $comment: Defines the number of C3 symmetry restraints. For each, three segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 100 + maximum: 10 minimum: 0 - rair_sta_7_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_7_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_8: + c3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C3 symmetry + segment + $comment: Residue number of first residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C3 symmetry + segment + $comment: Residue number of last residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C3 segment + description: Segment ID of first C3 segment + $comment: Segment ID of first C3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C3 symmetry + segment + $comment: Residue number of first residue in the second C3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C3 symmetry + segment + $comment: Residue number of last residue in the second C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C3 segment + description: Segment ID of second C3 segment + $comment: Segment ID of second C3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C3 symmetry + segment + $comment: Residue number of first residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C3 symmetry + segment + $comment: Residue number of last residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C3 segment + description: Segment ID of third C3 segment + $comment: Segment ID of third C3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc4sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of C4 symmetry restraints + description: Defines the number of C4 symmetry restraints. + $comment: Defines the number of C4 symmetry restraints. For each, four segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 100 + maximum: 10 minimum: 0 - rair_sta_8_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_8_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_9: + c4sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C4 symmetry + segment + $comment: Residue number of first residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C4 symmetry + segment + $comment: Residue number of last residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C4 segment + description: Segment ID of first C4 segment + $comment: Segment ID of first C4 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C4 symmetry + segment + $comment: Residue number of first residue in the second C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C4 symmetry + segment + $comment: Residue number of last residue in the second C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C4 segment + description: Segment ID of second C4 segment + $comment: Segment ID of second C4 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C4 symmetry + segment + $comment: Residue number of first residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C4 symmetry + segment + $comment: Residue number of last residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C4 segment + description: Segment ID of third C4 segment + $comment: Segment ID of third C4 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C4 symmetry + segment + $comment: Residue number of first residue in the fourth C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C4 symmetry + segment + $comment: Residue number of last residue in the fourth C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C4 segment + description: Segment ID of fourth C4 segment + $comment: Segment ID of fourth C4 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc5sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of C5 symmetry restraints + description: Defines the number of C5 symmetry restraints. + $comment: Defines the number of C5 symmetry restraints. For each, five segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 100 + maximum: 10 minimum: 0 - rair_sta_9_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_9_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_10: + c5sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C5 symmetry + segment + $comment: Residue number of first residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C5 symmetry + segment + $comment: Residue number of last residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C5 segment + description: Segment ID of first C5 segment + $comment: Segment ID of first C5 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C5 symmetry + segment + $comment: Residue number of first residue in the second C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C5 symmetry + segment + $comment: Residue number of last residue in the second C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C5 segment + description: Segment ID of second C5 segment + $comment: Segment ID of second C5 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C5 symmetry + segment + $comment: Residue number of first residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C5 symmetry + segment + $comment: Residue number of last residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C5 segment + description: Segment ID of third C5 segment + $comment: Segment ID of third C5 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C5 symmetry + segment + $comment: Residue number of first residue in the fourth C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C5 symmetry + segment + $comment: Residue number of last residue in the fourth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C5 segment + description: Segment ID of fourth C5 segment + $comment: Segment ID of fourth C5 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C5 symmetry + segment + $comment: Residue number of first residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C5 symmetry + segment + $comment: Residue number of last residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C5 segment + description: Segment ID of fifth C5 segment + $comment: Segment ID of fifth C5 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc6sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of C6 symmetry restraints + description: Defines the number of C6 symmetry restraints. + $comment: Defines the number of C6 symmetry restraints. For each, six segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 100 + maximum: 10 minimum: 0 - rair_sta_10_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_10_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_11: + c6sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C6 symmetry + segment + $comment: Residue number of first residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C6 symmetry + segment + $comment: Residue number of last residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C6 segment + description: Segment ID of first C6 segment + $comment: Segment ID of first C6 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C6 symmetry + segment + $comment: Residue number of first residue in the second C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C6 symmetry + segment + $comment: Residue number of last residue in the second C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C6 segment + description: Segment ID of second C6 segment + $comment: Segment ID of second C6 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C6 symmetry + segment + $comment: Residue number of first residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C6 symmetry + segment + $comment: Residue number of last residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C6 segment + description: Segment ID of third C6 segment + $comment: Segment ID of third C6 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C6 symmetry + segment + $comment: Residue number of first residue in the fourth C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C6 symmetry + segment + $comment: Residue number of last residue in the fourth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C6 segment + description: Segment ID of fourth C6 segment + $comment: Segment ID of fourth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C6 symmetry + segment + $comment: Residue number of first residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C6 symmetry + segment + $comment: Residue number of last residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C6 segment + description: Segment ID of fifth C6 segment + $comment: Segment ID of fifth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta6: + title: Residue number of first residue + description: Residue number of first residue in the sixth C6 symmetry + segment + $comment: Residue number of first residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end6: + title: Residue number of last residue + description: Residue number of last residue in the sixth C6 symmetry + segment + $comment: Residue number of last residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg6: + title: Segment ID of sixth C6 segment + description: Segment ID of sixth C6 segment + $comment: Segment ID of sixth C6 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + nums3sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of S3 symmetry restraints + description: Defines the number of S3 symmetry restraints. + $comment: Defines the number of S3 symmetry restraints. For each, three segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 100 + maximum: 10 minimum: 0 - rair_sta_11_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_11_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_12: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + s3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first S3 symmetry + segment + $comment: Residue number of first residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first S3 symmetry + segment + $comment: Residue number of last residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first S3 segment + description: Segment ID of first S3 segment + $comment: Segment ID of first S3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second S3 symmetry + segment + $comment: Residue number of first residue in the second S3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second S3 symmetry + segment + $comment: Residue number of last residue in the second S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second S3 segment + description: Segment ID of second S3 segment + $comment: Segment ID of second S3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third S3 symmetry + segment + $comment: Residue number of first residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third S3 symmetry + segment + $comment: Residue number of last residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third S3 segment + description: Segment ID of third S3 segment + $comment: Segment ID of third S3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + ncs_on: + default: false + title: Non-crystallographic symmetry restraints + description: Non-crystallographic symmetry restraints to ensure two molecules + will have the same conformation. + $comment: Non-crystallographic symmetry restraints to ensure two molecules + will have the same conformation. This does not apply any symmetry between + the two molecules but rather defines restraints such as the RMSD between + those is 0. + type: boolean + kncs: + default: 1.0 + title: Force constant for non-crystallographic restraints + description: Force constant for non-crystallographic restraints + $comment: Force constant for non-crystallographic restraints type: number - maximum: 100 + maximum: 1000 minimum: 0 - rair_sta_12_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_12_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_13: + numncs: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of non-crystallographic symmetry restraints + description: Number of non-crystallographic symmetry restraints (NCS). + $comment: Number of non-crystallographic symmetry restraints. For each pairs + of segments will have to be defined. Note that those must contain exactly + the same residues/atom combinations. type: number maximum: 100 minimum: 0 - rair_sta_13_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_13_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + ncs: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first NCS segment + $comment: Residue number of first residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first NCS segment + $comment: Residue number of last residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first NCS segment + description: Segment ID of first NCS segment + $comment: Segment ID of first NCS segment + type: string + minLength: 0 + maxLength: 100 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second NCS segment + $comment: Residue number of first residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second NCS segment + $comment: Residue number of last residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second NCS segment + description: Segment ID of second NCS segment + $comment: Segment ID of second NCS segment + type: string + minLength: 0 + maxLength: 100 + required: [] + additionalProperties: false + w_dist: + default: 0.01 + title: Weight of the distance restraint energy + description: Weight of the distance restraints energy in the scoring function + $comment: Weight of the distance restraints energy in the scoring function. + Note that this is different from the force constants used during the calculations. type: number maximum: 9999 - minimum: -9999 - nrair_14: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 minimum: 0 - rair_sta_14_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_14_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + w_air: + default: 0.01 + title: Weight of the distance restraint energy + description: Weight of the distance restraints energy in the scoring function + $comment: Weight of the distance restraints energy in the scoring function. + Note that this is different from the force constants used during the calculations. type: number maximum: 9999 - minimum: -9999 - nrair_15: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 minimum: 0 - rair_sta_15_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints + w_bsa: + default: -0.01 + title: Weight of the buried surface area term + description: Weight of the buried surface area term in the scoring function + $comment: Weight of the buried surface area (BSA) term in the scoring function. + Note that the BSA is only used for scoring. type: number maximum: 9999 minimum: -9999 - rair_end_15_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + w_cdih: + default: 0.0 + title: Weight of the dihedral angle restraint energy + description: Weight of the dihedral angle restraints energy in the scoring + function + $comment: Weight of the dihedral angle restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. type: number maximum: 9999 - minimum: -9999 - nrair_16: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 minimum: 0 - rair_sta_16_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_16_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + w_desolv: + default: 1.0 + title: Weight of the desolvation energy term + description: Weight of the desolvation energy term in the scoring function + $comment: Weight of the desolvation energy term in the scoring function. Note + that the desolvation energy is only used for scoring. type: number maximum: 9999 minimum: -9999 - nrair_17: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 - minimum: 0 - rair_sta_17_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints + w_elec: + default: 1.0 + title: Weight of the intermolecular electrostatic energy + description: Weight of the intermolecular electrostatic energy in the scoring + function + $comment: Weight of the intermolecular electrostatic energy in the scoring + function. Note that this does not affect the electostatic energy during + the rigidbody minimization. type: number maximum: 9999 minimum: -9999 - rair_end_17_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + w_sym: + default: 0.1 + title: Weight of the symmetry restraint energy + description: Weight of the symmetry restraints energy in the scoring function + $comment: Weight of the symmetry restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. type: number maximum: 9999 - minimum: -9999 - nrair_18: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 minimum: 0 - rair_sta_18_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints + w_vdw: + default: 0.01 + title: Weight of the intermolecular van der Waals energy + description: Weight of the intermolecular van der Waals energy in the scoring + function + $comment: Weight of the intermolecular van der Waals energy in the scoring + function. Note that this does not affect the van der Waals energy during + the rigidbody minimization. type: number maximum: 9999 minimum: -9999 - rair_end_18_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_19: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 - minimum: 0 - rair_sta_19_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_19_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_20: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 - minimum: 0 - rair_sta_20_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_20_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - surfrest: - default: false - title: Surface contact restraints - description: Surface contact restraints between molecules - $comment: Surface contact restraints between molecules. These are defined - as an ambiguous distance restraint between all CA,BB or N1 atoms of two - molecules (for small ligands all atoms are considered). The upper limit - is set to 7A (or 4.5A in case of small ligands). Note that this option is - computationally more expensive than the center of mass restraints (see cmrest). - type: boolean - ksurf: - default: 1.0 - title: Surface contact restraints force constant - description: Force constant applied to the surface contact restraints. - $comment: Force constant applied to the surface contact restraints. - type: number - maximum: 1000 - minimum: 0 - sampling: - default: 1000 - title: Number of models to generate - description: Number of rigidbody docking models to generate - $comment: Number of rigidbody docking models to generate - type: number - maximum: 50000 - minimum: 1 - crossdock: - default: true - title: Cross docking of starting ensembles - description: In case ensembles of starting structures are provided, if set - to true, takes all possible combinations for the docking. - $comment: This variable controls on starting models are combined in case ensembles - of starting structures are provided. If set to true, all possible combinations - of starting models will be used for the docking. If set to false, the first - model from molecule1 will be combined with the first model from molecule2 - and so on. - type: boolean - ntrials: - default: 5 - title: Number of internal docking trials - description: Number of internal docking trials. Only the best model will be - written to disk. - $comment: Number of internal docking trials. HADDOCK will repeat the docking - internally multiple times, ranking them internally and only writing the - best model to disk. - type: number - maximum: 100 - minimum: 1 - rotate180: - default: true - title: Sample 180-rotated solutions - description: If true, HADDOCK will rotate the molecule by 180 degree around - an axis perpendicular to the interface. - $comment: This parameter controls the sampling of 180 degree rotated solutions. - If set to true, HADDOCK will rotate the molecule by 180 degree around an - axis perpendicular to the interface. - type: boolean - randorien: - default: true - type: boolean - inter_rigid: - default: 1.0 - title: Scaling of intermolecular interactions - description: Scaling of intermolecular interactions - $comment: Scaling of intermolecular interactions. This allows in particular - to scale down intermolecular interactions to reach buried sites (recommended - value for this is 0.01). If scaled-down do note that the van der Waals intermolecular - energy might be bad because of clashes. In that case it is best to also - set the weight of the van der Waals energy term to 0 (w_vdw). - type: number - maximum: 1 - minimum: 0 - tolerance: - default: 0 - title: Failure tolerance percentage - description: Percentage of allowed failures for a module to successfully complete - $comment: Percentage of allowed failures for a module to successfully complete - type: number - maximum: 99 - minimum: 0 - sym_on: - default: false - title: Symmetry restraints - description: Enables symmetry restraints - $comment: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 - supported) and the segments to which those apply must be defined. In addition - a custom symmetry restraint file can be supplied (symrest_fname). - type: boolean - ksym: - default: 10.0 - title: Force constant for symmetry restraints - description: Force constant for symmetry restraints - $comment: Force constant for symmetry restraints - type: number - maximum: 1000 - minimum: 0 - symtbl_fname: - title: Custom symmetry restraints filename - description: Filename of the custom symmetry restraints file - $comment: Filename of the custom symmetry restraints file. - type: string - format: uri-reference - numc2sym: - default: 0 - title: Number of C2 symmetry restraints - description: Defines the number of C2 symmetry restraints. - $comment: Defines the number of C2 symmetry restraints. For each, a pair of - segments on which the symmetry restraint is applied will have to be defined. - Those must all have the same length. - type: number - maximum: 40 - minimum: 0 - c2sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C2 symmetry segment - $comment: Residue number of first residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C2 symmetry segment - $comment: Residue number of last residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg1_1: - default: '' - title: Segment ID of first C2 segment - description: Segment ID of first C2 segment - $comment: Segment ID of first C2 segment - type: string - minLength: 0 - maxLength: 4 - c2sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C2 symmetry segment - $comment: Residue number of first residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C2 symmetry segment - $comment: Residue number of last residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg2_1: - default: '' - title: Segment ID of second C2 segment - description: Segment ID of second C2 segment - $comment: Segment ID of second C2 segment - type: string - minLength: 0 - maxLength: 4 - numc3sym: - default: 0 - title: Number of C3 symmetry restraints - description: Defines the number of C3 symmetry restraints. - $comment: Defines the number of C3 symmetry restraints. For each, three segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C3 symmetry segment - $comment: Residue number of first residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C3 symmetry segment - $comment: Residue number of last residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg1_1: - default: '' - title: Segment ID of first C3 segment - description: Segment ID of first C3 segment - $comment: Segment ID of first C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C3 symmetry segment - $comment: Residue number of first residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C3 symmetry segment - $comment: Residue number of last residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg2_1: - default: '' - title: Segment ID of second C3 segment - description: Segment ID of second C3 segment - $comment: Segment ID of second C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C3 symmetry segment - $comment: Residue number of first residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C3 symmetry segment - $comment: Residue number of last residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg3_1: - default: '' - title: Segment ID of third C3 segment - description: Segment ID of third C3 segment - $comment: Segment ID of third C3 segment - type: string - minLength: 0 - maxLength: 4 - numc4sym: - default: 0 - title: Number of C4 symmetry restraints - description: Defines the number of C4 symmetry restraints. - $comment: Defines the number of C4 symmetry restraints. For each, four segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c4sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C4 symmetry segment - $comment: Residue number of first residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C4 symmetry segment - $comment: Residue number of last residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg1_1: - default: '' - title: Segment ID of first C4 segment - description: Segment ID of first C4 segment - $comment: Segment ID of first C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C4 symmetry segment - $comment: Residue number of first residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C4 symmetry segment - $comment: Residue number of last residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg2_1: - default: '' - title: Segment ID of second C4 segment - description: Segment ID of second C4 segment - $comment: Segment ID of second C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C4 symmetry segment - $comment: Residue number of first residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C4 symmetry segment - $comment: Residue number of last residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg3_1: - default: '' - title: Segment ID of third C4 segment - description: Segment ID of third C4 segment - $comment: Segment ID of third C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C4 symmetry segment - $comment: Residue number of first residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C4 symmetry segment - $comment: Residue number of last residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg4_1: - default: '' - title: Segment ID of fourth C4 segment - description: Segment ID of fourth C4 segment - $comment: Segment ID of fourth C4 segment - type: string - minLength: 0 - maxLength: 4 - numc5sym: - default: 0 - title: Number of C5 symmetry restraints - description: Defines the number of C5 symmetry restraints. - $comment: Defines the number of C5 symmetry restraints. For each, five segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c5sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C5 symmetry segment - $comment: Residue number of first residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C5 symmetry segment - $comment: Residue number of last residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg1_1: - default: '' - title: Segment ID of first C5 segment - description: Segment ID of first C5 segment - $comment: Segment ID of first C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C5 symmetry segment - $comment: Residue number of first residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C5 symmetry segment - $comment: Residue number of last residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg2_1: - default: '' - title: Segment ID of second C5 segment - description: Segment ID of second C5 segment - $comment: Segment ID of second C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C5 symmetry segment - $comment: Residue number of first residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C5 symmetry segment - $comment: Residue number of last residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg3_1: - default: '' - title: Segment ID of third C5 segment - description: Segment ID of third C5 segment - $comment: Segment ID of third C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C5 symmetry segment - $comment: Residue number of first residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C5 symmetry segment - $comment: Residue number of last residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg4_1: - default: '' - title: Segment ID of fourth C5 segment - description: Segment ID of fourth C5 segment - $comment: Segment ID of fourth C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C5 symmetry segment - $comment: Residue number of first residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C5 symmetry segment - $comment: Residue number of last residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg5_1: - default: '' - title: Segment ID of fifth C5 segment - description: Segment ID of fifth C5 segment - $comment: Segment ID of fifth C5 segment - type: string - minLength: 0 - maxLength: 4 - numc6sym: - default: 0 - title: Number of C6 symmetry restraints - description: Defines the number of C6 symmetry restraints. - $comment: Defines the number of C6 symmetry restraints. For each, six segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c6sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C6 symmetry segment - $comment: Residue number of first residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C6 symmetry segment - $comment: Residue number of last residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg1_1: - default: '' - title: Segment ID of first C6 segment - description: Segment ID of first C6 segment - $comment: Segment ID of first C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C6 symmetry segment - $comment: Residue number of first residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C6 symmetry segment - $comment: Residue number of last residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg2_1: - default: '' - title: Segment ID of second C6 segment - description: Segment ID of second C6 segment - $comment: Segment ID of second C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C6 symmetry segment - $comment: Residue number of first residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C6 symmetry segment - $comment: Residue number of last residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg3_1: - default: '' - title: Segment ID of third C6 segment - description: Segment ID of third C6 segment - $comment: Segment ID of third C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C6 symmetry segment - $comment: Residue number of first residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C6 symmetry segment - $comment: Residue number of last residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg4_1: - default: '' - title: Segment ID of fourth C6 segment - description: Segment ID of fourth C6 segment - $comment: Segment ID of fourth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C6 symmetry segment - $comment: Residue number of first residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C6 symmetry segment - $comment: Residue number of last residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg5_1: - default: '' - title: Segment ID of fifth C6 segment - description: Segment ID of fifth C6 segment - $comment: Segment ID of fifth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta6_1: - title: Residue number of first residue - description: Residue number of first residue in the sixth C6 symmetry segment - $comment: Residue number of first residue in the sixth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end6_1: - title: Residue number of last residue - description: Residue number of last residue in the sixth C6 symmetry segment - $comment: Residue number of last residue in the sixth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg6_1: - default: '' - title: Segment ID of sixth C6 segment - description: Segment ID of sixth C6 segment - $comment: Segment ID of sixth C6 segment - type: string - minLength: 0 - maxLength: 4 - nums3sym: - default: 0 - title: Number of S3 symmetry restraints - description: Defines the number of S3 symmetry restraints. - $comment: Defines the number of S3 symmetry restraints. For each, three segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - s3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first S3 symmetry segment - $comment: Residue number of first residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first S3 symmetry segment - $comment: Residue number of last residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg1_1: - default: '' - title: Segment ID of first S3 segment - description: Segment ID of first S3 segment - $comment: Segment ID of first S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second S3 symmetry segment - $comment: Residue number of first residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second S3 symmetry segment - $comment: Residue number of last residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg2_1: - default: '' - title: Segment ID of second S3 segment - description: Segment ID of second S3 segment - $comment: Segment ID of second S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third S3 symmetry segment - $comment: Residue number of first residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third S3 symmetry segment - $comment: Residue number of last residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg3_1: - default: '' - title: Segment ID of third S3 segment - description: Segment ID of third S3 segment - $comment: Segment ID of third S3 segment - type: string - minLength: 0 - maxLength: 4 - ncs_on: - default: false - title: Non-crystallographic symmetry restraints - description: Non-crystallographic symmetry restraints to ensure two molecules - will have the same conformation. - $comment: Non-crystallographic symmetry restraints to ensure two molecules - will have the same conformation. This does not apply any symmetry between - the two molecules but rather defines restraints such as the RMSD between - those is 0. - type: boolean - kncs: - default: 1.0 - title: Force constant for non-crystallographic restraints - description: Force constant for non-crystallographic restraints - $comment: Force constant for non-crystallographic restraints - type: number - maximum: 1000 - minimum: 0 - numncs: - default: 0 - title: Number of non-crystallographic symmetry restraints - description: Number of non-crystallographic symmetry restraints (NCS). - $comment: Number of non-crystallographic symmetry restraints. For each pairs - of segments will have to be defined. Note that those must contain exactly - the same residues/atom combinations. - type: number - maximum: 100 - minimum: 0 - ncs_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first NCS segment - $comment: Residue number of first residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first NCS segment - $comment: Residue number of last residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg1_1: - default: '' - title: Segment ID of first NCS segment - description: Segment ID of first NCS segment - $comment: Segment ID of first NCS segment - type: string - minLength: 0 - maxLength: 100 - ncs_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second NCS segment - $comment: Residue number of first residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second NCS segment - $comment: Residue number of last residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg2_1: - default: '' - title: Segment ID of second NCS segment - description: Segment ID of second NCS segment - $comment: Segment ID of second NCS segment - type: string - minLength: 0 - maxLength: 100 - w_dist: - default: 0.01 - title: Weight of the distance restraint energy - description: Weight of the distance restraints energy in the scoring function - $comment: Weight of the distance restraints energy in the scoring function. - Note that this is different from the force constants used during the calculations. - type: number - maximum: 9999 - minimum: 0 - w_air: - default: 0.01 - title: Weight of the distance restraint energy - description: Weight of the distance restraints energy in the scoring function - $comment: Weight of the distance restraints energy in the scoring function. - Note that this is different from the force constants used during the calculations. - type: number - maximum: 9999 - minimum: 0 - w_bsa: - default: -0.01 - title: Weight of the buried surface area term - description: Weight of the buried surface area term in the scoring function - $comment: Weight of the buried surface area (BSA) term in the scoring function. - Note that the BSA is only used for scoring. - type: number - maximum: 9999 - minimum: -9999 - w_cdih: - default: 0.0 - title: Weight of the dihedral angle restraint energy - description: Weight of the dihedral angle restraints energy in the scoring - function - $comment: Weight of the dihedral angle restraints energy in the scoring function. - Note that this is different from the force constant used during the calculations. - type: number - maximum: 9999 - minimum: 0 - w_desolv: - default: 1.0 - title: Weight of the desolvation energy term - description: Weight of the desolvation energy term in the scoring function - $comment: Weight of the desolvation energy term in the scoring function. Note - that the desolvation energy is only used for scoring. - type: number - maximum: 9999 - minimum: -9999 - w_elec: - default: 1.0 - title: Weight of the intermolecular electrostatic energy - description: Weight of the intermolecular electrostatic energy in the scoring - function - $comment: Weight of the intermolecular electrostatic energy in the scoring - function. Note that this does not affect the electostatic energy during - the rigidbody minimization. - type: number - maximum: 9999 - minimum: -9999 - w_sym: - default: 0.1 - title: Weight of the symmetry restraint energy - description: Weight of the symmetry restraints energy in the scoring function - $comment: Weight of the symmetry restraints energy in the scoring function. - Note that this is different from the force constant used during the calculations. - type: number - maximum: 9999 - minimum: 0 - w_vdw: - default: 0.01 - title: Weight of the intermolecular van der Waals energy - description: Weight of the intermolecular van der Waals energy in the scoring - function - $comment: Weight of the intermolecular van der Waals energy in the scoring - function. Note that this does not affect the van der Waals energy during - the rigidbody minimization. - type: number - maximum: 9999 - minimum: -9999 - ligand_param_fname: - title: Custom ligand parameter file - description: Ligand parameter file in CNS format - $comment: Ligand parameter file in CNS format containing all force field parameters - (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported - by default by HADDOCK - type: string - format: uri-reference - ligand_top_fname: - title: Custom ligand topology file - description: Ligand topology file in CNS format - $comment: Ligand topology file in CNS format containing the ligand topologies - (atoms, masses, charges, bond definitions...) for any ligand not supported - by default by HADDOCK - type: string - format: uri-reference - elecflag: - default: true - title: Include electrostatics energy - description: Include electrostatics energy during the calculations. - $comment: Include electrostatics energy during the calculations. If set to - false electrostatics will not be considered. - type: boolean - dielec: - default: rdie - title: Constant (cdie) or distance-dependent dielectric (rdie) constant. - description: Use a constant (cdie option) or a distance-dependent dielectric - (rdie) constant in the Coulomb potential. - $comment: Use a constant (cdie option) or a distance-dependent dielectric - (rdie) constant in the Coulomb potential. A distance dependent dielectric - constant will effectively scale down the electrostatic energy by having - a 1/r**2 dependency instead of 1/r - type: string - minLength: 0 - maxLength: 4 - enum: - - cdie - - rdie - epsilon: - default: 10.0 - title: Dielectric constant - description: Dielectric constant for the electrostatic Coulomb energy term. - $comment: Dielectric constant for the electrostatic Coulomb energy term. + ligand_param_fname: + title: Custom ligand parameter file + description: Ligand parameter file in CNS format + $comment: Ligand parameter file in CNS format containing all force field parameters + (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported + by default by HADDOCK + type: string + format: uri-reference + ligand_top_fname: + title: Custom ligand topology file + description: Ligand topology file in CNS format + $comment: Ligand topology file in CNS format containing the ligand topologies + (atoms, masses, charges, bond definitions...) for any ligand not supported + by default by HADDOCK + type: string + format: uri-reference + elecflag: + default: true + title: Include electrostatics energy + description: Include electrostatics energy during the calculations. + $comment: Include electrostatics energy during the calculations. If set to + false electrostatics will not be considered. + type: boolean + dielec: + default: rdie + title: Constant (cdie) or distance-dependent dielectric (rdie) constant. + description: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. + $comment: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. A distance dependent dielectric + constant will effectively scale down the electrostatic energy by having + a 1/r**2 dependency instead of 1/r + type: string + minLength: 0 + maxLength: 4 + enum: + - cdie + - rdie + epsilon: + default: 10.0 + title: Dielectric constant + description: Dielectric constant for the electrostatic Coulomb energy term. + $comment: Dielectric constant for the electrostatic Coulomb energy term. type: number maximum: 78 minimum: 1 required: [] additionalProperties: false uiSchema: - mol_fix_origin_1: - ui:group: molecule - mol_fix_origin_2: - ui:group: molecule - mol_fix_origin_3: - ui:group: molecule - mol_fix_origin_4: - ui:group: molecule - mol_fix_origin_5: - ui:group: molecule - mol_fix_origin_6: - ui:group: molecule - mol_fix_origin_7: - ui:group: molecule - mol_fix_origin_8: + mol_fix_origin: ui:group: molecule - mol_fix_origin_9: - ui:group: molecule - mol_fix_origin_10: - ui:group: molecule - mol_fix_origin_11: - ui:group: molecule - mol_fix_origin_12: - ui:group: molecule - mol_fix_origin_13: - ui:group: molecule - mol_fix_origin_14: - ui:group: molecule - mol_fix_origin_15: - ui:group: molecule - mol_fix_origin_16: - ui:group: molecule - mol_fix_origin_17: - ui:group: molecule - mol_fix_origin_18: - ui:group: molecule - mol_fix_origin_19: - ui:group: molecule - mol_fix_origin_20: - ui:group: molecule - mol_shape_1: - ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: - ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: - ui:group: molecule - mol_shape_10: - ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file @@ -2226,125 +1580,9 @@ nodes: ui:group: ab initio mode ranair: ui:group: ab initio mode - nrair_1: - ui:group: ab initio mode - rair_sta_1_1: + nrair: ui:group: ab initio mode - rair_end_1_1: - ui:group: ab initio mode - nrair_2: - ui:group: ab initio mode - rair_sta_2_1: - ui:group: ab initio mode - rair_end_2_1: - ui:group: ab initio mode - nrair_3: - ui:group: ab initio mode - rair_sta_3_1: - ui:group: ab initio mode - rair_end_3_1: - ui:group: ab initio mode - nrair_4: - ui:group: ab initio mode - rair_sta_4_1: - ui:group: ab initio mode - rair_end_4_1: - ui:group: ab initio mode - nrair_5: - ui:group: ab initio mode - rair_sta_5_1: - ui:group: ab initio mode - rair_end_5_1: - ui:group: ab initio mode - nrair_6: - ui:group: ab initio mode - rair_sta_6_1: - ui:group: ab initio mode - rair_end_6_1: - ui:group: ab initio mode - nrair_7: - ui:group: ab initio mode - rair_sta_7_1: - ui:group: ab initio mode - rair_end_7_1: - ui:group: ab initio mode - nrair_8: - ui:group: ab initio mode - rair_sta_8_1: - ui:group: ab initio mode - rair_end_8_1: - ui:group: ab initio mode - nrair_9: - ui:group: ab initio mode - rair_sta_9_1: - ui:group: ab initio mode - rair_end_9_1: - ui:group: ab initio mode - nrair_10: - ui:group: ab initio mode - rair_sta_10_1: - ui:group: ab initio mode - rair_end_10_1: - ui:group: ab initio mode - nrair_11: - ui:group: ab initio mode - rair_sta_11_1: - ui:group: ab initio mode - rair_end_11_1: - ui:group: ab initio mode - nrair_12: - ui:group: ab initio mode - rair_sta_12_1: - ui:group: ab initio mode - rair_end_12_1: - ui:group: ab initio mode - nrair_13: - ui:group: ab initio mode - rair_sta_13_1: - ui:group: ab initio mode - rair_end_13_1: - ui:group: ab initio mode - nrair_14: - ui:group: ab initio mode - rair_sta_14_1: - ui:group: ab initio mode - rair_end_14_1: - ui:group: ab initio mode - nrair_15: - ui:group: ab initio mode - rair_sta_15_1: - ui:group: ab initio mode - rair_end_15_1: - ui:group: ab initio mode - nrair_16: - ui:group: ab initio mode - rair_sta_16_1: - ui:group: ab initio mode - rair_end_16_1: - ui:group: ab initio mode - nrair_17: - ui:group: ab initio mode - rair_sta_17_1: - ui:group: ab initio mode - rair_end_17_1: - ui:group: ab initio mode - nrair_18: - ui:group: ab initio mode - rair_sta_18_1: - ui:group: ab initio mode - rair_end_18_1: - ui:group: ab initio mode - nrair_19: - ui:group: ab initio mode - rair_sta_19_1: - ui:group: ab initio mode - rair_end_19_1: - ui:group: ab initio mode - nrair_20: - ui:group: ab initio mode - rair_sta_20_1: - ui:group: ab initio mode - rair_end_20_1: + rair: ui:group: ab initio mode surfrest: ui:group: ab initio mode @@ -2373,171 +1611,35 @@ nodes: ui:group: symmetry numc2sym: ui:group: symmetry - c2sym_sta1_1: - ui:group: symmetry - c2sym_end1_1: - ui:group: symmetry - c2sym_seg1_1: - ui:group: symmetry - c2sym_sta2_1: - ui:group: symmetry - c2sym_end2_1: - ui:group: symmetry - c2sym_seg2_1: + c2sym: ui:group: symmetry numc3sym: ui:group: symmetry - c3sym_sta1_1: - ui:group: symmetry - c3sym_end1_1: - ui:group: symmetry - c3sym_seg1_1: - ui:group: symmetry - c3sym_sta2_1: - ui:group: symmetry - c3sym_end2_1: - ui:group: symmetry - c3sym_seg2_1: - ui:group: symmetry - c3sym_sta3_1: - ui:group: symmetry - c3sym_end3_1: - ui:group: symmetry - c3sym_seg3_1: + c3sym: ui:group: symmetry numc4sym: ui:group: symmetry - c4sym_sta1_1: - ui:group: symmetry - c4sym_end1_1: - ui:group: symmetry - c4sym_seg1_1: - ui:group: symmetry - c4sym_sta2_1: - ui:group: symmetry - c4sym_end2_1: - ui:group: symmetry - c4sym_seg2_1: - ui:group: symmetry - c4sym_sta3_1: - ui:group: symmetry - c4sym_end3_1: - ui:group: symmetry - c4sym_seg3_1: - ui:group: symmetry - c4sym_sta4_1: - ui:group: symmetry - c4sym_end4_1: - ui:group: symmetry - c4sym_seg4_1: + c4sym: ui:group: symmetry numc5sym: ui:group: symmetry - c5sym_sta1_1: - ui:group: symmetry - c5sym_end1_1: - ui:group: symmetry - c5sym_seg1_1: - ui:group: symmetry - c5sym_sta2_1: - ui:group: symmetry - c5sym_end2_1: - ui:group: symmetry - c5sym_seg2_1: - ui:group: symmetry - c5sym_sta3_1: - ui:group: symmetry - c5sym_end3_1: - ui:group: symmetry - c5sym_seg3_1: - ui:group: symmetry - c5sym_sta4_1: - ui:group: symmetry - c5sym_end4_1: - ui:group: symmetry - c5sym_seg4_1: - ui:group: symmetry - c5sym_sta5_1: - ui:group: symmetry - c5sym_end5_1: - ui:group: symmetry - c5sym_seg5_1: + c5sym: ui:group: symmetry numc6sym: ui:group: symmetry - c6sym_sta1_1: - ui:group: symmetry - c6sym_end1_1: - ui:group: symmetry - c6sym_seg1_1: - ui:group: symmetry - c6sym_sta2_1: - ui:group: symmetry - c6sym_end2_1: - ui:group: symmetry - c6sym_seg2_1: - ui:group: symmetry - c6sym_sta3_1: - ui:group: symmetry - c6sym_end3_1: - ui:group: symmetry - c6sym_seg3_1: - ui:group: symmetry - c6sym_sta4_1: - ui:group: symmetry - c6sym_end4_1: - ui:group: symmetry - c6sym_seg4_1: - ui:group: symmetry - c6sym_sta5_1: - ui:group: symmetry - c6sym_end5_1: - ui:group: symmetry - c6sym_seg5_1: - ui:group: symmetry - c6sym_sta6_1: - ui:group: symmetry - c6sym_end6_1: - ui:group: symmetry - c6sym_seg6_1: + c6sym: ui:group: symmetry nums3sym: ui:group: symmetry - s3sym_sta1_1: - ui:group: symmetry - s3sym_end1_1: - ui:group: symmetry - s3sym_seg1_1: - ui:group: symmetry - s3sym_sta2_1: - ui:group: symmetry - s3sym_end2_1: - ui:group: symmetry - s3sym_seg2_1: - ui:group: symmetry - s3sym_sta3_1: - ui:group: symmetry - s3sym_end3_1: - ui:group: symmetry - s3sym_seg3_1: - ui:group: symmetry - ncs_on: - ui:group: symmetry - kncs: - ui:group: symmetry - numncs: - ui:group: symmetry - ncs_sta1_1: - ui:group: symmetry - ncs_end1_1: + s3sym: ui:group: symmetry - ncs_seg1_1: + ncs_on: ui:group: symmetry - ncs_sta2_1: + kncs: ui:group: symmetry - ncs_end2_1: + numncs: ui:group: symmetry - ncs_seg2_1: + ncs: ui:group: symmetry w_dist: ui:group: scoring @@ -2567,6 +1669,47 @@ nodes: ui:group: force field epsilon: ui:group: force field + tomlSchema: + mol_fix_origin: + indexed: true + mol_shape: + indexed: true + nrair: + indexed: true + rair: + indexed: true + items: + indexed: true + items: + flatten: true + c2sym: + indexed: true + items: + flatten: true + c3sym: + indexed: true + items: + flatten: true + c4sym: + indexed: true + items: + flatten: true + c5sym: + indexed: true + items: + flatten: true + c6sym: + indexed: true + items: + flatten: true + s3sym: + indexed: true + items: + flatten: true + ncs: + indexed: true + items: + flatten: true - id: lightdock category: sampling label: Run Lightdock as a HADDOCK3 module. @@ -2605,12 +1748,10 @@ nodes: minLength: 0 maxLength: 100 receptor_active: - default: '' type: string minLength: 0 maxLength: 100 receptor_passive: - default: '' type: string minLength: 0 maxLength: 100 @@ -2620,12 +1761,10 @@ nodes: minLength: 0 maxLength: 100 ligand_active: - default: '' type: string minLength: 0 maxLength: 100 ligand_passive: - default: '' type: string minLength: 0 maxLength: 100 @@ -2641,6 +1780,7 @@ nodes: required: [] additionalProperties: false uiSchema: {} + tomlSchema: {} - id: topoaa category: topology label: Create and manage CNS all-atom topology. @@ -2694,1226 +1834,79 @@ nodes: type: number maximum: 99 minimum: 0 - mol1: - type: object - properties: - prot_segid: - default: A - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol2: - type: object - properties: - prot_segid: - default: B - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol3: - type: object - properties: - prot_segid: - default: C - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol4: - type: object - properties: - prot_segid: - default: D - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol5: - type: object - properties: - prot_segid: - default: E - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol6: - type: object - properties: - prot_segid: - default: F - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol7: - type: object - properties: - prot_segid: - default: G - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol8: - type: object - properties: - prot_segid: - default: H - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol9: - type: object - properties: - prot_segid: - default: I - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol10: - type: object - properties: - prot_segid: - default: J - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol11: - type: object - properties: - prot_segid: - default: K - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol12: - type: object - properties: - prot_segid: - default: L - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol13: - type: object - properties: - prot_segid: - default: M - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol14: - type: object - properties: - prot_segid: - default: N - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol15: - type: object - properties: - prot_segid: - default: O - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol16: - type: object - properties: - prot_segid: - default: P - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol17: - type: object - properties: - prot_segid: - default: Q - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol18: - type: object - properties: - prot_segid: - default: R - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol19: - type: object - properties: - prot_segid: - default: S - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol20: - type: object - properties: - prot_segid: - default: T - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false + mol: + title: Input molecule configuration + description: Specific molecule configuration + $comment: You can expand this parameter and associated sub-parameters to the + other input molecules. For example, if you input three molecules, you can + define mol1, mol2, and mol3 subparameters. Those not defined will be populated + with the defaults. + type: array + items: + type: object + properties: + prot_segid: + default: A + title: Segment ID + description: Segment ID assigned to this molecule + $comment: Segment ID assigned to this molecule in CNS. Used to distinguish + different molecules + type: string + minLength: 0 + maxLength: 4 + cyclicpept: + default: false + title: Cyclic peptide + description: Defines the molecule as a cyclic peptide + $comment: This option defines the molecule as a cyclic peptide and HADDOCK + will generate a peptide bond between the N- and C-ter provided those + are within 2A. This cutoff can be changed in the generate-topology.cns + script. + type: boolean + nhisd: + default: 0 + title: Number of HISD residue + description: Defines the number of HISD residues (neutral HIS with the + proton on the ND atom) residues when autohis=false + $comment: Defines the number of HISD residues (neutral HIS with the + proton on the ND atom) residues. The corresponding residue numbers + must be defined in the following parameter (hisd_1, hisd_2, ...). + Add as many as needed. Note that HIS is interpreted as a charged Histidine) + type: number + maximum: 9999 + minimum: 0 + hisd: + type: array + items: + title: HISD residue number + description: Residue number of the Histidine to be defined as HISD + $comment: Residue number of the Histidine to be defined as HISD + type: number + maximum: 9999 + minimum: -9999 + nhise: + default: 0 + title: Number of HISE residue + description: Defines the number of HISE residues (neutral HIS with the + proton on the NE atom) residues when autohis=false + $comment: Defines the number of HISE residues (neutral HIS with the + proton on the NE atom) residues. The corresponding residue numbers + must be defined in the following parameter (hise_1, hise_2, ...). + Add as many as needed. Note that HIS is interpreted as a charged Histidine) + type: number + maximum: 9999 + minimum: 0 + hise: + type: array + items: + title: HISE residue number + description: Residue number of the Histidine to be defined as HISE + $comment: Residue number of the Histidine to be defined as HISE + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false required: [] additionalProperties: false uiSchema: @@ -3929,46 +1922,18 @@ nodes: ui:group: force field tolerance: ui:group: module - mol1: - ui:field: collapsible - mol2: - ui:field: collapsible - mol3: - ui:field: collapsible - mol4: - ui:field: collapsible - mol5: - ui:field: collapsible - mol6: - ui:field: collapsible - mol7: - ui:field: collapsible - mol8: - ui:field: collapsible - mol9: - ui:field: collapsible - mol10: - ui:field: collapsible - mol11: - ui:field: collapsible - mol12: - ui:field: collapsible - mol13: - ui:field: collapsible - mol14: - ui:field: collapsible - mol15: - ui:field: collapsible - mol16: - ui:field: collapsible - mol17: - ui:field: collapsible - mol18: - ui:field: collapsible - mol19: - ui:field: collapsible - mol20: - ui:field: collapsible + mol: + ui:group: input molecules + tomlSchema: + mol: + indexed: true + items: + sectioned: true + properties: + hisd: + indexed: true + hise: + indexed: true - id: emscoring category: scoring label: HADDOCK3 scoring module. @@ -3976,203 +1941,447 @@ nodes: schema: type: object properties: + w_bsa: + default: 0.0 + title: Weight of the buried surface area term + description: Weight of the buried surface area term in the scoring function + $comment: Weight of the buried surface area (BSA) term in the scoring function. + Note that the BSA is only used for scoring. + type: number + maximum: 9999 + minimum: -9999 + w_cdih: + default: 0.0 + title: Weight of the dihedral angle restraint energy + description: Weight of the dihedral angle restraints energy in the scoring + function + $comment: Weight of the dihedral angle restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. + type: number + maximum: 9999 + minimum: 0 + w_desolv: + default: 1.0 + title: Weight of the desolvation energy term + description: Weight of the desolvation energy term in the scoring function + $comment: Weight of the desolvation energy term in the scoring function. Note + that the desolvation energy is only used for scoring. + type: number + maximum: 9999 + minimum: -9999 + w_elec: + default: 0.2 + title: Weight of the intermolecular electrostatic energy + description: Weight of the intermolecular electrostatic energy in the scoring + function + $comment: Weight of the intermolecular electrostatic energy in the scoring + function. Note that this does not affect the electostatic energy during + the EM minimization. + type: number + maximum: 9999 + minimum: -9999 + w_vdw: + default: 1.0 + title: Weight of the intermolecular van der Waals energy + description: Weight of the intermolecular van der Waals energy in the scoring + function + $comment: Weight of the intermolecular van der Waals energy in the scoring + function. Note that this does not affect the van der Waals energy during + the EM minimization. + type: number + maximum: 9999 + minimum: -9999 + ligand_param_fname: + title: Custom ligand parameter file + description: Ligand parameter file in CNS format + $comment: Ligand parameter file in CNS format containing all force field parameters + (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported + by default by HADDOCK + type: string + format: uri-reference + ligand_top_fname: + title: Custom ligand topology file + description: Ligand topology file in CNS format + $comment: Ligand topology file in CNS format containing the ligand topologies + (atoms, masses, charges, bond definitions...) for any ligand not supported + by default by HADDOCK + type: string + format: uri-reference + elecflag: + default: true + title: Include electrostatics energy + description: Include electrostatics energy during the calculations. + $comment: Include electrostatics energy during the calculations. If set to + false electrostatics will not be considered. + type: boolean + dielec: + default: cdie + title: Constant (cdie) or distance-dependent dielectric (rdie) constant. + description: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. + $comment: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. A distance dependent dielectric + constant will effectively scale down the electrostatic energy by having + a 1/r**2 dependency instead of 1/r + type: string + minLength: 0 + maxLength: 4 + enum: + - cdie + - rdie + epsilon: + default: 1.0 + title: Dielectric constant + description: Dielectric constant for the electrostatic Coulomb energy term. + $comment: Dielectric constant for the electrostatic Coulomb energy term. + type: number + maximum: 78 + minimum: 1 + dihedflag: + default: true + type: boolean + individualize: + default: true + title: Individualise models + description: Treat each model in the PDB ensemble as a separate entity. + $comment: Treat each model in the PDB ensemble as a separate entity. This + means that for each a separate topology file will be generated. The models + in the ensemble can thus correspond to different molecules. + type: boolean + nemsteps: + default: 50 + title: Number of EM steps + description: Number of energy minimisation steps to perform. + $comment: Number of energy minimisation steps to perform. Note that the effective + number might be smaller if the minimisation converges earlier. + type: number + maximum: 10000 + minimum: 1 tolerance: - default: 5 + default: 0 + title: Failure tolerance percentage + description: Percentage of allowed failures for a module to successfully complete + $comment: Percentage of allowed failures for a module to successfully complete + type: number + maximum: 99 + minimum: 0 + required: [] + additionalProperties: false + uiSchema: + w_bsa: + ui:group: scoring + w_cdih: + ui:group: scoring + w_desolv: + ui:group: scoring + w_elec: + ui:group: scoring + w_vdw: + ui:group: scoring + ligand_param_fname: + ui:widget: file + ui:group: force field + ligand_top_fname: + ui:widget: file + ui:group: force field + elecflag: + ui:group: force field + dielec: + ui:group: force field + epsilon: + ui:group: force field + dihedflag: + ui:group: force field + individualize: + ui:group: sampling + nemsteps: + ui:group: sampling + tolerance: + ui:group: module + tomlSchema: {} +- id: mdscoring + category: scoring + label: HADDOCK3 scoring module. + description: HADDOCK3 module to perform energy minimization scoring. + schema: + type: object + properties: + w_bsa: + default: 0.0 + title: Weight of the buried surface area term + description: Weight of the buried surface area term in the scoring function + $comment: Weight of the buried surface area (BSA) term in the scoring function. + Note that the BSA is only used for scoring. + type: number + maximum: 9999 + minimum: -9999 + w_cdih: + default: 0.0 + title: Weight of the dihedral angle restraint energy + description: Weight of the dihedral angle restraints energy in the scoring + function + $comment: Weight of the dihedral angle restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. + type: number + maximum: 9999 + minimum: 0 + w_desolv: + default: 1.0 + title: Weight of the desolvation energy term + description: Weight of the desolvation energy term in the scoring function + $comment: Weight of the desolvation energy term in the scoring function. Note + that the desolvation energy is only used for scoring. + type: number + maximum: 9999 + minimum: -9999 + w_elec: + default: 0.2 + title: Weight of the intermolecular electrostatic energy + description: Weight of the intermolecular electrostatic energy in the scoring + function + $comment: Weight of the intermolecular electrostatic energy in the scoring + function. Note that this does not affect the electostatic energy during + the EM minimization. + type: number + maximum: 9999 + minimum: -9999 + w_vdw: + default: 1.0 + title: Weight of the intermolecular van der Waals energy + description: Weight of the intermolecular van der Waals energy in the scoring + function + $comment: Weight of the intermolecular van der Waals energy in the scoring + function. Note that this does not affect the van der Waals energy during + the EM minimization. type: number maximum: 9999 minimum: -9999 - log_level: - default: verbose + contactairs: + default: false + title: Contact restraints + description: Contact restraints between molecules + $comment: Contact restraints between molecules. These are defined as ambiguous + distance restraint between each residue of a molecule and all residues of + the other molecules with 5A from that residue. This can be used to restraint + the contacts between the interfaces. Note that this can generate a large + number of ambiguous restraints and slow down the computations + type: boolean + kcont: + default: 1.0 + title: Contact restraints force constant + description: Force constant applied to the contact restraints. + $comment: Force constant applied to the contact restraints. + type: number + maximum: 1000 + minimum: 0 + ssdihed: + default: none + title: Define automatically backbone dihedral angle restraints + description: If turned on, this option will automatically defined backbone + dihedral angle restraints for the selected regions. + $comment: This option allows to utomatically defined backbone dihedral angle + restraints for the selected regions. The restraints will be defined for + the phi and psi backbone dihedral angles of amino acids, with the target + value taken from the measured angle in the input structure, and the error + bound defined by the error_dih parameter. Those restraints can be applied + to the entire structure (all), the alpha/beta secondary structure elements + (alphabeta) or only to the alpha helical regions (alpha). Those are automatically + detected based on the measured dihedral angle combinations. type: string minLength: 0 maxLength: 100 + enum: + - none + - all + - alpha + - alphabeta + error_dih: + default: 10 + title: Force constant for backbone dihedral angle restraints + description: Force constant for backbone dihedral angle restraints (ssdihed + option) + $comment: Force constant for backbone dihedral angle restraints (ssdihed option) + type: number + maximum: 1000 + minimum: 0 + dnarest_on: + default: false + title: Restrain the DNA conformation + description: Automatically creates restraints to maintain the conformation + of DNA/RNA + $comment: 'This option allows to restraint the conformation of nucleic acids + based on the values from the input structures. The following restraints + will be automatically defined: - single base planarity - sugar pucker - + phosphate backbone diherdral angle restraints - Watson-Crick base pairing' + type: boolean ligand_param_fname: + title: Custom ligand parameter file + description: Ligand parameter file in CNS format + $comment: Ligand parameter file in CNS format containing all force field parameters + (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported + by default by HADDOCK type: string format: uri-reference ligand_top_fname: + title: Custom ligand topology file + description: Ligand topology file in CNS format + $comment: Ligand topology file in CNS format containing the ligand topologies + (atoms, masses, charges, bond definitions...) for any ligand not supported + by default by HADDOCK type: string format: uri-reference - individualize: - default: true - type: boolean - nemsteps: - default: 40 - type: number - maximum: 9999 - minimum: -9999 elecflag: default: true + title: Include electrostatics energy + description: Include electrostatics energy during the calculations. + $comment: Include electrostatics energy during the calculations. If set to + false electrostatics will not be considered. type: boolean dielec: default: cdie + title: Constant (cdie) or distance-dependent dielectric (rdie) constant. + description: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. + $comment: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. A distance dependent dielectric + constant will effectively scale down the electrostatic energy by having + a 1/r**2 dependency instead of 1/r type: string minLength: 0 - maxLength: 100 + maxLength: 4 + enum: + - cdie + - rdie epsilon: default: 1.0 + title: Dielectric constant + description: Dielectric constant for the electrostatic Coulomb energy term. + $comment: Dielectric constant for the electrostatic Coulomb energy term. type: number - maximum: 9999 - minimum: -9999 + maximum: 78 + minimum: 1 dihedflag: default: true type: boolean - par_nonbonded: - default: OPLSX + individualize: + default: true + title: Individualise models + description: Treat each model in the PDB ensemble as a separate entity. + $comment: Treat each model in the PDB ensemble as a separate entity. This + means that for each a separate topology file will be generated. The models + in the ensemble can thus correspond to different molecules. + type: boolean + solvent: + default: water + title: Solvent + description: Solvent to use during the short MD refinement + $comment: Solvent to use during the short MD refinement. Water and DMSO are + supported. A solvent shelll is generated by shifting pre-equilibrated boxes + around the complex. For water an 8A water shell is generated and for DMSO + a 12.5A shell. For DMSO, type: string minLength: 0 maxLength: 100 - w_air: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_bsa: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_cdih: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_dani: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_deint: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_desolv: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - w_dist: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_elec: - default: 0.2 - type: number - maximum: 9999 - minimum: -9999 - w_lcc: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_rg: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_sani: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_sym: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_vdw: - default: 1.0 + enum: + - water + - dmso + nemsteps: + default: 200 + title: Number of EM steps + description: Number of energy minimisation steps to perform. + $comment: Number of energy minimisation steps to perform in the various EM + stages of this refinement protocol. Note that the effective number might + be smaller if the minimisation converges earlier. type: number - maximum: 9999 - minimum: -9999 - w_vean: - default: 0.0 + maximum: 10000 + minimum: 1 + waterheatsteps: + default: 100 + title: Number of MD steps for the heating + description: Number of MD steps for the heating phase. + $comment: Number of MD steps for the heating phase. The heating consists of + three successive short molecular dynamics simluations at 100, 200 and 300 + Kelvin. type: number - maximum: 9999 - minimum: -9999 - w_xpcs: - default: 0.0 + maximum: 10000 + minimum: 0 + watersteps: + default: 1250 + title: Number of MD steps at 300K. + description: Number of MD steps for 300K simulation. + $comment: Number of MD steps for 300K simulation. This is the sampling state + of the refinement. type: number - maximum: 9999 - minimum: -9999 - w_xrdc: - default: 0.0 + maximum: 100000 + minimum: 0 + watercoolsteps: + default: 500 + title: Number of MD steps for the cooling + description: Number of MD steps for the cooling phase. + $comment: Number of MD steps for the cooling phase. The cooling consists of + three successive short molecular dynamics simluations at 300, 200 and 100 + Kelvin. type: number - maximum: 9999 - minimum: -9999 - w_zres: - default: 0.0 + maximum: 10000 + minimum: 0 + tolerance: + default: 0 + title: Failure tolerance percentage + description: Percentage of allowed failures for a module to successfully complete + $comment: Percentage of allowed failures for a module to successfully complete type: number - maximum: 9999 - minimum: -9999 - shape_1: - default: false - type: boolean - shape_2: - default: false - type: boolean - shape_3: - default: false - type: boolean - shape_4: - default: false - type: boolean - shape_5: - default: false - type: boolean - shape_6: - default: false - type: boolean - shape_7: - default: false - type: boolean - shape_8: - default: false - type: boolean - shape_9: - default: false - type: boolean - shape_10: - default: false - type: boolean - shape_11: - default: false - type: boolean - shape_12: - default: false - type: boolean - shape_13: - default: false - type: boolean - shape_14: - default: false - type: boolean - shape_15: - default: false - type: boolean - shape_16: - default: false - type: boolean - shape_17: - default: false - type: boolean - shape_18: - default: false - type: boolean - shape_19: - default: false - type: boolean - shape_20: - default: false - type: boolean + maximum: 99 + minimum: 0 required: [] additionalProperties: false uiSchema: + w_bsa: + ui:group: scoring + w_cdih: + ui:group: scoring + w_desolv: + ui:group: scoring + w_elec: + ui:group: scoring + w_vdw: + ui:group: scoring + contactairs: + ui:group: distance restraints + kcont: + ui:group: distance restraints + ssdihed: + ui:group: dihedral restraints + error_dih: + ui:group: dihedral restraints + dnarest_on: + ui:group: other restraints ligand_param_fname: ui:widget: file + ui:group: force field ligand_top_fname: ui:widget: file + ui:group: force field + elecflag: + ui:group: force field + dielec: + ui:group: force field + epsilon: + ui:group: force field + dihedflag: + ui:group: force field + individualize: + ui:group: sampling + nemsteps: + ui:group: sampling + waterheatsteps: + ui:group: sampling + watersteps: + ui:group: sampling + watercoolsteps: + ui:group: sampling + tolerance: + ui:group: module + tomlSchema: {} - id: flexref category: refinement label: HADDOCK3 module for flexible refinement. @@ -4180,246 +2389,22 @@ nodes: schema: type: object properties: - mol_fix_origin_1: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_2: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_3: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_4: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_5: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_6: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_7: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_8: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_9: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_10: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_11: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_12: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_13: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_14: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_15: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_16: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_17: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_18: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_19: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_20: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + mol_fix_origin: + type: array + items: + default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. + type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -4876,344 +2861,392 @@ nodes: type: number maximum: 40 minimum: 0 - c2sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C2 symmetry segment - $comment: Residue number of first residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C2 symmetry segment - $comment: Residue number of last residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg1_1: - default: '' - title: Segment ID of first C2 segment - description: Segment ID of first C2 segment - $comment: Segment ID of first C2 segment - type: string - minLength: 0 - maxLength: 4 - c2sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C2 symmetry segment - $comment: Residue number of first residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C2 symmetry segment - $comment: Residue number of last residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg2_1: - default: '' - title: Segment ID of second C2 segment - description: Segment ID of second C2 segment - $comment: Segment ID of second C2 segment - type: string - minLength: 0 - maxLength: 4 + c2sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C2 symmetry + segment + $comment: Residue number of first residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C2 symmetry + segment + $comment: Residue number of last residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C2 segment + description: Segment ID of first C2 segment + $comment: Segment ID of first C2 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C2 symmetry + segment + $comment: Residue number of first residue in the second C2 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C2 symmetry + segment + $comment: Residue number of last residue in the second C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C2 segment + description: Segment ID of second C2 segment + $comment: Segment ID of second C2 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc3sym: default: 0 title: Number of C3 symmetry restraints description: Defines the number of C3 symmetry restraints. $comment: Defines the number of C3 symmetry restraints. For each, three segments on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C3 symmetry segment - $comment: Residue number of first residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C3 symmetry segment - $comment: Residue number of last residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg1_1: - default: '' - title: Segment ID of first C3 segment - description: Segment ID of first C3 segment - $comment: Segment ID of first C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C3 symmetry segment - $comment: Residue number of first residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C3 symmetry segment - $comment: Residue number of last residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg2_1: - default: '' - title: Segment ID of second C3 segment - description: Segment ID of second C3 segment - $comment: Segment ID of second C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C3 symmetry segment - $comment: Residue number of first residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C3 symmetry segment - $comment: Residue number of last residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg3_1: - default: '' - title: Segment ID of third C3 segment - description: Segment ID of third C3 segment - $comment: Segment ID of third C3 segment - type: string - minLength: 0 - maxLength: 4 - numc4sym: - default: 0 - title: Number of C4 symmetry restraints - description: Defines the number of C4 symmetry restraints. - $comment: Defines the number of C4 symmetry restraints. For each, four segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c4sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C4 symmetry segment - $comment: Residue number of first residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C4 symmetry segment - $comment: Residue number of last residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg1_1: - default: '' - title: Segment ID of first C4 segment - description: Segment ID of first C4 segment - $comment: Segment ID of first C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C4 symmetry segment - $comment: Residue number of first residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C4 symmetry segment - $comment: Residue number of last residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg2_1: - default: '' - title: Segment ID of second C4 segment - description: Segment ID of second C4 segment - $comment: Segment ID of second C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C4 symmetry segment - $comment: Residue number of first residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C4 symmetry segment - $comment: Residue number of last residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg3_1: - default: '' - title: Segment ID of third C4 segment - description: Segment ID of third C4 segment - $comment: Segment ID of third C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C4 symmetry segment - $comment: Residue number of first residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C4 symmetry segment - $comment: Residue number of last residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg4_1: - default: '' - title: Segment ID of fourth C4 segment - description: Segment ID of fourth C4 segment - $comment: Segment ID of fourth C4 segment - type: string - minLength: 0 - maxLength: 4 - numc5sym: - default: 0 - title: Number of C5 symmetry restraints - description: Defines the number of C5 symmetry restraints. - $comment: Defines the number of C5 symmetry restraints. For each, five segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c5sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C5 symmetry segment - $comment: Residue number of first residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C5 symmetry segment - $comment: Residue number of last residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg1_1: - default: '' - title: Segment ID of first C5 segment - description: Segment ID of first C5 segment - $comment: Segment ID of first C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C5 symmetry segment - $comment: Residue number of first residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C5 symmetry segment - $comment: Residue number of last residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg2_1: - default: '' - title: Segment ID of second C5 segment - description: Segment ID of second C5 segment - $comment: Segment ID of second C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C5 symmetry segment - $comment: Residue number of first residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C5 symmetry segment - $comment: Residue number of last residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg3_1: - default: '' - title: Segment ID of third C5 segment - description: Segment ID of third C5 segment - $comment: Segment ID of third C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C5 symmetry segment - $comment: Residue number of first residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C5 symmetry segment - $comment: Residue number of last residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg4_1: - default: '' - title: Segment ID of fourth C5 segment - description: Segment ID of fourth C5 segment - $comment: Segment ID of fourth C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C5 symmetry segment - $comment: Residue number of first residue in the fifth C5 symmetry segment + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - c5sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C5 symmetry segment - $comment: Residue number of last residue in the fifth C5 symmetry segment + maximum: 10 + minimum: 0 + c3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C3 symmetry + segment + $comment: Residue number of first residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C3 symmetry + segment + $comment: Residue number of last residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C3 segment + description: Segment ID of first C3 segment + $comment: Segment ID of first C3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C3 symmetry + segment + $comment: Residue number of first residue in the second C3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C3 symmetry + segment + $comment: Residue number of last residue in the second C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C3 segment + description: Segment ID of second C3 segment + $comment: Segment ID of second C3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C3 symmetry + segment + $comment: Residue number of first residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C3 symmetry + segment + $comment: Residue number of last residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C3 segment + description: Segment ID of third C3 segment + $comment: Segment ID of third C3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc4sym: + default: 0 + title: Number of C4 symmetry restraints + description: Defines the number of C4 symmetry restraints. + $comment: Defines the number of C4 symmetry restraints. For each, four segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - c5sym_seg5_1: - default: '' - title: Segment ID of fifth C5 segment - description: Segment ID of fifth C5 segment - $comment: Segment ID of fifth C5 segment - type: string - minLength: 0 - maxLength: 4 + maximum: 10 + minimum: 0 + c4sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C4 symmetry + segment + $comment: Residue number of first residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C4 symmetry + segment + $comment: Residue number of last residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C4 segment + description: Segment ID of first C4 segment + $comment: Segment ID of first C4 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C4 symmetry + segment + $comment: Residue number of first residue in the second C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C4 symmetry + segment + $comment: Residue number of last residue in the second C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C4 segment + description: Segment ID of second C4 segment + $comment: Segment ID of second C4 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C4 symmetry + segment + $comment: Residue number of first residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C4 symmetry + segment + $comment: Residue number of last residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C4 segment + description: Segment ID of third C4 segment + $comment: Segment ID of third C4 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C4 symmetry + segment + $comment: Residue number of first residue in the fourth C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C4 symmetry + segment + $comment: Residue number of last residue in the fourth C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C4 segment + description: Segment ID of fourth C4 segment + $comment: Segment ID of fourth C4 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc5sym: + default: 0 + title: Number of C5 symmetry restraints + description: Defines the number of C5 symmetry restraints. + $comment: Defines the number of C5 symmetry restraints. For each, five segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. + type: number + maximum: 10 + minimum: 0 + c5sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C5 symmetry + segment + $comment: Residue number of first residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C5 symmetry + segment + $comment: Residue number of last residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C5 segment + description: Segment ID of first C5 segment + $comment: Segment ID of first C5 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C5 symmetry + segment + $comment: Residue number of first residue in the second C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C5 symmetry + segment + $comment: Residue number of last residue in the second C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C5 segment + description: Segment ID of second C5 segment + $comment: Segment ID of second C5 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C5 symmetry + segment + $comment: Residue number of first residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C5 symmetry + segment + $comment: Residue number of last residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C5 segment + description: Segment ID of third C5 segment + $comment: Segment ID of third C5 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C5 symmetry + segment + $comment: Residue number of first residue in the fourth C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C5 symmetry + segment + $comment: Residue number of last residue in the fourth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C5 segment + description: Segment ID of fourth C5 segment + $comment: Segment ID of fourth C5 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C5 symmetry + segment + $comment: Residue number of first residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C5 symmetry + segment + $comment: Residue number of last residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C5 segment + description: Segment ID of fifth C5 segment + $comment: Segment ID of fifth C5 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc6sym: default: 0 title: Number of C6 symmetry restraints @@ -5224,138 +3257,153 @@ nodes: type: number maximum: 10 minimum: 0 - c6sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C6 symmetry segment - $comment: Residue number of first residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C6 symmetry segment - $comment: Residue number of last residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg1_1: - default: '' - title: Segment ID of first C6 segment - description: Segment ID of first C6 segment - $comment: Segment ID of first C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C6 symmetry segment - $comment: Residue number of first residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C6 symmetry segment - $comment: Residue number of last residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg2_1: - default: '' - title: Segment ID of second C6 segment - description: Segment ID of second C6 segment - $comment: Segment ID of second C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C6 symmetry segment - $comment: Residue number of first residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C6 symmetry segment - $comment: Residue number of last residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg3_1: - default: '' - title: Segment ID of third C6 segment - description: Segment ID of third C6 segment - $comment: Segment ID of third C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C6 symmetry segment - $comment: Residue number of first residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C6 symmetry segment - $comment: Residue number of last residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg4_1: - default: '' - title: Segment ID of fourth C6 segment - description: Segment ID of fourth C6 segment - $comment: Segment ID of fourth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C6 symmetry segment - $comment: Residue number of first residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C6 symmetry segment - $comment: Residue number of last residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg5_1: - default: '' - title: Segment ID of fifth C6 segment - description: Segment ID of fifth C6 segment - $comment: Segment ID of fifth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta6_1: - title: Residue number of first residue - description: Residue number of first residue in the sixth C6 symmetry segment - $comment: Residue number of first residue in the sixth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end6_1: - title: Residue number of last residue - description: Residue number of last residue in the sixth C6 symmetry segment - $comment: Residue number of last residue in the sixth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg6_1: - default: '' - title: Segment ID of sixth C6 segment - description: Segment ID of sixth C6 segment - $comment: Segment ID of sixth C6 segment - type: string - minLength: 0 - maxLength: 4 + c6sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C6 symmetry + segment + $comment: Residue number of first residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C6 symmetry + segment + $comment: Residue number of last residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C6 segment + description: Segment ID of first C6 segment + $comment: Segment ID of first C6 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C6 symmetry + segment + $comment: Residue number of first residue in the second C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C6 symmetry + segment + $comment: Residue number of last residue in the second C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C6 segment + description: Segment ID of second C6 segment + $comment: Segment ID of second C6 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C6 symmetry + segment + $comment: Residue number of first residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C6 symmetry + segment + $comment: Residue number of last residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C6 segment + description: Segment ID of third C6 segment + $comment: Segment ID of third C6 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C6 symmetry + segment + $comment: Residue number of first residue in the fourth C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C6 symmetry + segment + $comment: Residue number of last residue in the fourth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C6 segment + description: Segment ID of fourth C6 segment + $comment: Segment ID of fourth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C6 symmetry + segment + $comment: Residue number of first residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C6 symmetry + segment + $comment: Residue number of last residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C6 segment + description: Segment ID of fifth C6 segment + $comment: Segment ID of fifth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta6: + title: Residue number of first residue + description: Residue number of first residue in the sixth C6 symmetry + segment + $comment: Residue number of first residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end6: + title: Residue number of last residue + description: Residue number of last residue in the sixth C6 symmetry + segment + $comment: Residue number of last residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg6: + title: Segment ID of sixth C6 segment + description: Segment ID of sixth C6 segment + $comment: Segment ID of sixth C6 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false nums3sym: default: 0 title: Number of S3 symmetry restraints @@ -5366,72 +3414,83 @@ nodes: type: number maximum: 10 minimum: 0 - s3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first S3 symmetry segment - $comment: Residue number of first residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first S3 symmetry segment - $comment: Residue number of last residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg1_1: - default: '' - title: Segment ID of first S3 segment - description: Segment ID of first S3 segment - $comment: Segment ID of first S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second S3 symmetry segment - $comment: Residue number of first residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second S3 symmetry segment - $comment: Residue number of last residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg2_1: - default: '' - title: Segment ID of second S3 segment - description: Segment ID of second S3 segment - $comment: Segment ID of second S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third S3 symmetry segment - $comment: Residue number of first residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third S3 symmetry segment - $comment: Residue number of last residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg3_1: - default: '' - title: Segment ID of third S3 segment - description: Segment ID of third S3 segment - $comment: Segment ID of third S3 segment - type: string - minLength: 0 - maxLength: 4 + s3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first S3 symmetry + segment + $comment: Residue number of first residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first S3 symmetry + segment + $comment: Residue number of last residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first S3 segment + description: Segment ID of first S3 segment + $comment: Segment ID of first S3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second S3 symmetry + segment + $comment: Residue number of first residue in the second S3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second S3 symmetry + segment + $comment: Residue number of last residue in the second S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second S3 segment + description: Segment ID of second S3 segment + $comment: Segment ID of second S3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third S3 symmetry + segment + $comment: Residue number of first residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third S3 symmetry + segment + $comment: Residue number of last residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third S3 segment + description: Segment ID of third S3 segment + $comment: Segment ID of third S3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false ncs_on: default: false title: Non-crystallographic symmetry restraints @@ -5460,50 +3519,55 @@ nodes: type: number maximum: 100 minimum: 0 - ncs_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first NCS segment - $comment: Residue number of first residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first NCS segment - $comment: Residue number of last residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg1_1: - default: '' - title: Segment ID of first NCS segment - description: Segment ID of first NCS segment - $comment: Segment ID of first NCS segment - type: string - minLength: 0 - maxLength: 100 - ncs_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second NCS segment - $comment: Residue number of first residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second NCS segment - $comment: Residue number of last residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg2_1: - default: '' - title: Segment ID of second NCS segment - description: Segment ID of second NCS segment - $comment: Segment ID of second NCS segment - type: string - minLength: 0 - maxLength: 100 + ncs: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first NCS segment + $comment: Residue number of first residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first NCS segment + $comment: Residue number of last residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first NCS segment + description: Segment ID of first NCS segment + $comment: Segment ID of first NCS segment + type: string + minLength: 0 + maxLength: 100 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second NCS segment + $comment: Residue number of first residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second NCS segment + $comment: Residue number of last residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second NCS segment + description: Segment ID of second NCS segment + $comment: Segment ID of second NCS segment + type: string + minLength: 0 + maxLength: 100 + required: [] + additionalProperties: false w_air: default: 0.1 title: Weight of the distance restraint energy @@ -5618,6 +3682,13 @@ nodes: type: number maximum: 78 minimum: 1 + dihedflag: + default: true + title: Use torsion angle dihedral energy term + description: Turns on the torsion angle dihedral energy terms of the force + field. + $comment: Turns on the torsion angle dihedral energy terms of the force field. + type: boolean sampling_factor: default: 1 title: Sampling factor for each starting model @@ -5709,20 +3780,31 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_1_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 + seg: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the semi-flexible + segment. + $comment: Residue number defining the start of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: Ending residue number + description: Residue number defining the end of the semi-flexible + segment. + $comment: Residue number defining the end of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nseg2: default: -1 title: Number of semi-flexible segments @@ -5738,20 +3820,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_2_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg3: default: -1 title: Number of semi-flexible segments @@ -5767,20 +3835,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_3_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg4: default: -1 title: Number of semi-flexible segments @@ -5796,20 +3850,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_4_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg5: default: -1 title: Number of semi-flexible segments @@ -5825,20 +3865,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_5_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg6: default: -1 title: Number of semi-flexible segments @@ -5854,20 +3880,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_6_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg7: default: -1 title: Number of semi-flexible segments @@ -5883,20 +3895,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_7_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg8: default: -1 title: Number of semi-flexible segments @@ -5912,20 +3910,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_8_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg9: default: -1 title: Number of semi-flexible segments @@ -5941,20 +3925,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_9_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg10: default: -1 title: Number of semi-flexible segments @@ -5970,20 +3940,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_10_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg11: default: -1 title: Number of semi-flexible segments @@ -5999,20 +3955,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_11_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg12: default: -1 title: Number of semi-flexible segments @@ -6028,20 +3970,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_12_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg13: default: -1 title: Number of semi-flexible segments @@ -6057,20 +3985,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_13_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg14: default: -1 title: Number of semi-flexible segments @@ -6086,20 +4000,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_14_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg15: default: -1 title: Number of semi-flexible segments @@ -6115,20 +4015,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_15_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg16: default: -1 title: Number of semi-flexible segments @@ -6144,20 +4030,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_16_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg17: default: -1 title: Number of semi-flexible segments @@ -6173,20 +4045,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_17_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg18: default: -1 title: Number of semi-flexible segments @@ -6199,23 +4057,9 @@ nodes: segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. - type: number - maximum: 1000 - minimum: -1 - seg_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_18_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 + type: number + maximum: 1000 + minimum: -1 nseg19: default: -1 title: Number of semi-flexible segments @@ -6231,20 +4075,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_19_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg20: default: -1 title: Number of semi-flexible segments @@ -6260,20 +4090,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_20_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle1: default: 0 title: Number of fully flexible segments @@ -6284,20 +4100,32 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_1_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 + fle: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the fully flexible + segment. + $comment: Residue number defining the start of the fully flexible + segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: End residue number + description: Residue number defining the end of the fully flexible + segment. + $comment: Residue number defining the end of the fully flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nfle2: default: 0 title: Number of fully flexible segments @@ -6308,20 +4136,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_2_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle3: default: 0 title: Number of fully flexible segments @@ -6332,20 +4146,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_3_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle4: default: 0 title: Number of fully flexible segments @@ -6356,20 +4156,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_4_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle5: default: 0 title: Number of fully flexible segments @@ -6380,20 +4166,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_5_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle6: default: 0 title: Number of fully flexible segments @@ -6404,20 +4176,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_6_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle7: default: 0 title: Number of fully flexible segments @@ -6428,20 +4186,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_7_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle8: default: 0 title: Number of fully flexible segments @@ -6452,20 +4196,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_8_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle9: default: 0 title: Number of fully flexible segments @@ -6476,20 +4206,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_9_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle10: default: 0 title: Number of fully flexible segments @@ -6500,20 +4216,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_10_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle11: default: 0 title: Number of fully flexible segments @@ -6524,20 +4226,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_11_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle12: default: 0 title: Number of fully flexible segments @@ -6548,20 +4236,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_12_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle13: default: 0 title: Number of fully flexible segments @@ -6572,20 +4246,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_13_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle14: default: 0 title: Number of fully flexible segments @@ -6596,20 +4256,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_14_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle15: default: 0 title: Number of fully flexible segments @@ -6620,20 +4266,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_15_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle16: default: 0 title: Number of fully flexible segments @@ -6644,20 +4276,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_16_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle17: default: 0 title: Number of fully flexible segments @@ -6668,20 +4286,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_17_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle18: default: 0 title: Number of fully flexible segments @@ -6692,20 +4296,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_18_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle19: default: 0 title: Number of fully flexible segments @@ -6716,20 +4306,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_19_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle20: default: 0 title: Number of fully flexible segments @@ -6740,102 +4316,12 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_20_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 required: [] additionalProperties: false uiSchema: - mol_fix_origin_1: - ui:group: molecule - mol_fix_origin_2: - ui:group: molecule - mol_fix_origin_3: - ui:group: molecule - mol_fix_origin_4: - ui:group: molecule - mol_fix_origin_5: - ui:group: molecule - mol_fix_origin_6: - ui:group: molecule - mol_fix_origin_7: - ui:group: molecule - mol_fix_origin_8: - ui:group: molecule - mol_fix_origin_9: - ui:group: molecule - mol_fix_origin_10: - ui:group: molecule - mol_fix_origin_11: - ui:group: molecule - mol_fix_origin_12: - ui:group: molecule - mol_fix_origin_13: - ui:group: molecule - mol_fix_origin_14: - ui:group: molecule - mol_fix_origin_15: - ui:group: molecule - mol_fix_origin_16: - ui:group: molecule - mol_fix_origin_17: - ui:group: molecule - mol_fix_origin_18: - ui:group: molecule - mol_fix_origin_19: - ui:group: molecule - mol_fix_origin_20: - ui:group: molecule - mol_shape_1: - ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: + mol_fix_origin: ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: - ui:group: molecule - mol_shape_10: - ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file @@ -6912,153 +4398,27 @@ nodes: ui:group: symmetry numc2sym: ui:group: symmetry - c2sym_sta1_1: - ui:group: symmetry - c2sym_end1_1: - ui:group: symmetry - c2sym_seg1_1: - ui:group: symmetry - c2sym_sta2_1: - ui:group: symmetry - c2sym_end2_1: - ui:group: symmetry - c2sym_seg2_1: + c2sym: ui:group: symmetry numc3sym: ui:group: symmetry - c3sym_sta1_1: - ui:group: symmetry - c3sym_end1_1: - ui:group: symmetry - c3sym_seg1_1: - ui:group: symmetry - c3sym_sta2_1: - ui:group: symmetry - c3sym_end2_1: - ui:group: symmetry - c3sym_seg2_1: - ui:group: symmetry - c3sym_sta3_1: - ui:group: symmetry - c3sym_end3_1: - ui:group: symmetry - c3sym_seg3_1: + c3sym: ui:group: symmetry numc4sym: ui:group: symmetry - c4sym_sta1_1: - ui:group: symmetry - c4sym_end1_1: - ui:group: symmetry - c4sym_seg1_1: - ui:group: symmetry - c4sym_sta2_1: - ui:group: symmetry - c4sym_end2_1: - ui:group: symmetry - c4sym_seg2_1: - ui:group: symmetry - c4sym_sta3_1: - ui:group: symmetry - c4sym_end3_1: - ui:group: symmetry - c4sym_seg3_1: - ui:group: symmetry - c4sym_sta4_1: - ui:group: symmetry - c4sym_end4_1: - ui:group: symmetry - c4sym_seg4_1: + c4sym: ui:group: symmetry numc5sym: ui:group: symmetry - c5sym_sta1_1: - ui:group: symmetry - c5sym_end1_1: - ui:group: symmetry - c5sym_seg1_1: - ui:group: symmetry - c5sym_sta2_1: - ui:group: symmetry - c5sym_end2_1: - ui:group: symmetry - c5sym_seg2_1: - ui:group: symmetry - c5sym_sta3_1: - ui:group: symmetry - c5sym_end3_1: - ui:group: symmetry - c5sym_seg3_1: - ui:group: symmetry - c5sym_sta4_1: - ui:group: symmetry - c5sym_end4_1: - ui:group: symmetry - c5sym_seg4_1: - ui:group: symmetry - c5sym_sta5_1: - ui:group: symmetry - c5sym_end5_1: - ui:group: symmetry - c5sym_seg5_1: + c5sym: ui:group: symmetry numc6sym: ui:group: symmetry - c6sym_sta1_1: - ui:group: symmetry - c6sym_end1_1: - ui:group: symmetry - c6sym_seg1_1: - ui:group: symmetry - c6sym_sta2_1: - ui:group: symmetry - c6sym_end2_1: - ui:group: symmetry - c6sym_seg2_1: - ui:group: symmetry - c6sym_sta3_1: - ui:group: symmetry - c6sym_end3_1: - ui:group: symmetry - c6sym_seg3_1: - ui:group: symmetry - c6sym_sta4_1: - ui:group: symmetry - c6sym_end4_1: - ui:group: symmetry - c6sym_seg4_1: - ui:group: symmetry - c6sym_sta5_1: - ui:group: symmetry - c6sym_end5_1: - ui:group: symmetry - c6sym_seg5_1: - ui:group: symmetry - c6sym_sta6_1: - ui:group: symmetry - c6sym_end6_1: - ui:group: symmetry - c6sym_seg6_1: + c6sym: ui:group: symmetry nums3sym: ui:group: symmetry - s3sym_sta1_1: - ui:group: symmetry - s3sym_end1_1: - ui:group: symmetry - s3sym_seg1_1: - ui:group: symmetry - s3sym_sta2_1: - ui:group: symmetry - s3sym_end2_1: - ui:group: symmetry - s3sym_seg2_1: - ui:group: symmetry - s3sym_sta3_1: - ui:group: symmetry - s3sym_end3_1: - ui:group: symmetry - s3sym_seg3_1: + s3sym: ui:group: symmetry ncs_on: ui:group: symmetry @@ -7066,17 +4426,7 @@ nodes: ui:group: symmetry numncs: ui:group: symmetry - ncs_sta1_1: - ui:group: symmetry - ncs_end1_1: - ui:group: symmetry - ncs_seg1_1: - ui:group: symmetry - ncs_sta2_1: - ui:group: symmetry - ncs_end2_1: - ui:group: symmetry - ncs_seg2_1: + ncs: ui:group: symmetry w_air: ui:group: scoring @@ -7104,6 +4454,8 @@ nodes: ui:group: force field epsilon: ui:group: force field + dihedflag: + ui:group: force field sampling_factor: ui:group: sampling nemsteps: @@ -7120,244 +4472,133 @@ nodes: ui:group: module nseg1: ui:group: flexibility - seg_sta_1_1: - ui:group: flexibility - seg_end_1_1: - ui:group: flexibility - nseg2: - ui:group: flexibility - seg_sta_2_1: - ui:group: flexibility - seg_end_2_1: - ui:group: flexibility - nseg3: - ui:group: flexibility - seg_sta_3_1: - ui:group: flexibility - seg_end_3_1: - ui:group: flexibility - nseg4: - ui:group: flexibility - seg_sta_4_1: + seg: ui:group: flexibility - seg_end_4_1: + nseg2: ui:group: flexibility - nseg5: + nseg3: ui:group: flexibility - seg_sta_5_1: + nseg4: ui:group: flexibility - seg_end_5_1: + nseg5: ui:group: flexibility nseg6: ui:group: flexibility - seg_sta_6_1: - ui:group: flexibility - seg_end_6_1: - ui:group: flexibility nseg7: ui:group: flexibility - seg_sta_7_1: - ui:group: flexibility - seg_end_7_1: - ui:group: flexibility nseg8: ui:group: flexibility - seg_sta_8_1: - ui:group: flexibility - seg_end_8_1: - ui:group: flexibility nseg9: ui:group: flexibility - seg_sta_9_1: - ui:group: flexibility - seg_end_9_1: - ui:group: flexibility nseg10: ui:group: flexibility - seg_sta_10_1: - ui:group: flexibility - seg_end_10_1: - ui:group: flexibility nseg11: ui:group: flexibility - seg_sta_11_1: - ui:group: flexibility - seg_end_11_1: - ui:group: flexibility nseg12: ui:group: flexibility - seg_sta_12_1: - ui:group: flexibility - seg_end_12_1: - ui:group: flexibility nseg13: ui:group: flexibility - seg_sta_13_1: - ui:group: flexibility - seg_end_13_1: - ui:group: flexibility nseg14: ui:group: flexibility - seg_sta_14_1: - ui:group: flexibility - seg_end_14_1: - ui:group: flexibility nseg15: ui:group: flexibility - seg_sta_15_1: - ui:group: flexibility - seg_end_15_1: - ui:group: flexibility nseg16: ui:group: flexibility - seg_sta_16_1: - ui:group: flexibility - seg_end_16_1: - ui:group: flexibility nseg17: ui:group: flexibility - seg_sta_17_1: - ui:group: flexibility - seg_end_17_1: - ui:group: flexibility nseg18: ui:group: flexibility - seg_sta_18_1: - ui:group: flexibility - seg_end_18_1: - ui:group: flexibility nseg19: ui:group: flexibility - seg_sta_19_1: - ui:group: flexibility - seg_end_19_1: - ui:group: flexibility nseg20: ui:group: flexibility - seg_sta_20_1: - ui:group: flexibility - seg_end_20_1: - ui:group: flexibility nfle1: ui:group: flexibility - fle_sta_1_1: - ui:group: flexibility - fle_end_1_1: + fle: ui:group: flexibility nfle2: ui:group: flexibility - fle_sta_2_1: - ui:group: flexibility - fle_end_2_1: - ui:group: flexibility nfle3: ui:group: flexibility - fle_sta_3_1: - ui:group: flexibility - fle_end_3_1: - ui:group: flexibility nfle4: ui:group: flexibility - fle_sta_4_1: - ui:group: flexibility - fle_end_4_1: - ui:group: flexibility nfle5: ui:group: flexibility - fle_sta_5_1: - ui:group: flexibility - fle_end_5_1: - ui:group: flexibility nfle6: ui:group: flexibility - fle_sta_6_1: - ui:group: flexibility - fle_end_6_1: - ui:group: flexibility nfle7: ui:group: flexibility - fle_sta_7_1: - ui:group: flexibility - fle_end_7_1: - ui:group: flexibility nfle8: ui:group: flexibility - fle_sta_8_1: - ui:group: flexibility - fle_end_8_1: - ui:group: flexibility nfle9: ui:group: flexibility - fle_sta_9_1: - ui:group: flexibility - fle_end_9_1: - ui:group: flexibility nfle10: ui:group: flexibility - fle_sta_10_1: - ui:group: flexibility - fle_end_10_1: - ui:group: flexibility nfle11: ui:group: flexibility - fle_sta_11_1: - ui:group: flexibility - fle_end_11_1: - ui:group: flexibility nfle12: ui:group: flexibility - fle_sta_12_1: - ui:group: flexibility - fle_end_12_1: - ui:group: flexibility nfle13: ui:group: flexibility - fle_sta_13_1: - ui:group: flexibility - fle_end_13_1: - ui:group: flexibility nfle14: ui:group: flexibility - fle_sta_14_1: - ui:group: flexibility - fle_end_14_1: - ui:group: flexibility nfle15: ui:group: flexibility - fle_sta_15_1: - ui:group: flexibility - fle_end_15_1: - ui:group: flexibility nfle16: ui:group: flexibility - fle_sta_16_1: - ui:group: flexibility - fle_end_16_1: - ui:group: flexibility nfle17: ui:group: flexibility - fle_sta_17_1: - ui:group: flexibility - fle_end_17_1: - ui:group: flexibility nfle18: ui:group: flexibility - fle_sta_18_1: - ui:group: flexibility - fle_end_18_1: - ui:group: flexibility nfle19: ui:group: flexibility - fle_sta_19_1: - ui:group: flexibility - fle_end_19_1: - ui:group: flexibility nfle20: ui:group: flexibility - fle_sta_20_1: - ui:group: flexibility - fle_end_20_1: - ui:group: flexibility + tomlSchema: + mol_fix_origin: + indexed: true + mol_shape: + indexed: true + c2sym: + indexed: true + items: + flatten: true + c3sym: + indexed: true + items: + flatten: true + c4sym: + indexed: true + items: + flatten: true + c5sym: + indexed: true + items: + flatten: true + c6sym: + indexed: true + items: + flatten: true + s3sym: + indexed: true + items: + flatten: true + ncs: + indexed: true + items: + flatten: true + seg: + indexed: true + items: + indexed: true + items: + flatten: true + fle: + indexed: true + items: + indexed: true + items: + flatten: true - id: mdref category: refinement label: HADDOCK3 module for water refinement. @@ -7365,246 +4606,22 @@ nodes: schema: type: object properties: - mol_fix_origin_1: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_2: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_3: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_4: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_5: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_6: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_7: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_8: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_9: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_10: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_11: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_12: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_13: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_14: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_15: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_16: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_17: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_18: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_19: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_20: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + mol_fix_origin: + type: array + items: + default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. + type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -7834,50 +4851,60 @@ nodes: type: number maximum: 40 minimum: 0 - c2sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C2 symmetry segment - $comment: Residue number of first residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C2 symmetry segment - $comment: Residue number of last residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg1_1: - default: '' - title: Segment ID of first C2 segment - description: Segment ID of first C2 segment - $comment: Segment ID of first C2 segment - type: string - minLength: 0 - maxLength: 4 - c2sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C2 symmetry segment - $comment: Residue number of first residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C2 symmetry segment - $comment: Residue number of last residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg2_1: - default: '' - title: Segment ID of second C2 segment - description: Segment ID of second C2 segment - $comment: Segment ID of second C2 segment - type: string - minLength: 0 - maxLength: 4 + c2sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C2 symmetry + segment + $comment: Residue number of first residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C2 symmetry + segment + $comment: Residue number of last residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C2 segment + description: Segment ID of first C2 segment + $comment: Segment ID of first C2 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C2 symmetry + segment + $comment: Residue number of first residue in the second C2 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C2 symmetry + segment + $comment: Residue number of last residue in the second C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C2 segment + description: Segment ID of second C2 segment + $comment: Segment ID of second C2 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc3sym: default: 0 title: Number of C3 symmetry restraints @@ -7888,170 +4915,194 @@ nodes: type: number maximum: 10 minimum: 0 - c3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C3 symmetry segment - $comment: Residue number of first residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C3 symmetry segment - $comment: Residue number of last residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg1_1: - default: '' - title: Segment ID of first C3 segment - description: Segment ID of first C3 segment - $comment: Segment ID of first C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C3 symmetry segment - $comment: Residue number of first residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C3 symmetry segment - $comment: Residue number of last residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg2_1: - default: '' - title: Segment ID of second C3 segment - description: Segment ID of second C3 segment - $comment: Segment ID of second C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C3 symmetry segment - $comment: Residue number of first residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C3 symmetry segment - $comment: Residue number of last residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg3_1: - default: '' - title: Segment ID of third C3 segment - description: Segment ID of third C3 segment - $comment: Segment ID of third C3 segment - type: string - minLength: 0 - maxLength: 4 + c3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C3 symmetry + segment + $comment: Residue number of first residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C3 symmetry + segment + $comment: Residue number of last residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C3 segment + description: Segment ID of first C3 segment + $comment: Segment ID of first C3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C3 symmetry + segment + $comment: Residue number of first residue in the second C3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C3 symmetry + segment + $comment: Residue number of last residue in the second C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C3 segment + description: Segment ID of second C3 segment + $comment: Segment ID of second C3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C3 symmetry + segment + $comment: Residue number of first residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C3 symmetry + segment + $comment: Residue number of last residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C3 segment + description: Segment ID of third C3 segment + $comment: Segment ID of third C3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc4sym: default: 0 - title: Number of C4 symmetry restraints - description: Defines the number of C4 symmetry restraints. - $comment: Defines the number of C4 symmetry restraints. For each, four segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c4sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C4 symmetry segment - $comment: Residue number of first residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C4 symmetry segment - $comment: Residue number of last residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg1_1: - default: '' - title: Segment ID of first C4 segment - description: Segment ID of first C4 segment - $comment: Segment ID of first C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C4 symmetry segment - $comment: Residue number of first residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C4 symmetry segment - $comment: Residue number of last residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg2_1: - default: '' - title: Segment ID of second C4 segment - description: Segment ID of second C4 segment - $comment: Segment ID of second C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C4 symmetry segment - $comment: Residue number of first residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C4 symmetry segment - $comment: Residue number of last residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg3_1: - default: '' - title: Segment ID of third C4 segment - description: Segment ID of third C4 segment - $comment: Segment ID of third C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C4 symmetry segment - $comment: Residue number of first residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C4 symmetry segment - $comment: Residue number of last residue in the fourth C4 symmetry segment + title: Number of C4 symmetry restraints + description: Defines the number of C4 symmetry restraints. + $comment: Defines the number of C4 symmetry restraints. For each, four segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - c4sym_seg4_1: - default: '' - title: Segment ID of fourth C4 segment - description: Segment ID of fourth C4 segment - $comment: Segment ID of fourth C4 segment - type: string - minLength: 0 - maxLength: 4 + maximum: 10 + minimum: 0 + c4sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C4 symmetry + segment + $comment: Residue number of first residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C4 symmetry + segment + $comment: Residue number of last residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C4 segment + description: Segment ID of first C4 segment + $comment: Segment ID of first C4 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C4 symmetry + segment + $comment: Residue number of first residue in the second C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C4 symmetry + segment + $comment: Residue number of last residue in the second C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C4 segment + description: Segment ID of second C4 segment + $comment: Segment ID of second C4 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C4 symmetry + segment + $comment: Residue number of first residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C4 symmetry + segment + $comment: Residue number of last residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C4 segment + description: Segment ID of third C4 segment + $comment: Segment ID of third C4 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C4 symmetry + segment + $comment: Residue number of first residue in the fourth C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C4 symmetry + segment + $comment: Residue number of last residue in the fourth C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C4 segment + description: Segment ID of fourth C4 segment + $comment: Segment ID of fourth C4 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc5sym: default: 0 title: Number of C5 symmetry restraints @@ -8062,116 +5113,130 @@ nodes: type: number maximum: 10 minimum: 0 - c5sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C5 symmetry segment - $comment: Residue number of first residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C5 symmetry segment - $comment: Residue number of last residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg1_1: - default: '' - title: Segment ID of first C5 segment - description: Segment ID of first C5 segment - $comment: Segment ID of first C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C5 symmetry segment - $comment: Residue number of first residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C5 symmetry segment - $comment: Residue number of last residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg2_1: - default: '' - title: Segment ID of second C5 segment - description: Segment ID of second C5 segment - $comment: Segment ID of second C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C5 symmetry segment - $comment: Residue number of first residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C5 symmetry segment - $comment: Residue number of last residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg3_1: - default: '' - title: Segment ID of third C5 segment - description: Segment ID of third C5 segment - $comment: Segment ID of third C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C5 symmetry segment - $comment: Residue number of first residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C5 symmetry segment - $comment: Residue number of last residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg4_1: - default: '' - title: Segment ID of fourth C5 segment - description: Segment ID of fourth C5 segment - $comment: Segment ID of fourth C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C5 symmetry segment - $comment: Residue number of first residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C5 symmetry segment - $comment: Residue number of last residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg5_1: - default: '' - title: Segment ID of fifth C5 segment - description: Segment ID of fifth C5 segment - $comment: Segment ID of fifth C5 segment - type: string - minLength: 0 - maxLength: 4 + c5sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C5 symmetry + segment + $comment: Residue number of first residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C5 symmetry + segment + $comment: Residue number of last residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C5 segment + description: Segment ID of first C5 segment + $comment: Segment ID of first C5 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C5 symmetry + segment + $comment: Residue number of first residue in the second C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C5 symmetry + segment + $comment: Residue number of last residue in the second C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C5 segment + description: Segment ID of second C5 segment + $comment: Segment ID of second C5 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C5 symmetry + segment + $comment: Residue number of first residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C5 symmetry + segment + $comment: Residue number of last residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C5 segment + description: Segment ID of third C5 segment + $comment: Segment ID of third C5 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C5 symmetry + segment + $comment: Residue number of first residue in the fourth C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C5 symmetry + segment + $comment: Residue number of last residue in the fourth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C5 segment + description: Segment ID of fourth C5 segment + $comment: Segment ID of fourth C5 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C5 symmetry + segment + $comment: Residue number of first residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C5 symmetry + segment + $comment: Residue number of last residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C5 segment + description: Segment ID of fifth C5 segment + $comment: Segment ID of fifth C5 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc6sym: default: 0 title: Number of C6 symmetry restraints @@ -8182,138 +5247,153 @@ nodes: type: number maximum: 10 minimum: 0 - c6sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C6 symmetry segment - $comment: Residue number of first residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C6 symmetry segment - $comment: Residue number of last residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg1_1: - default: '' - title: Segment ID of first C6 segment - description: Segment ID of first C6 segment - $comment: Segment ID of first C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C6 symmetry segment - $comment: Residue number of first residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C6 symmetry segment - $comment: Residue number of last residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg2_1: - default: '' - title: Segment ID of second C6 segment - description: Segment ID of second C6 segment - $comment: Segment ID of second C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C6 symmetry segment - $comment: Residue number of first residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C6 symmetry segment - $comment: Residue number of last residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg3_1: - default: '' - title: Segment ID of third C6 segment - description: Segment ID of third C6 segment - $comment: Segment ID of third C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C6 symmetry segment - $comment: Residue number of first residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C6 symmetry segment - $comment: Residue number of last residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg4_1: - default: '' - title: Segment ID of fourth C6 segment - description: Segment ID of fourth C6 segment - $comment: Segment ID of fourth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C6 symmetry segment - $comment: Residue number of first residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C6 symmetry segment - $comment: Residue number of last residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg5_1: - default: '' - title: Segment ID of fifth C6 segment - description: Segment ID of fifth C6 segment - $comment: Segment ID of fifth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta6_1: - title: Residue number of first residue - description: Residue number of first residue in the sixth C6 symmetry segment - $comment: Residue number of first residue in the sixth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end6_1: - title: Residue number of last residue - description: Residue number of last residue in the sixth C6 symmetry segment - $comment: Residue number of last residue in the sixth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg6_1: - default: '' - title: Segment ID of sixth C6 segment - description: Segment ID of sixth C6 segment - $comment: Segment ID of sixth C6 segment - type: string - minLength: 0 - maxLength: 4 + c6sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C6 symmetry + segment + $comment: Residue number of first residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C6 symmetry + segment + $comment: Residue number of last residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C6 segment + description: Segment ID of first C6 segment + $comment: Segment ID of first C6 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C6 symmetry + segment + $comment: Residue number of first residue in the second C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C6 symmetry + segment + $comment: Residue number of last residue in the second C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C6 segment + description: Segment ID of second C6 segment + $comment: Segment ID of second C6 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C6 symmetry + segment + $comment: Residue number of first residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C6 symmetry + segment + $comment: Residue number of last residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C6 segment + description: Segment ID of third C6 segment + $comment: Segment ID of third C6 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C6 symmetry + segment + $comment: Residue number of first residue in the fourth C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C6 symmetry + segment + $comment: Residue number of last residue in the fourth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C6 segment + description: Segment ID of fourth C6 segment + $comment: Segment ID of fourth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C6 symmetry + segment + $comment: Residue number of first residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C6 symmetry + segment + $comment: Residue number of last residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C6 segment + description: Segment ID of fifth C6 segment + $comment: Segment ID of fifth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta6: + title: Residue number of first residue + description: Residue number of first residue in the sixth C6 symmetry + segment + $comment: Residue number of first residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end6: + title: Residue number of last residue + description: Residue number of last residue in the sixth C6 symmetry + segment + $comment: Residue number of last residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg6: + title: Segment ID of sixth C6 segment + description: Segment ID of sixth C6 segment + $comment: Segment ID of sixth C6 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false nums3sym: default: 0 title: Number of S3 symmetry restraints @@ -8324,72 +5404,83 @@ nodes: type: number maximum: 10 minimum: 0 - s3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first S3 symmetry segment - $comment: Residue number of first residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first S3 symmetry segment - $comment: Residue number of last residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg1_1: - default: '' - title: Segment ID of first S3 segment - description: Segment ID of first S3 segment - $comment: Segment ID of first S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second S3 symmetry segment - $comment: Residue number of first residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second S3 symmetry segment - $comment: Residue number of last residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg2_1: - default: '' - title: Segment ID of second S3 segment - description: Segment ID of second S3 segment - $comment: Segment ID of second S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third S3 symmetry segment - $comment: Residue number of first residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third S3 symmetry segment - $comment: Residue number of last residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg3_1: - default: '' - title: Segment ID of third S3 segment - description: Segment ID of third S3 segment - $comment: Segment ID of third S3 segment - type: string - minLength: 0 - maxLength: 4 + s3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first S3 symmetry + segment + $comment: Residue number of first residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first S3 symmetry + segment + $comment: Residue number of last residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first S3 segment + description: Segment ID of first S3 segment + $comment: Segment ID of first S3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second S3 symmetry + segment + $comment: Residue number of first residue in the second S3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second S3 symmetry + segment + $comment: Residue number of last residue in the second S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second S3 segment + description: Segment ID of second S3 segment + $comment: Segment ID of second S3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third S3 symmetry + segment + $comment: Residue number of first residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third S3 symmetry + segment + $comment: Residue number of last residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third S3 segment + description: Segment ID of third S3 segment + $comment: Segment ID of third S3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false ncs_on: default: false title: Non-crystallographic symmetry restraints @@ -8418,50 +5509,55 @@ nodes: type: number maximum: 100 minimum: 0 - ncs_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first NCS segment - $comment: Residue number of first residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first NCS segment - $comment: Residue number of last residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg1_1: - default: '' - title: Segment ID of first NCS segment - description: Segment ID of first NCS segment - $comment: Segment ID of first NCS segment - type: string - minLength: 0 - maxLength: 100 - ncs_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second NCS segment - $comment: Residue number of first residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second NCS segment - $comment: Residue number of last residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg2_1: - default: '' - title: Segment ID of second NCS segment - description: Segment ID of second NCS segment - $comment: Segment ID of second NCS segment - type: string - minLength: 0 - maxLength: 100 + ncs: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first NCS segment + $comment: Residue number of first residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first NCS segment + $comment: Residue number of last residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first NCS segment + description: Segment ID of first NCS segment + $comment: Segment ID of first NCS segment + type: string + minLength: 0 + maxLength: 100 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second NCS segment + $comment: Residue number of first residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second NCS segment + $comment: Residue number of last residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second NCS segment + description: Segment ID of second NCS segment + $comment: Segment ID of second NCS segment + type: string + minLength: 0 + maxLength: 100 + required: [] + additionalProperties: false w_air: default: 0.1 title: Weight of the distance restraint energy @@ -8576,6 +5672,13 @@ nodes: type: number maximum: 78 minimum: 1 + dihedflag: + default: true + title: Use torsion angle dihedral energy term + description: Turns on the torsion angle dihedral energy terms of the force + field. + $comment: Turns on the torsion angle dihedral energy terms of the force field. + type: boolean sampling_factor: default: 1 title: Sampling factor for each starting model @@ -8660,20 +5763,31 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_1_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 + seg: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the semi-flexible + segment. + $comment: Residue number defining the start of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: Ending residue number + description: Residue number defining the end of the semi-flexible + segment. + $comment: Residue number defining the end of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nseg2: default: -1 title: Number of semi-flexible segments @@ -8689,20 +5803,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_2_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg3: default: -1 title: Number of semi-flexible segments @@ -8718,20 +5818,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_3_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg4: default: -1 title: Number of semi-flexible segments @@ -8747,20 +5833,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_4_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg5: default: -1 title: Number of semi-flexible segments @@ -8776,20 +5848,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_5_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg6: default: -1 title: Number of semi-flexible segments @@ -8805,20 +5863,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_6_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg7: default: -1 title: Number of semi-flexible segments @@ -8834,20 +5878,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_7_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg8: default: -1 title: Number of semi-flexible segments @@ -8863,20 +5893,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_8_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg9: default: -1 title: Number of semi-flexible segments @@ -8892,20 +5908,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_9_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg10: default: -1 title: Number of semi-flexible segments @@ -8921,20 +5923,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_10_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg11: default: -1 title: Number of semi-flexible segments @@ -8950,20 +5938,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_11_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg12: default: -1 title: Number of semi-flexible segments @@ -8979,20 +5953,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_12_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg13: default: -1 title: Number of semi-flexible segments @@ -9008,20 +5968,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_13_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg14: default: -1 title: Number of semi-flexible segments @@ -9033,24 +5979,10 @@ nodes: of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy - minimisation. If nseg is set to 0, then the molecule will be kept ridig. - type: number - maximum: 1000 - minimum: -1 - seg_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_14_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: -1 nseg15: default: -1 title: Number of semi-flexible segments @@ -9066,20 +5998,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_15_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg16: default: -1 title: Number of semi-flexible segments @@ -9095,20 +6013,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_16_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg17: default: -1 title: Number of semi-flexible segments @@ -9124,20 +6028,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_17_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg18: default: -1 title: Number of semi-flexible segments @@ -9153,20 +6043,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_18_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg19: default: -1 title: Number of semi-flexible segments @@ -9182,20 +6058,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_19_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg20: default: -1 title: Number of semi-flexible segments @@ -9211,20 +6073,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_20_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle1: default: 0 title: Number of fully flexible segments @@ -9235,20 +6083,32 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_1_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 + fle: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the fully flexible + segment. + $comment: Residue number defining the start of the fully flexible + segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: End residue number + description: Residue number defining the end of the fully flexible + segment. + $comment: Residue number defining the end of the fully flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nfle2: default: 0 title: Number of fully flexible segments @@ -9259,20 +6119,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_2_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle3: default: 0 title: Number of fully flexible segments @@ -9283,20 +6129,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_3_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle4: default: 0 title: Number of fully flexible segments @@ -9307,20 +6139,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_4_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle5: default: 0 title: Number of fully flexible segments @@ -9331,20 +6149,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_5_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle6: default: 0 title: Number of fully flexible segments @@ -9355,20 +6159,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_6_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle7: default: 0 title: Number of fully flexible segments @@ -9379,20 +6169,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_7_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle8: default: 0 title: Number of fully flexible segments @@ -9403,20 +6179,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_8_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle9: default: 0 title: Number of fully flexible segments @@ -9427,20 +6189,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_9_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle10: default: 0 title: Number of fully flexible segments @@ -9451,20 +6199,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_10_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle11: default: 0 title: Number of fully flexible segments @@ -9475,20 +6209,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_11_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle12: default: 0 title: Number of fully flexible segments @@ -9499,20 +6219,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_12_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle13: default: 0 title: Number of fully flexible segments @@ -9523,20 +6229,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_13_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle14: default: 0 title: Number of fully flexible segments @@ -9547,20 +6239,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_14_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle15: default: 0 title: Number of fully flexible segments @@ -9571,20 +6249,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_15_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle16: default: 0 title: Number of fully flexible segments @@ -9595,20 +6259,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_16_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle17: default: 0 title: Number of fully flexible segments @@ -9619,20 +6269,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_17_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle18: default: 0 title: Number of fully flexible segments @@ -9643,20 +6279,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_18_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle19: default: 0 title: Number of fully flexible segments @@ -9667,20 +6289,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_19_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle20: default: 0 title: Number of fully flexible segments @@ -9691,102 +6299,12 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_20_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 required: [] additionalProperties: false uiSchema: - mol_fix_origin_1: - ui:group: molecule - mol_fix_origin_2: - ui:group: molecule - mol_fix_origin_3: - ui:group: molecule - mol_fix_origin_4: - ui:group: molecule - mol_fix_origin_5: - ui:group: molecule - mol_fix_origin_6: - ui:group: molecule - mol_fix_origin_7: - ui:group: molecule - mol_fix_origin_8: - ui:group: molecule - mol_fix_origin_9: - ui:group: molecule - mol_fix_origin_10: - ui:group: molecule - mol_fix_origin_11: - ui:group: molecule - mol_fix_origin_12: - ui:group: molecule - mol_fix_origin_13: - ui:group: molecule - mol_fix_origin_14: - ui:group: molecule - mol_fix_origin_15: - ui:group: molecule - mol_fix_origin_16: - ui:group: molecule - mol_fix_origin_17: - ui:group: molecule - mol_fix_origin_18: - ui:group: molecule - mol_fix_origin_19: - ui:group: molecule - mol_fix_origin_20: - ui:group: molecule - mol_shape_1: - ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: - ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: - ui:group: molecule - mol_shape_10: + mol_fix_origin: ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file @@ -9821,171 +6339,45 @@ nodes: ui:widget: file ui:group: dihedral restraints dihedrals_on: - ui:group: dihedral restraints - dihedrals_scale: - ui:group: dihedral restraints - ssdihed: - ui:group: dihedral restraints - error_dih: - ui:group: dihedral restraints - dnarest_on: - ui:group: other restraints - sym_on: - ui:group: symmetry - ksym: - ui:group: symmetry - symtbl_fname: - ui:widget: file - ui:group: symmetry - numc2sym: - ui:group: symmetry - c2sym_sta1_1: - ui:group: symmetry - c2sym_end1_1: - ui:group: symmetry - c2sym_seg1_1: - ui:group: symmetry - c2sym_sta2_1: - ui:group: symmetry - c2sym_end2_1: - ui:group: symmetry - c2sym_seg2_1: - ui:group: symmetry - numc3sym: - ui:group: symmetry - c3sym_sta1_1: - ui:group: symmetry - c3sym_end1_1: - ui:group: symmetry - c3sym_seg1_1: - ui:group: symmetry - c3sym_sta2_1: - ui:group: symmetry - c3sym_end2_1: - ui:group: symmetry - c3sym_seg2_1: - ui:group: symmetry - c3sym_sta3_1: - ui:group: symmetry - c3sym_end3_1: - ui:group: symmetry - c3sym_seg3_1: - ui:group: symmetry - numc4sym: - ui:group: symmetry - c4sym_sta1_1: - ui:group: symmetry - c4sym_end1_1: - ui:group: symmetry - c4sym_seg1_1: - ui:group: symmetry - c4sym_sta2_1: - ui:group: symmetry - c4sym_end2_1: - ui:group: symmetry - c4sym_seg2_1: - ui:group: symmetry - c4sym_sta3_1: - ui:group: symmetry - c4sym_end3_1: - ui:group: symmetry - c4sym_seg3_1: - ui:group: symmetry - c4sym_sta4_1: - ui:group: symmetry - c4sym_end4_1: - ui:group: symmetry - c4sym_seg4_1: - ui:group: symmetry - numc5sym: - ui:group: symmetry - c5sym_sta1_1: - ui:group: symmetry - c5sym_end1_1: - ui:group: symmetry - c5sym_seg1_1: - ui:group: symmetry - c5sym_sta2_1: - ui:group: symmetry - c5sym_end2_1: + ui:group: dihedral restraints + dihedrals_scale: + ui:group: dihedral restraints + ssdihed: + ui:group: dihedral restraints + error_dih: + ui:group: dihedral restraints + dnarest_on: + ui:group: other restraints + sym_on: ui:group: symmetry - c5sym_seg2_1: + ksym: ui:group: symmetry - c5sym_sta3_1: + symtbl_fname: + ui:widget: file ui:group: symmetry - c5sym_end3_1: + numc2sym: ui:group: symmetry - c5sym_seg3_1: + c2sym: ui:group: symmetry - c5sym_sta4_1: + numc3sym: ui:group: symmetry - c5sym_end4_1: + c3sym: ui:group: symmetry - c5sym_seg4_1: + numc4sym: ui:group: symmetry - c5sym_sta5_1: + c4sym: ui:group: symmetry - c5sym_end5_1: + numc5sym: ui:group: symmetry - c5sym_seg5_1: + c5sym: ui:group: symmetry numc6sym: ui:group: symmetry - c6sym_sta1_1: - ui:group: symmetry - c6sym_end1_1: - ui:group: symmetry - c6sym_seg1_1: - ui:group: symmetry - c6sym_sta2_1: - ui:group: symmetry - c6sym_end2_1: - ui:group: symmetry - c6sym_seg2_1: - ui:group: symmetry - c6sym_sta3_1: - ui:group: symmetry - c6sym_end3_1: - ui:group: symmetry - c6sym_seg3_1: - ui:group: symmetry - c6sym_sta4_1: - ui:group: symmetry - c6sym_end4_1: - ui:group: symmetry - c6sym_seg4_1: - ui:group: symmetry - c6sym_sta5_1: - ui:group: symmetry - c6sym_end5_1: - ui:group: symmetry - c6sym_seg5_1: - ui:group: symmetry - c6sym_sta6_1: - ui:group: symmetry - c6sym_end6_1: - ui:group: symmetry - c6sym_seg6_1: + c6sym: ui:group: symmetry nums3sym: ui:group: symmetry - s3sym_sta1_1: - ui:group: symmetry - s3sym_end1_1: - ui:group: symmetry - s3sym_seg1_1: - ui:group: symmetry - s3sym_sta2_1: - ui:group: symmetry - s3sym_end2_1: - ui:group: symmetry - s3sym_seg2_1: - ui:group: symmetry - s3sym_sta3_1: - ui:group: symmetry - s3sym_end3_1: - ui:group: symmetry - s3sym_seg3_1: + s3sym: ui:group: symmetry ncs_on: ui:group: symmetry @@ -9993,17 +6385,7 @@ nodes: ui:group: symmetry numncs: ui:group: symmetry - ncs_sta1_1: - ui:group: symmetry - ncs_end1_1: - ui:group: symmetry - ncs_seg1_1: - ui:group: symmetry - ncs_sta2_1: - ui:group: symmetry - ncs_end2_1: - ui:group: symmetry - ncs_seg2_1: + ncs: ui:group: symmetry w_air: ui:group: scoring @@ -10031,6 +6413,8 @@ nodes: ui:group: force field epsilon: ui:group: force field + dihedflag: + ui:group: force field sampling_factor: ui:group: sampling nemsteps: @@ -10045,491 +6429,156 @@ nodes: ui:group: module nseg1: ui:group: flexibility - seg_sta_1_1: - ui:group: flexibility - seg_end_1_1: + seg: ui:group: flexibility nseg2: ui:group: flexibility - seg_sta_2_1: - ui:group: flexibility - seg_end_2_1: - ui:group: flexibility nseg3: ui:group: flexibility - seg_sta_3_1: - ui:group: flexibility - seg_end_3_1: - ui:group: flexibility nseg4: ui:group: flexibility - seg_sta_4_1: - ui:group: flexibility - seg_end_4_1: - ui:group: flexibility nseg5: ui:group: flexibility - seg_sta_5_1: - ui:group: flexibility - seg_end_5_1: - ui:group: flexibility nseg6: ui:group: flexibility - seg_sta_6_1: - ui:group: flexibility - seg_end_6_1: - ui:group: flexibility nseg7: ui:group: flexibility - seg_sta_7_1: - ui:group: flexibility - seg_end_7_1: - ui:group: flexibility nseg8: ui:group: flexibility - seg_sta_8_1: - ui:group: flexibility - seg_end_8_1: - ui:group: flexibility nseg9: ui:group: flexibility - seg_sta_9_1: - ui:group: flexibility - seg_end_9_1: - ui:group: flexibility nseg10: ui:group: flexibility - seg_sta_10_1: - ui:group: flexibility - seg_end_10_1: - ui:group: flexibility nseg11: ui:group: flexibility - seg_sta_11_1: - ui:group: flexibility - seg_end_11_1: - ui:group: flexibility nseg12: ui:group: flexibility - seg_sta_12_1: - ui:group: flexibility - seg_end_12_1: - ui:group: flexibility nseg13: ui:group: flexibility - seg_sta_13_1: - ui:group: flexibility - seg_end_13_1: - ui:group: flexibility nseg14: ui:group: flexibility - seg_sta_14_1: - ui:group: flexibility - seg_end_14_1: - ui:group: flexibility nseg15: ui:group: flexibility - seg_sta_15_1: - ui:group: flexibility - seg_end_15_1: - ui:group: flexibility nseg16: ui:group: flexibility - seg_sta_16_1: - ui:group: flexibility - seg_end_16_1: - ui:group: flexibility nseg17: ui:group: flexibility - seg_sta_17_1: - ui:group: flexibility - seg_end_17_1: - ui:group: flexibility nseg18: ui:group: flexibility - seg_sta_18_1: - ui:group: flexibility - seg_end_18_1: - ui:group: flexibility nseg19: ui:group: flexibility - seg_sta_19_1: - ui:group: flexibility - seg_end_19_1: - ui:group: flexibility - nseg20: - ui:group: flexibility - seg_sta_20_1: - ui:group: flexibility - seg_end_20_1: - ui:group: flexibility - nfle1: - ui:group: flexibility - fle_sta_1_1: - ui:group: flexibility - fle_end_1_1: - ui:group: flexibility - nfle2: - ui:group: flexibility - fle_sta_2_1: - ui:group: flexibility - fle_end_2_1: - ui:group: flexibility - nfle3: - ui:group: flexibility - fle_sta_3_1: - ui:group: flexibility - fle_end_3_1: - ui:group: flexibility - nfle4: - ui:group: flexibility - fle_sta_4_1: - ui:group: flexibility - fle_end_4_1: - ui:group: flexibility - nfle5: - ui:group: flexibility - fle_sta_5_1: - ui:group: flexibility - fle_end_5_1: - ui:group: flexibility - nfle6: - ui:group: flexibility - fle_sta_6_1: - ui:group: flexibility - fle_end_6_1: - ui:group: flexibility - nfle7: - ui:group: flexibility - fle_sta_7_1: - ui:group: flexibility - fle_end_7_1: - ui:group: flexibility - nfle8: - ui:group: flexibility - fle_sta_8_1: - ui:group: flexibility - fle_end_8_1: - ui:group: flexibility - nfle9: - ui:group: flexibility - fle_sta_9_1: - ui:group: flexibility - fle_end_9_1: - ui:group: flexibility - nfle10: - ui:group: flexibility - fle_sta_10_1: - ui:group: flexibility - fle_end_10_1: - ui:group: flexibility - nfle11: - ui:group: flexibility - fle_sta_11_1: - ui:group: flexibility - fle_end_11_1: - ui:group: flexibility - nfle12: - ui:group: flexibility - fle_sta_12_1: - ui:group: flexibility - fle_end_12_1: - ui:group: flexibility - nfle13: - ui:group: flexibility - fle_sta_13_1: - ui:group: flexibility - fle_end_13_1: - ui:group: flexibility - nfle14: - ui:group: flexibility - fle_sta_14_1: - ui:group: flexibility - fle_end_14_1: - ui:group: flexibility - nfle15: - ui:group: flexibility - fle_sta_15_1: - ui:group: flexibility - fle_end_15_1: - ui:group: flexibility - nfle16: - ui:group: flexibility - fle_sta_16_1: - ui:group: flexibility - fle_end_16_1: - ui:group: flexibility - nfle17: - ui:group: flexibility - fle_sta_17_1: - ui:group: flexibility - fle_end_17_1: - ui:group: flexibility - nfle18: - ui:group: flexibility - fle_sta_18_1: - ui:group: flexibility - fle_end_18_1: - ui:group: flexibility - nfle19: - ui:group: flexibility - fle_sta_19_1: - ui:group: flexibility - fle_end_19_1: - ui:group: flexibility - nfle20: - ui:group: flexibility - fle_sta_20_1: - ui:group: flexibility - fle_end_20_1: - ui:group: flexibility -- id: emref - category: refinement - label: HADDOCK3 module for energy minimization refinement. - description: HADDOCK3 module energy minimization refinement. - schema: - type: object - properties: - mol_fix_origin_1: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_2: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_3: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_4: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_5: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_6: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_7: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_8: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_9: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_10: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_11: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_12: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_13: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_14: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_15: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_16: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_17: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_18: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_19: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_20: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + nseg20: + ui:group: flexibility + nfle1: + ui:group: flexibility + fle: + ui:group: flexibility + nfle2: + ui:group: flexibility + nfle3: + ui:group: flexibility + nfle4: + ui:group: flexibility + nfle5: + ui:group: flexibility + nfle6: + ui:group: flexibility + nfle7: + ui:group: flexibility + nfle8: + ui:group: flexibility + nfle9: + ui:group: flexibility + nfle10: + ui:group: flexibility + nfle11: + ui:group: flexibility + nfle12: + ui:group: flexibility + nfle13: + ui:group: flexibility + nfle14: + ui:group: flexibility + nfle15: + ui:group: flexibility + nfle16: + ui:group: flexibility + nfle17: + ui:group: flexibility + nfle18: + ui:group: flexibility + nfle19: + ui:group: flexibility + nfle20: + ui:group: flexibility + tomlSchema: + mol_fix_origin: + indexed: true + mol_shape: + indexed: true + c2sym: + indexed: true + items: + flatten: true + c3sym: + indexed: true + items: + flatten: true + c4sym: + indexed: true + items: + flatten: true + c5sym: + indexed: true + items: + flatten: true + c6sym: + indexed: true + items: + flatten: true + s3sym: + indexed: true + items: + flatten: true + ncs: + indexed: true + items: + flatten: true + seg: + indexed: true + items: + indexed: true + items: + flatten: true + fle: + indexed: true + items: + indexed: true + items: + flatten: true +- id: emref + category: refinement + label: HADDOCK3 module for energy minimization refinement. + description: HADDOCK3 module energy minimization refinement. + schema: + type: object + properties: + mol_fix_origin: + type: array + items: + default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. + type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -10718,50 +6767,60 @@ nodes: type: number maximum: 40 minimum: 0 - c2sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C2 symmetry segment - $comment: Residue number of first residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C2 symmetry segment - $comment: Residue number of last residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg1_1: - default: '' - title: Segment ID of first C2 segment - description: Segment ID of first C2 segment - $comment: Segment ID of first C2 segment - type: string - minLength: 0 - maxLength: 4 - c2sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C2 symmetry segment - $comment: Residue number of first residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C2 symmetry segment - $comment: Residue number of last residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg2_1: - default: '' - title: Segment ID of second C2 segment - description: Segment ID of second C2 segment - $comment: Segment ID of second C2 segment - type: string - minLength: 0 - maxLength: 4 + c2sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C2 symmetry + segment + $comment: Residue number of first residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C2 symmetry + segment + $comment: Residue number of last residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C2 segment + description: Segment ID of first C2 segment + $comment: Segment ID of first C2 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C2 symmetry + segment + $comment: Residue number of first residue in the second C2 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C2 symmetry + segment + $comment: Residue number of last residue in the second C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C2 segment + description: Segment ID of second C2 segment + $comment: Segment ID of second C2 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc3sym: default: 0 title: Number of C3 symmetry restraints @@ -10772,72 +6831,83 @@ nodes: type: number maximum: 10 minimum: 0 - c3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C3 symmetry segment - $comment: Residue number of first residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C3 symmetry segment - $comment: Residue number of last residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg1_1: - default: '' - title: Segment ID of first C3 segment - description: Segment ID of first C3 segment - $comment: Segment ID of first C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C3 symmetry segment - $comment: Residue number of first residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C3 symmetry segment - $comment: Residue number of last residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg2_1: - default: '' - title: Segment ID of second C3 segment - description: Segment ID of second C3 segment - $comment: Segment ID of second C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C3 symmetry segment - $comment: Residue number of first residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C3 symmetry segment - $comment: Residue number of last residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg3_1: - default: '' - title: Segment ID of third C3 segment - description: Segment ID of third C3 segment - $comment: Segment ID of third C3 segment - type: string - minLength: 0 - maxLength: 4 + c3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C3 symmetry + segment + $comment: Residue number of first residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C3 symmetry + segment + $comment: Residue number of last residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C3 segment + description: Segment ID of first C3 segment + $comment: Segment ID of first C3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C3 symmetry + segment + $comment: Residue number of first residue in the second C3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C3 symmetry + segment + $comment: Residue number of last residue in the second C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C3 segment + description: Segment ID of second C3 segment + $comment: Segment ID of second C3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C3 symmetry + segment + $comment: Residue number of first residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C3 symmetry + segment + $comment: Residue number of last residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C3 segment + description: Segment ID of third C3 segment + $comment: Segment ID of third C3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc4sym: default: 0 title: Number of C4 symmetry restraints @@ -10848,356 +6918,398 @@ nodes: type: number maximum: 10 minimum: 0 - c4sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C4 symmetry segment - $comment: Residue number of first residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C4 symmetry segment - $comment: Residue number of last residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg1_1: - default: '' - title: Segment ID of first C4 segment - description: Segment ID of first C4 segment - $comment: Segment ID of first C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C4 symmetry segment - $comment: Residue number of first residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C4 symmetry segment - $comment: Residue number of last residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg2_1: - default: '' - title: Segment ID of second C4 segment - description: Segment ID of second C4 segment - $comment: Segment ID of second C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C4 symmetry segment - $comment: Residue number of first residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C4 symmetry segment - $comment: Residue number of last residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg3_1: - default: '' - title: Segment ID of third C4 segment - description: Segment ID of third C4 segment - $comment: Segment ID of third C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C4 symmetry segment - $comment: Residue number of first residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C4 symmetry segment - $comment: Residue number of last residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg4_1: - default: '' - title: Segment ID of fourth C4 segment - description: Segment ID of fourth C4 segment - $comment: Segment ID of fourth C4 segment - type: string - minLength: 0 - maxLength: 4 + c4sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C4 symmetry + segment + $comment: Residue number of first residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C4 symmetry + segment + $comment: Residue number of last residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C4 segment + description: Segment ID of first C4 segment + $comment: Segment ID of first C4 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C4 symmetry + segment + $comment: Residue number of first residue in the second C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C4 symmetry + segment + $comment: Residue number of last residue in the second C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C4 segment + description: Segment ID of second C4 segment + $comment: Segment ID of second C4 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C4 symmetry + segment + $comment: Residue number of first residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C4 symmetry + segment + $comment: Residue number of last residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C4 segment + description: Segment ID of third C4 segment + $comment: Segment ID of third C4 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C4 symmetry + segment + $comment: Residue number of first residue in the fourth C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C4 symmetry + segment + $comment: Residue number of last residue in the fourth C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C4 segment + description: Segment ID of fourth C4 segment + $comment: Segment ID of fourth C4 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc5sym: default: 0 title: Number of C5 symmetry restraints description: Defines the number of C5 symmetry restraints. $comment: Defines the number of C5 symmetry restraints. For each, five segments on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c5sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C5 symmetry segment - $comment: Residue number of first residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C5 symmetry segment - $comment: Residue number of last residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg1_1: - default: '' - title: Segment ID of first C5 segment - description: Segment ID of first C5 segment - $comment: Segment ID of first C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C5 symmetry segment - $comment: Residue number of first residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C5 symmetry segment - $comment: Residue number of last residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg2_1: - default: '' - title: Segment ID of second C5 segment - description: Segment ID of second C5 segment - $comment: Segment ID of second C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C5 symmetry segment - $comment: Residue number of first residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C5 symmetry segment - $comment: Residue number of last residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg3_1: - default: '' - title: Segment ID of third C5 segment - description: Segment ID of third C5 segment - $comment: Segment ID of third C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C5 symmetry segment - $comment: Residue number of first residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C5 symmetry segment - $comment: Residue number of last residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg4_1: - default: '' - title: Segment ID of fourth C5 segment - description: Segment ID of fourth C5 segment - $comment: Segment ID of fourth C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C5 symmetry segment - $comment: Residue number of first residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C5 symmetry segment - $comment: Residue number of last residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg5_1: - default: '' - title: Segment ID of fifth C5 segment - description: Segment ID of fifth C5 segment - $comment: Segment ID of fifth C5 segment - type: string - minLength: 0 - maxLength: 4 - numc6sym: - default: 0 - title: Number of C6 symmetry restraints - description: Defines the number of C6 symmetry restraints. - $comment: Defines the number of C6 symmetry restraints. For each, six segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c6sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C6 symmetry segment - $comment: Residue number of first residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C6 symmetry segment - $comment: Residue number of last residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg1_1: - default: '' - title: Segment ID of first C6 segment - description: Segment ID of first C6 segment - $comment: Segment ID of first C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C6 symmetry segment - $comment: Residue number of first residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C6 symmetry segment - $comment: Residue number of last residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg2_1: - default: '' - title: Segment ID of second C6 segment - description: Segment ID of second C6 segment - $comment: Segment ID of second C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C6 symmetry segment - $comment: Residue number of first residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C6 symmetry segment - $comment: Residue number of last residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg3_1: - default: '' - title: Segment ID of third C6 segment - description: Segment ID of third C6 segment - $comment: Segment ID of third C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C6 symmetry segment - $comment: Residue number of first residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C6 symmetry segment - $comment: Residue number of last residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg4_1: - default: '' - title: Segment ID of fourth C6 segment - description: Segment ID of fourth C6 segment - $comment: Segment ID of fourth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C6 symmetry segment - $comment: Residue number of first residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C6 symmetry segment - $comment: Residue number of last residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg5_1: - default: '' - title: Segment ID of fifth C6 segment - description: Segment ID of fifth C6 segment - $comment: Segment ID of fifth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta6_1: - title: Residue number of first residue - description: Residue number of first residue in the sixth C6 symmetry segment - $comment: Residue number of first residue in the sixth C6 symmetry segment + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - c6sym_end6_1: - title: Residue number of last residue - description: Residue number of last residue in the sixth C6 symmetry segment - $comment: Residue number of last residue in the sixth C6 symmetry segment + maximum: 10 + minimum: 0 + c5sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C5 symmetry + segment + $comment: Residue number of first residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C5 symmetry + segment + $comment: Residue number of last residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C5 segment + description: Segment ID of first C5 segment + $comment: Segment ID of first C5 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C5 symmetry + segment + $comment: Residue number of first residue in the second C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C5 symmetry + segment + $comment: Residue number of last residue in the second C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C5 segment + description: Segment ID of second C5 segment + $comment: Segment ID of second C5 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C5 symmetry + segment + $comment: Residue number of first residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C5 symmetry + segment + $comment: Residue number of last residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C5 segment + description: Segment ID of third C5 segment + $comment: Segment ID of third C5 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C5 symmetry + segment + $comment: Residue number of first residue in the fourth C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C5 symmetry + segment + $comment: Residue number of last residue in the fourth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C5 segment + description: Segment ID of fourth C5 segment + $comment: Segment ID of fourth C5 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C5 symmetry + segment + $comment: Residue number of first residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C5 symmetry + segment + $comment: Residue number of last residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C5 segment + description: Segment ID of fifth C5 segment + $comment: Segment ID of fifth C5 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc6sym: + default: 0 + title: Number of C6 symmetry restraints + description: Defines the number of C6 symmetry restraints. + $comment: Defines the number of C6 symmetry restraints. For each, six segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - c6sym_seg6_1: - default: '' - title: Segment ID of sixth C6 segment - description: Segment ID of sixth C6 segment - $comment: Segment ID of sixth C6 segment - type: string - minLength: 0 - maxLength: 4 + maximum: 10 + minimum: 0 + c6sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C6 symmetry + segment + $comment: Residue number of first residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C6 symmetry + segment + $comment: Residue number of last residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C6 segment + description: Segment ID of first C6 segment + $comment: Segment ID of first C6 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C6 symmetry + segment + $comment: Residue number of first residue in the second C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C6 symmetry + segment + $comment: Residue number of last residue in the second C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C6 segment + description: Segment ID of second C6 segment + $comment: Segment ID of second C6 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C6 symmetry + segment + $comment: Residue number of first residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C6 symmetry + segment + $comment: Residue number of last residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C6 segment + description: Segment ID of third C6 segment + $comment: Segment ID of third C6 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C6 symmetry + segment + $comment: Residue number of first residue in the fourth C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C6 symmetry + segment + $comment: Residue number of last residue in the fourth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C6 segment + description: Segment ID of fourth C6 segment + $comment: Segment ID of fourth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C6 symmetry + segment + $comment: Residue number of first residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C6 symmetry + segment + $comment: Residue number of last residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C6 segment + description: Segment ID of fifth C6 segment + $comment: Segment ID of fifth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta6: + title: Residue number of first residue + description: Residue number of first residue in the sixth C6 symmetry + segment + $comment: Residue number of first residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end6: + title: Residue number of last residue + description: Residue number of last residue in the sixth C6 symmetry + segment + $comment: Residue number of last residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg6: + title: Segment ID of sixth C6 segment + description: Segment ID of sixth C6 segment + $comment: Segment ID of sixth C6 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false nums3sym: default: 0 title: Number of S3 symmetry restraints @@ -11208,72 +7320,83 @@ nodes: type: number maximum: 10 minimum: 0 - s3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first S3 symmetry segment - $comment: Residue number of first residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first S3 symmetry segment - $comment: Residue number of last residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg1_1: - default: '' - title: Segment ID of first S3 segment - description: Segment ID of first S3 segment - $comment: Segment ID of first S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second S3 symmetry segment - $comment: Residue number of first residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second S3 symmetry segment - $comment: Residue number of last residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg2_1: - default: '' - title: Segment ID of second S3 segment - description: Segment ID of second S3 segment - $comment: Segment ID of second S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third S3 symmetry segment - $comment: Residue number of first residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third S3 symmetry segment - $comment: Residue number of last residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg3_1: - default: '' - title: Segment ID of third S3 segment - description: Segment ID of third S3 segment - $comment: Segment ID of third S3 segment - type: string - minLength: 0 - maxLength: 4 + s3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first S3 symmetry + segment + $comment: Residue number of first residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first S3 symmetry + segment + $comment: Residue number of last residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first S3 segment + description: Segment ID of first S3 segment + $comment: Segment ID of first S3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second S3 symmetry + segment + $comment: Residue number of first residue in the second S3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second S3 symmetry + segment + $comment: Residue number of last residue in the second S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second S3 segment + description: Segment ID of second S3 segment + $comment: Segment ID of second S3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third S3 symmetry + segment + $comment: Residue number of first residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third S3 symmetry + segment + $comment: Residue number of last residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third S3 segment + description: Segment ID of third S3 segment + $comment: Segment ID of third S3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false ncs_on: default: false title: Non-crystallographic symmetry restraints @@ -11302,50 +7425,55 @@ nodes: type: number maximum: 100 minimum: 0 - ncs_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first NCS segment - $comment: Residue number of first residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first NCS segment - $comment: Residue number of last residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg1_1: - default: '' - title: Segment ID of first NCS segment - description: Segment ID of first NCS segment - $comment: Segment ID of first NCS segment - type: string - minLength: 0 - maxLength: 100 - ncs_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second NCS segment - $comment: Residue number of first residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second NCS segment - $comment: Residue number of last residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg2_1: - default: '' - title: Segment ID of second NCS segment - description: Segment ID of second NCS segment - $comment: Segment ID of second NCS segment - type: string - minLength: 0 - maxLength: 100 + ncs: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first NCS segment + $comment: Residue number of first residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first NCS segment + $comment: Residue number of last residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first NCS segment + description: Segment ID of first NCS segment + $comment: Segment ID of first NCS segment + type: string + minLength: 0 + maxLength: 100 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second NCS segment + $comment: Residue number of first residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second NCS segment + $comment: Residue number of last residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second NCS segment + description: Segment ID of second NCS segment + $comment: Segment ID of second NCS segment + type: string + minLength: 0 + maxLength: 100 + required: [] + additionalProperties: false w_air: default: 0.1 title: Weight of the distance restraint energy @@ -11514,20 +7642,31 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_1_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 + seg: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the semi-flexible + segment. + $comment: Residue number defining the start of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: Ending residue number + description: Residue number defining the end of the semi-flexible + segment. + $comment: Residue number defining the end of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nseg2: default: -1 title: Number of semi-flexible segments @@ -11543,20 +7682,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_2_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg3: default: -1 title: Number of semi-flexible segments @@ -11572,20 +7697,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_3_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg4: default: -1 title: Number of semi-flexible segments @@ -11601,20 +7712,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_4_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg5: default: -1 title: Number of semi-flexible segments @@ -11630,20 +7727,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_5_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg6: default: -1 title: Number of semi-flexible segments @@ -11659,20 +7742,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_6_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg7: default: -1 title: Number of semi-flexible segments @@ -11688,20 +7757,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_7_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg8: default: -1 title: Number of semi-flexible segments @@ -11717,20 +7772,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_8_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg9: default: -1 title: Number of semi-flexible segments @@ -11746,20 +7787,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_9_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg10: default: -1 title: Number of semi-flexible segments @@ -11775,20 +7802,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_10_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg11: default: -1 title: Number of semi-flexible segments @@ -11804,20 +7817,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_11_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg12: default: -1 title: Number of semi-flexible segments @@ -11833,20 +7832,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_12_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg13: default: -1 title: Number of semi-flexible segments @@ -11862,20 +7847,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_13_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg14: default: -1 title: Number of semi-flexible segments @@ -11891,20 +7862,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_14_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg15: default: -1 title: Number of semi-flexible segments @@ -11920,20 +7877,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_15_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg16: default: -1 title: Number of semi-flexible segments @@ -11949,20 +7892,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_16_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg17: default: -1 title: Number of semi-flexible segments @@ -11978,20 +7907,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_17_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg18: default: -1 title: Number of semi-flexible segments @@ -12007,20 +7922,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_18_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg19: default: -1 title: Number of semi-flexible segments @@ -12036,20 +7937,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_19_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg20: default: -1 title: Number of semi-flexible segments @@ -12065,20 +7952,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_20_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle1: default: 0 title: Number of fully flexible segments @@ -12089,20 +7962,32 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_1_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 + fle: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the fully flexible + segment. + $comment: Residue number defining the start of the fully flexible + segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: End residue number + description: Residue number defining the end of the fully flexible + segment. + $comment: Residue number defining the end of the fully flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nfle2: default: 0 title: Number of fully flexible segments @@ -12113,20 +7998,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_2_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle3: default: 0 title: Number of fully flexible segments @@ -12137,20 +8008,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_3_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle4: default: 0 title: Number of fully flexible segments @@ -12161,20 +8018,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_4_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle5: default: 0 title: Number of fully flexible segments @@ -12185,20 +8028,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_5_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle6: default: 0 title: Number of fully flexible segments @@ -12209,20 +8038,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_6_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle7: default: 0 title: Number of fully flexible segments @@ -12233,20 +8048,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_7_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle8: default: 0 title: Number of fully flexible segments @@ -12257,20 +8058,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_8_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle9: default: 0 title: Number of fully flexible segments @@ -12281,20 +8068,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_9_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle10: default: 0 title: Number of fully flexible segments @@ -12305,20 +8078,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_10_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle11: default: 0 title: Number of fully flexible segments @@ -12329,20 +8088,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_11_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle12: default: 0 title: Number of fully flexible segments @@ -12353,20 +8098,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_12_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle13: default: 0 title: Number of fully flexible segments @@ -12377,20 +8108,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_13_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle14: default: 0 title: Number of fully flexible segments @@ -12401,20 +8118,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_14_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle15: default: 0 title: Number of fully flexible segments @@ -12425,20 +8128,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_15_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle16: default: 0 title: Number of fully flexible segments @@ -12449,20 +8138,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_16_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle17: default: 0 title: Number of fully flexible segments @@ -12473,20 +8148,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_17_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle18: default: 0 title: Number of fully flexible segments @@ -12497,20 +8158,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_18_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle19: default: 0 title: Number of fully flexible segments @@ -12521,20 +8168,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_19_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle20: default: 0 title: Number of fully flexible segments @@ -12545,102 +8178,12 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_20_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 required: [] additionalProperties: false uiSchema: - mol_fix_origin_1: - ui:group: molecule - mol_fix_origin_2: - ui:group: molecule - mol_fix_origin_3: - ui:group: molecule - mol_fix_origin_4: - ui:group: molecule - mol_fix_origin_5: + mol_fix_origin: ui:group: molecule - mol_fix_origin_6: - ui:group: molecule - mol_fix_origin_7: - ui:group: molecule - mol_fix_origin_8: - ui:group: molecule - mol_fix_origin_9: - ui:group: molecule - mol_fix_origin_10: - ui:group: molecule - mol_fix_origin_11: - ui:group: molecule - mol_fix_origin_12: - ui:group: molecule - mol_fix_origin_13: - ui:group: molecule - mol_fix_origin_14: - ui:group: molecule - mol_fix_origin_15: - ui:group: molecule - mol_fix_origin_16: - ui:group: molecule - mol_fix_origin_17: - ui:group: molecule - mol_fix_origin_18: - ui:group: molecule - mol_fix_origin_19: - ui:group: molecule - mol_fix_origin_20: - ui:group: molecule - mol_shape_1: - ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: - ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: - ui:group: molecule - mol_shape_10: - ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file @@ -12687,153 +8230,27 @@ nodes: ui:group: symmetry numc2sym: ui:group: symmetry - c2sym_sta1_1: - ui:group: symmetry - c2sym_end1_1: - ui:group: symmetry - c2sym_seg1_1: - ui:group: symmetry - c2sym_sta2_1: - ui:group: symmetry - c2sym_end2_1: - ui:group: symmetry - c2sym_seg2_1: + c2sym: ui:group: symmetry numc3sym: ui:group: symmetry - c3sym_sta1_1: - ui:group: symmetry - c3sym_end1_1: - ui:group: symmetry - c3sym_seg1_1: - ui:group: symmetry - c3sym_sta2_1: - ui:group: symmetry - c3sym_end2_1: - ui:group: symmetry - c3sym_seg2_1: - ui:group: symmetry - c3sym_sta3_1: - ui:group: symmetry - c3sym_end3_1: - ui:group: symmetry - c3sym_seg3_1: + c3sym: ui:group: symmetry numc4sym: ui:group: symmetry - c4sym_sta1_1: - ui:group: symmetry - c4sym_end1_1: - ui:group: symmetry - c4sym_seg1_1: - ui:group: symmetry - c4sym_sta2_1: - ui:group: symmetry - c4sym_end2_1: - ui:group: symmetry - c4sym_seg2_1: - ui:group: symmetry - c4sym_sta3_1: - ui:group: symmetry - c4sym_end3_1: - ui:group: symmetry - c4sym_seg3_1: - ui:group: symmetry - c4sym_sta4_1: - ui:group: symmetry - c4sym_end4_1: - ui:group: symmetry - c4sym_seg4_1: + c4sym: ui:group: symmetry numc5sym: ui:group: symmetry - c5sym_sta1_1: - ui:group: symmetry - c5sym_end1_1: - ui:group: symmetry - c5sym_seg1_1: - ui:group: symmetry - c5sym_sta2_1: - ui:group: symmetry - c5sym_end2_1: - ui:group: symmetry - c5sym_seg2_1: - ui:group: symmetry - c5sym_sta3_1: - ui:group: symmetry - c5sym_end3_1: - ui:group: symmetry - c5sym_seg3_1: - ui:group: symmetry - c5sym_sta4_1: - ui:group: symmetry - c5sym_end4_1: - ui:group: symmetry - c5sym_seg4_1: - ui:group: symmetry - c5sym_sta5_1: - ui:group: symmetry - c5sym_end5_1: - ui:group: symmetry - c5sym_seg5_1: + c5sym: ui:group: symmetry numc6sym: ui:group: symmetry - c6sym_sta1_1: - ui:group: symmetry - c6sym_end1_1: - ui:group: symmetry - c6sym_seg1_1: - ui:group: symmetry - c6sym_sta2_1: - ui:group: symmetry - c6sym_end2_1: - ui:group: symmetry - c6sym_seg2_1: - ui:group: symmetry - c6sym_sta3_1: - ui:group: symmetry - c6sym_end3_1: - ui:group: symmetry - c6sym_seg3_1: - ui:group: symmetry - c6sym_sta4_1: - ui:group: symmetry - c6sym_end4_1: - ui:group: symmetry - c6sym_seg4_1: - ui:group: symmetry - c6sym_sta5_1: - ui:group: symmetry - c6sym_end5_1: - ui:group: symmetry - c6sym_seg5_1: - ui:group: symmetry - c6sym_sta6_1: - ui:group: symmetry - c6sym_end6_1: - ui:group: symmetry - c6sym_seg6_1: + c6sym: ui:group: symmetry nums3sym: ui:group: symmetry - s3sym_sta1_1: - ui:group: symmetry - s3sym_end1_1: - ui:group: symmetry - s3sym_seg1_1: - ui:group: symmetry - s3sym_sta2_1: - ui:group: symmetry - s3sym_end2_1: - ui:group: symmetry - s3sym_seg2_1: - ui:group: symmetry - s3sym_sta3_1: - ui:group: symmetry - s3sym_end3_1: - ui:group: symmetry - s3sym_seg3_1: + s3sym: ui:group: symmetry ncs_on: ui:group: symmetry @@ -12841,17 +8258,7 @@ nodes: ui:group: symmetry numncs: ui:group: symmetry - ncs_sta1_1: - ui:group: symmetry - ncs_end1_1: - ui:group: symmetry - ncs_seg1_1: - ui:group: symmetry - ncs_sta2_1: - ui:group: symmetry - ncs_end2_1: - ui:group: symmetry - ncs_seg2_1: + ncs: ui:group: symmetry w_air: ui:group: scoring @@ -12879,6 +8286,8 @@ nodes: ui:group: force field epsilon: ui:group: force field + dihedflag: + ui:group: force field sampling: ui:group: sampling sampling_factor: @@ -12889,243 +8298,132 @@ nodes: ui:group: module nseg1: ui:group: flexibility - seg_sta_1_1: - ui:group: flexibility - seg_end_1_1: + seg: ui:group: flexibility nseg2: ui:group: flexibility - seg_sta_2_1: - ui:group: flexibility - seg_end_2_1: - ui:group: flexibility nseg3: ui:group: flexibility - seg_sta_3_1: - ui:group: flexibility - seg_end_3_1: - ui:group: flexibility nseg4: ui:group: flexibility - seg_sta_4_1: - ui:group: flexibility - seg_end_4_1: - ui:group: flexibility nseg5: ui:group: flexibility - seg_sta_5_1: - ui:group: flexibility - seg_end_5_1: - ui:group: flexibility nseg6: ui:group: flexibility - seg_sta_6_1: - ui:group: flexibility - seg_end_6_1: - ui:group: flexibility nseg7: ui:group: flexibility - seg_sta_7_1: - ui:group: flexibility - seg_end_7_1: - ui:group: flexibility nseg8: ui:group: flexibility - seg_sta_8_1: - ui:group: flexibility - seg_end_8_1: - ui:group: flexibility nseg9: ui:group: flexibility - seg_sta_9_1: - ui:group: flexibility - seg_end_9_1: - ui:group: flexibility nseg10: ui:group: flexibility - seg_sta_10_1: - ui:group: flexibility - seg_end_10_1: - ui:group: flexibility nseg11: ui:group: flexibility - seg_sta_11_1: - ui:group: flexibility - seg_end_11_1: - ui:group: flexibility nseg12: ui:group: flexibility - seg_sta_12_1: - ui:group: flexibility - seg_end_12_1: - ui:group: flexibility nseg13: ui:group: flexibility - seg_sta_13_1: - ui:group: flexibility - seg_end_13_1: - ui:group: flexibility nseg14: ui:group: flexibility - seg_sta_14_1: - ui:group: flexibility - seg_end_14_1: - ui:group: flexibility nseg15: ui:group: flexibility - seg_sta_15_1: - ui:group: flexibility - seg_end_15_1: - ui:group: flexibility nseg16: ui:group: flexibility - seg_sta_16_1: - ui:group: flexibility - seg_end_16_1: - ui:group: flexibility nseg17: ui:group: flexibility - seg_sta_17_1: - ui:group: flexibility - seg_end_17_1: - ui:group: flexibility nseg18: ui:group: flexibility - seg_sta_18_1: - ui:group: flexibility - seg_end_18_1: - ui:group: flexibility nseg19: ui:group: flexibility - seg_sta_19_1: - ui:group: flexibility - seg_end_19_1: - ui:group: flexibility nseg20: ui:group: flexibility - seg_sta_20_1: - ui:group: flexibility - seg_end_20_1: - ui:group: flexibility nfle1: ui:group: flexibility - fle_sta_1_1: - ui:group: flexibility - fle_end_1_1: + fle: ui:group: flexibility nfle2: ui:group: flexibility - fle_sta_2_1: - ui:group: flexibility - fle_end_2_1: - ui:group: flexibility nfle3: ui:group: flexibility - fle_sta_3_1: - ui:group: flexibility - fle_end_3_1: - ui:group: flexibility nfle4: ui:group: flexibility - fle_sta_4_1: - ui:group: flexibility - fle_end_4_1: - ui:group: flexibility nfle5: ui:group: flexibility - fle_sta_5_1: - ui:group: flexibility - fle_end_5_1: - ui:group: flexibility nfle6: ui:group: flexibility - fle_sta_6_1: - ui:group: flexibility - fle_end_6_1: - ui:group: flexibility nfle7: ui:group: flexibility - fle_sta_7_1: - ui:group: flexibility - fle_end_7_1: - ui:group: flexibility nfle8: ui:group: flexibility - fle_sta_8_1: - ui:group: flexibility - fle_end_8_1: - ui:group: flexibility nfle9: ui:group: flexibility - fle_sta_9_1: - ui:group: flexibility - fle_end_9_1: - ui:group: flexibility nfle10: ui:group: flexibility - fle_sta_10_1: - ui:group: flexibility - fle_end_10_1: - ui:group: flexibility nfle11: ui:group: flexibility - fle_sta_11_1: - ui:group: flexibility - fle_end_11_1: - ui:group: flexibility nfle12: ui:group: flexibility - fle_sta_12_1: - ui:group: flexibility - fle_end_12_1: - ui:group: flexibility nfle13: ui:group: flexibility - fle_sta_13_1: - ui:group: flexibility - fle_end_13_1: - ui:group: flexibility nfle14: ui:group: flexibility - fle_sta_14_1: - ui:group: flexibility - fle_end_14_1: - ui:group: flexibility nfle15: ui:group: flexibility - fle_sta_15_1: - ui:group: flexibility - fle_end_15_1: - ui:group: flexibility nfle16: ui:group: flexibility - fle_sta_16_1: - ui:group: flexibility - fle_end_16_1: - ui:group: flexibility nfle17: ui:group: flexibility - fle_sta_17_1: - ui:group: flexibility - fle_end_17_1: - ui:group: flexibility nfle18: ui:group: flexibility - fle_sta_18_1: - ui:group: flexibility - fle_end_18_1: - ui:group: flexibility nfle19: ui:group: flexibility - fle_sta_19_1: - ui:group: flexibility - fle_end_19_1: - ui:group: flexibility nfle20: ui:group: flexibility - fle_sta_20_1: - ui:group: flexibility - fle_end_20_1: - ui:group: flexibility + tomlSchema: + mol_fix_origin: + indexed: true + mol_shape: + indexed: true + c2sym: + indexed: true + items: + flatten: true + c3sym: + indexed: true + items: + flatten: true + c4sym: + indexed: true + items: + flatten: true + c5sym: + indexed: true + items: + flatten: true + c6sym: + indexed: true + items: + flatten: true + s3sym: + indexed: true + items: + flatten: true + ncs: + indexed: true + items: + flatten: true + seg: + indexed: true + items: + indexed: true + items: + flatten: true + fle: + indexed: true + items: + indexed: true + items: + flatten: true examples: docking-protein-ligand: /examples/docking-protein-ligand.zip diff --git a/public/catalog/haddock3.guru.yaml b/public/catalog/haddock3.guru.yaml index 6a548215..06341265 100644 --- a/public/catalog/haddock3.guru.yaml +++ b/public/catalog/haddock3.guru.yaml @@ -14,18 +14,23 @@ global: schema: type: object properties: + run_dir: + title: Run directory + description: Folder to store the HADDOCK3 run + $comment: The new folder that will be created to save the HADDOCK3 run + type: string + format: uri-reference molecules: - title: Molecules + title: Input Molecules + description: The input molecules that will be used for docking. + $comment: Molecules must be provided in PDB format. These PDB files can be + single molecules or ensembles using the MODEL/ENDMDL statements. type: array minItems: 1 maxItems: 20 items: type: string format: uri-reference - run_dir: - title: Run directory - type: string - format: uri-reference cns_exec: title: Path to the CNS executable description: If not provided, HADDOCK3 will use the cns path configured during @@ -73,7 +78,6 @@ global: - slurm - torque queue: - default: '' title: Queue name description: Name of the batch queue to which jobs will be submitted $comment: Name of the batch queue to which jobs will be submitted. If not @@ -115,7 +119,6 @@ global: purpose to allow to edit the scripts without touching the main installation. type: boolean required: - - molecules - run_dir additionalProperties: false uiSchema: @@ -141,6 +144,7 @@ global: ui:group: execution self_contained: ui:group: execution + tomlSchema: {} nodes: - id: clustfcc category: analysis @@ -177,6 +181,7 @@ nodes: uiSchema: executable: ui:widget: file + tomlSchema: {} - id: seletop category: analysis label: HADDOCK3 module to select a top cluster/model. @@ -192,6 +197,7 @@ nodes: required: [] additionalProperties: false uiSchema: {} + tomlSchema: {} - id: seletopclusts category: analysis label: HADDOCK3 module to select a top cluster/model. @@ -213,6 +219,7 @@ nodes: required: [] additionalProperties: false uiSchema: {} + tomlSchema: {} - id: caprieval category: analysis label: Calculate CAPRI metrics. @@ -221,79 +228,186 @@ nodes: type: object properties: reference_fname: + title: Reference structure + description: Structure to be used when calculating the CAPRI metrics. + $comment: Reference tructure to be used when calculating the CAPRI metrics. + If none is defined then the lowest scoring model is selected by default. type: string format: uri-reference irmsd: default: true + title: Calculate I-RMSD + description: Performs Interface RMSD calculations. + $comment: Calculates the Interface Root Mean Square Deviation. This calculate + the RMSD of interface backbone atoms after fitting on the interface backbone + atoms. The interface is idenfied based on intermolecular contacts shorter + than the defined irmsd_cutoff. type: boolean fnat: default: true + title: Calculate FNAT + description: Performs FNAT calculations. + $comment: Calculates the Fraction of Native Contacts. This evaluates how many + contacts observed in the reference are present in the model. The distance + cutoff used to define intermolecular contacts is defined by the fnat_cutoff + parameter. type: boolean lrmsd: default: true + title: Calculate L-RMSD + description: Performs Ligand RMSD calculations. + $comment: Calculates the Ligand Root Mean Square Deviation. This calculation + is done by superimposing the receptors (defined by the receptor_chain parameter) + and then evaluating the RMSD on the ligands (defined by the ligand_chain + parameter). Superposition and RMSD calculations are done on backbone heavy + atoms. type: boolean ilrmsd: default: true + title: Calculate I-L-RMSD + description: Performs Interface Ligand RMSD calculations. + $comment: Calculates the Interface Ligand Root Mean Square Deviation. This + calculation is done by superimposing the model and the target on the interface + backbone atoms of the receptor (defined by the receptor_chain parameter) + and calculating the RMSD on all heavy atoms of the ligand (defined by the + ligand_chain parameter). type: boolean dockq: default: true + title: Calculate DockQ + description: Evaluate DockQ. + $comment: Evaluate DockQ. A single continuous quality measure for protein + docked models based on the CAPRI criteria, a combination of i-RMSD, l-RMSD + and FNAT value. For details check the DockQ publication `DOI:10.1371/journal.pone.0161879` type: boolean irmsd_cutoff: default: 10.0 - type: number - maximum: 9999 - minimum: -9999 + title: "Distance cutoff (\xC5) used to define interface residues." + description: "Distance cutoff (\xC5) used to define interface residues based\ + \ on intermolecular contacts." + $comment: "Distance cutoff (\xC5) used to define interface residues based\ + \ on intermolecular contacts." + type: number + maximum: 20.0 + minimum: 3.0 fnat_cutoff: default: 5.0 - type: number - maximum: 9999 - minimum: -9999 - lrmsd_cutoff: - default: 10.0 - type: number - maximum: 9999 - minimum: -9999 + title: "Distance cutoff (\xC5) used to define interface contacts." + description: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." + $comment: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." + type: number + maximum: 20.0 + minimum: 3.0 receptor_chain: default: A - type: string - minLength: 0 - maxLength: 100 + title: Receptor ChainID + description: Receptor ChainID to be considered for the RMSD calculations. + $comment: Receptor ChainID to be considered for the RMSD calculations. This + determines which chain will be treated as the receptor for the L-RMSD and + for I-L-RMSD. + type: string + minLength: 1 + maxLength: 1 ligand_chain: default: B - type: string - minLength: 0 - maxLength: 100 - rankby: - default: score - type: string - minLength: 0 - maxLength: 100 - rank_ascending: - default: true - type: boolean + title: Ligand ChainID + description: Ligand ChainID to be considered for the RMSD calculations. + $comment: Ligand ChainID to be considered for the RMSD calculations. This + determines which chain will be treated as the ligand for the L-RMSD and + for I-L-RMSD. + type: string + minLength: 1 + maxLength: 1 sortby: default: score + title: Sort the structures/clusters in the output file by this value + description: Which value should be used to sort the output. + $comment: Which value should be used to sort the output, the output table + will be sorted accordingly. type: string minLength: 0 - maxLength: 100 + maxLength: 20 + enum: + - score + - irmsd + - lrmsd + - ilrmsd + - fnat + - dockq sort_ascending: default: true + title: Sort in ascending order + description: Sort in ascending order. + $comment: Sort in ascending order. type: boolean alignment_method: default: sequence + title: Alignment method used to match the numbering. + description: Which alignment method should be used to match the numbering. + $comment: Alignment method used to match the numbering. Sequence alignment + is haddock3-friendly but might not produce best results for structures that + are too different, for that use type: string minLength: 0 maxLength: 100 + enum: + - structure + - sequence lovoalign_exec: - default: '' + title: Location (path) of the LovoAlign executable + description: Location (path) of the LovoAlign executable. + $comment: Location (path) of the LovoAlign executable. type: string minLength: 0 - maxLength: 100 + maxLength: 200 + clt_threshold: + default: 4 + title: Threshold (n) used for the average evaluation in the cluster-based + output + description: Threshold (n) used for the average evaluation in the cluster-based + output. + $comment: Threshold (n) used for the average evaluation in the cluster-based + output. + type: number + maximum: 1000 + minimum: 1 required: [] additionalProperties: false uiSchema: reference_fname: ui:widget: file + ui:group: analysis + irmsd: + ui:group: analysis + fnat: + ui:group: analysis + lrmsd: + ui:group: analysis + ilrmsd: + ui:group: analysis + dockq: + ui:group: analysis + irmsd_cutoff: + ui:group: analysis + fnat_cutoff: + ui:group: analysis + receptor_chain: + ui:group: analysis + ligand_chain: + ui:group: analysis + sortby: + ui:group: analysis + sort_ascending: + ui:group: analysis + alignment_method: + ui:group: analysis + lovoalign_exec: + ui:group: analysis + clt_threshold: + ui:group: analysis + tomlSchema: {} - id: gdock category: sampling label: HADDOCK3 gdock integration module. @@ -309,6 +423,7 @@ nodes: uiSchema: ambig_fname: ui:widget: file + tomlSchema: {} - id: rigidbody category: sampling label: HADDOCK3 rigid-body docking module. @@ -316,246 +431,22 @@ nodes: schema: type: object properties: - mol_fix_origin_1: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_2: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_3: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_4: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_5: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_6: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_7: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_8: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_9: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_10: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_11: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_12: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_13: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_14: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_15: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_16: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_17: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_18: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_19: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_20: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + mol_fix_origin: + type: array + items: + default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. + type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -685,1431 +576,974 @@ nodes: sampled, but it is possible to define per molecule segments from which the random restraints will be defined (see the nrair_X parameter). type: boolean - nrair_1: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + nrair: + type: array + items: + default: 0 + title: Number of segments from which to pick random restraints + description: Defines the number of segments for this molecule from which + to randomly define random interaction restraints. + $comment: Defines the number of segments for this molecule from which to + randomly define random interaction restraints. Only solvent accessible + residues will be considered. See also the ranair parameter. + type: number + maximum: 100 + minimum: 0 + rair: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Starting residue number for segment from which to define + random interaction restraints + $comment: Starting residue number for segment from which to define + random interaction restraints + type: number + maximum: 9999 + minimum: -9999 + end: + title: Ending residue number + description: Ending residue number for segment from which to define + random interaction restraints + $comment: Ending residue number for segment from which to define random + interaction restraints + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false + surfrest: + default: false + title: Surface contact restraints + description: Surface contact restraints between molecules + $comment: Surface contact restraints between molecules. These are defined + as an ambiguous distance restraint between all CA,BB or N1 atoms of two + molecules (for small ligands all atoms are considered). The upper limit + is set to 7A (or 4.5A in case of small ligands). Note that this option is + computationally more expensive than the center of mass restraints (see cmrest). + type: boolean + ksurf: + default: 1.0 + title: Surface contact restraints force constant + description: Force constant applied to the surface contact restraints. + $comment: Force constant applied to the surface contact restraints. type: number - maximum: 100 + maximum: 1000 minimum: 0 - rair_sta_1_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_1_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + sampling: + default: 1000 + title: Number of models to generate + description: Number of rigidbody docking models to generate + $comment: Number of rigidbody docking models to generate type: number - maximum: 9999 - minimum: -9999 - nrair_2: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + maximum: 50000 + minimum: 1 + crossdock: + default: true + title: Cross docking of starting ensembles + description: In case ensembles of starting structures are provided, if set + to true, takes all possible combinations for the docking. + $comment: This variable controls on starting models are combined in case ensembles + of starting structures are provided. If set to true, all possible combinations + of starting models will be used for the docking. If set to false, the first + model from molecule1 will be combined with the first model from molecule2 + and so on. + type: boolean + ntrials: + default: 5 + title: Number of internal docking trials + description: Number of internal docking trials. Only the best model will be + written to disk. + $comment: Number of internal docking trials. HADDOCK will repeat the docking + internally multiple times, ranking them internally and only writing the + best model to disk. type: number maximum: 100 - minimum: 0 - rair_sta_2_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_2_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_3: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + minimum: 1 + rotate180: + default: true + title: Sample 180-rotated solutions + description: If true, HADDOCK will rotate the molecule by 180 degree around + an axis perpendicular to the interface. + $comment: This parameter controls the sampling of 180 degree rotated solutions. + If set to true, HADDOCK will rotate the molecule by 180 degree around an + axis perpendicular to the interface. + type: boolean + randorien: + default: true + type: boolean + rigidtrans: + default: true + title: Allow translation during EM + description: Enables translation during rigidbody energy minimization + $comment: Enables translation during rigidbody energy minimization. If set + to false, only a rotational energy minimization will be performed. + type: boolean + iniseed: + default: 917 + title: Random seed + description: Random seed used in CNS to initialize the random seed function + $comment: Random seed used in CNS to initialize the random seed function type: number - maximum: 100 + maximum: 9999999999999999 minimum: 0 - rair_sta_3_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_3_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_4: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + keepwater: + default: false + title: Write water molecules to output file + description: Write water molecules if present to the output file. + $comment: Write water molecules if present to the output file. + type: boolean + inter_rigid: + default: 1.0 + title: Scaling of intermolecular interactions + description: Scaling of intermolecular interactions + $comment: Scaling of intermolecular interactions. This allows in particular + to scale down intermolecular interactions to reach buried sites (recommended + value for this is 0.01). If scaled-down do note that the van der Waals intermolecular + energy might be bad because of clashes. In that case it is best to also + set the weight of the van der Waals energy term to 0 (w_vdw). type: number - maximum: 100 + maximum: 1 minimum: 0 - rair_sta_4_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_4_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_5: + tolerance: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Failure tolerance percentage + description: Percentage of allowed failures for a module to successfully complete + $comment: Percentage of allowed failures for a module to successfully complete type: number - maximum: 100 + maximum: 99 minimum: 0 - rair_sta_5_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_5_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_6: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 - minimum: 0 - rair_sta_6_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_6_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_7: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + log_level: + default: quiet + title: Log level verbosity for CNS + description: Set the log level verbosity for CNS + $comment: CNS, the computational engine used by HADDOCK can generate a lot + of output messages. This parameter controls the verbosity of CNS (verbose, + normal or quiet). + type: string + minLength: 0 + maxLength: 100 + enum: + - verbose + - normal + - quiet + sym_on: + default: false + title: Symmetry restraints + description: Enables symmetry restraints + $comment: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 + supported) and the segments to which those apply must be defined. In addition + a custom symmetry restraint file can be supplied (symrest_fname). + type: boolean + ksym: + default: 10.0 + title: Force constant for symmetry restraints + description: Force constant for symmetry restraints + $comment: Force constant for symmetry restraints type: number - maximum: 100 + maximum: 1000 minimum: 0 - rair_sta_7_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_7_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_8: + symtbl_fname: + title: Custom symmetry restraints filename + description: Filename of the custom symmetry restraints file + $comment: Filename of the custom symmetry restraints file. + type: string + format: uri-reference + numc2sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of C2 symmetry restraints + description: Defines the number of C2 symmetry restraints. + $comment: Defines the number of C2 symmetry restraints. For each, a pair of + segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. type: number - maximum: 100 + maximum: 40 minimum: 0 - rair_sta_8_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_8_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_9: + c2sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C2 symmetry + segment + $comment: Residue number of first residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C2 symmetry + segment + $comment: Residue number of last residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C2 segment + description: Segment ID of first C2 segment + $comment: Segment ID of first C2 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C2 symmetry + segment + $comment: Residue number of first residue in the second C2 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C2 symmetry + segment + $comment: Residue number of last residue in the second C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C2 segment + description: Segment ID of second C2 segment + $comment: Segment ID of second C2 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc3sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of C3 symmetry restraints + description: Defines the number of C3 symmetry restraints. + $comment: Defines the number of C3 symmetry restraints. For each, three segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 100 + maximum: 10 minimum: 0 - rair_sta_9_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_9_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_10: + c3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C3 symmetry + segment + $comment: Residue number of first residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C3 symmetry + segment + $comment: Residue number of last residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C3 segment + description: Segment ID of first C3 segment + $comment: Segment ID of first C3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C3 symmetry + segment + $comment: Residue number of first residue in the second C3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C3 symmetry + segment + $comment: Residue number of last residue in the second C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C3 segment + description: Segment ID of second C3 segment + $comment: Segment ID of second C3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C3 symmetry + segment + $comment: Residue number of first residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C3 symmetry + segment + $comment: Residue number of last residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C3 segment + description: Segment ID of third C3 segment + $comment: Segment ID of third C3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc4sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of C4 symmetry restraints + description: Defines the number of C4 symmetry restraints. + $comment: Defines the number of C4 symmetry restraints. For each, four segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 100 + maximum: 10 minimum: 0 - rair_sta_10_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_10_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_11: + c4sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C4 symmetry + segment + $comment: Residue number of first residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C4 symmetry + segment + $comment: Residue number of last residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C4 segment + description: Segment ID of first C4 segment + $comment: Segment ID of first C4 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C4 symmetry + segment + $comment: Residue number of first residue in the second C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C4 symmetry + segment + $comment: Residue number of last residue in the second C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C4 segment + description: Segment ID of second C4 segment + $comment: Segment ID of second C4 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C4 symmetry + segment + $comment: Residue number of first residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C4 symmetry + segment + $comment: Residue number of last residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C4 segment + description: Segment ID of third C4 segment + $comment: Segment ID of third C4 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C4 symmetry + segment + $comment: Residue number of first residue in the fourth C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C4 symmetry + segment + $comment: Residue number of last residue in the fourth C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C4 segment + description: Segment ID of fourth C4 segment + $comment: Segment ID of fourth C4 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc5sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of C5 symmetry restraints + description: Defines the number of C5 symmetry restraints. + $comment: Defines the number of C5 symmetry restraints. For each, five segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 100 + maximum: 10 minimum: 0 - rair_sta_11_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_11_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_12: + c5sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C5 symmetry + segment + $comment: Residue number of first residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C5 symmetry + segment + $comment: Residue number of last residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C5 segment + description: Segment ID of first C5 segment + $comment: Segment ID of first C5 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C5 symmetry + segment + $comment: Residue number of first residue in the second C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C5 symmetry + segment + $comment: Residue number of last residue in the second C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C5 segment + description: Segment ID of second C5 segment + $comment: Segment ID of second C5 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C5 symmetry + segment + $comment: Residue number of first residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C5 symmetry + segment + $comment: Residue number of last residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C5 segment + description: Segment ID of third C5 segment + $comment: Segment ID of third C5 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C5 symmetry + segment + $comment: Residue number of first residue in the fourth C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C5 symmetry + segment + $comment: Residue number of last residue in the fourth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C5 segment + description: Segment ID of fourth C5 segment + $comment: Segment ID of fourth C5 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C5 symmetry + segment + $comment: Residue number of first residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C5 symmetry + segment + $comment: Residue number of last residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C5 segment + description: Segment ID of fifth C5 segment + $comment: Segment ID of fifth C5 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc6sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of C6 symmetry restraints + description: Defines the number of C6 symmetry restraints. + $comment: Defines the number of C6 symmetry restraints. For each, six segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 100 + maximum: 10 minimum: 0 - rair_sta_12_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_12_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_13: + c6sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C6 symmetry + segment + $comment: Residue number of first residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C6 symmetry + segment + $comment: Residue number of last residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C6 segment + description: Segment ID of first C6 segment + $comment: Segment ID of first C6 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C6 symmetry + segment + $comment: Residue number of first residue in the second C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C6 symmetry + segment + $comment: Residue number of last residue in the second C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C6 segment + description: Segment ID of second C6 segment + $comment: Segment ID of second C6 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C6 symmetry + segment + $comment: Residue number of first residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C6 symmetry + segment + $comment: Residue number of last residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C6 segment + description: Segment ID of third C6 segment + $comment: Segment ID of third C6 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C6 symmetry + segment + $comment: Residue number of first residue in the fourth C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C6 symmetry + segment + $comment: Residue number of last residue in the fourth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C6 segment + description: Segment ID of fourth C6 segment + $comment: Segment ID of fourth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C6 symmetry + segment + $comment: Residue number of first residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C6 symmetry + segment + $comment: Residue number of last residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C6 segment + description: Segment ID of fifth C6 segment + $comment: Segment ID of fifth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta6: + title: Residue number of first residue + description: Residue number of first residue in the sixth C6 symmetry + segment + $comment: Residue number of first residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end6: + title: Residue number of last residue + description: Residue number of last residue in the sixth C6 symmetry + segment + $comment: Residue number of last residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg6: + title: Segment ID of sixth C6 segment + description: Segment ID of sixth C6 segment + $comment: Segment ID of sixth C6 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + nums3sym: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of S3 symmetry restraints + description: Defines the number of S3 symmetry restraints. + $comment: Defines the number of S3 symmetry restraints. For each, three segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 100 + maximum: 10 minimum: 0 - rair_sta_13_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_13_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_14: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + s3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first S3 symmetry + segment + $comment: Residue number of first residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first S3 symmetry + segment + $comment: Residue number of last residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first S3 segment + description: Segment ID of first S3 segment + $comment: Segment ID of first S3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second S3 symmetry + segment + $comment: Residue number of first residue in the second S3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second S3 symmetry + segment + $comment: Residue number of last residue in the second S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second S3 segment + description: Segment ID of second S3 segment + $comment: Segment ID of second S3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third S3 symmetry + segment + $comment: Residue number of first residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third S3 symmetry + segment + $comment: Residue number of last residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third S3 segment + description: Segment ID of third S3 segment + $comment: Segment ID of third S3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + ncs_on: + default: false + title: Non-crystallographic symmetry restraints + description: Non-crystallographic symmetry restraints to ensure two molecules + will have the same conformation. + $comment: Non-crystallographic symmetry restraints to ensure two molecules + will have the same conformation. This does not apply any symmetry between + the two molecules but rather defines restraints such as the RMSD between + those is 0. + type: boolean + kncs: + default: 1.0 + title: Force constant for non-crystallographic restraints + description: Force constant for non-crystallographic restraints + $comment: Force constant for non-crystallographic restraints type: number - maximum: 100 + maximum: 1000 minimum: 0 - rair_sta_14_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_14_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - nrair_15: + numncs: default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. + title: Number of non-crystallographic symmetry restraints + description: Number of non-crystallographic symmetry restraints (NCS). + $comment: Number of non-crystallographic symmetry restraints. For each pairs + of segments will have to be defined. Note that those must contain exactly + the same residues/atom combinations. type: number maximum: 100 minimum: 0 - rair_sta_15_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_15_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + ncs: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first NCS segment + $comment: Residue number of first residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first NCS segment + $comment: Residue number of last residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first NCS segment + description: Segment ID of first NCS segment + $comment: Segment ID of first NCS segment + type: string + minLength: 0 + maxLength: 100 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second NCS segment + $comment: Residue number of first residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second NCS segment + $comment: Residue number of last residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second NCS segment + description: Segment ID of second NCS segment + $comment: Segment ID of second NCS segment + type: string + minLength: 0 + maxLength: 100 + required: [] + additionalProperties: false + w_dist: + default: 0.01 + title: Weight of the distance restraint energy + description: Weight of the distance restraints energy in the scoring function + $comment: Weight of the distance restraints energy in the scoring function. + Note that this is different from the force constants used during the calculations. type: number maximum: 9999 - minimum: -9999 - nrair_16: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 minimum: 0 - rair_sta_16_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_16_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + w_air: + default: 0.01 + title: Weight of the distance restraint energy + description: Weight of the distance restraints energy in the scoring function + $comment: Weight of the distance restraints energy in the scoring function. + Note that this is different from the force constants used during the calculations. type: number maximum: 9999 - minimum: -9999 - nrair_17: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 minimum: 0 - rair_sta_17_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints + w_bsa: + default: -0.01 + title: Weight of the buried surface area term + description: Weight of the buried surface area term in the scoring function + $comment: Weight of the buried surface area (BSA) term in the scoring function. + Note that the BSA is only used for scoring. type: number maximum: 9999 minimum: -9999 - rair_end_17_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + w_cdih: + default: 0.0 + title: Weight of the dihedral angle restraint energy + description: Weight of the dihedral angle restraints energy in the scoring + function + $comment: Weight of the dihedral angle restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. type: number maximum: 9999 - minimum: -9999 - nrair_18: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 minimum: 0 - rair_sta_18_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_18_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + w_desolv: + default: 1.0 + title: Weight of the desolvation energy term + description: Weight of the desolvation energy term in the scoring function + $comment: Weight of the desolvation energy term in the scoring function. Note + that the desolvation energy is only used for scoring. type: number maximum: 9999 minimum: -9999 - nrair_19: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 - minimum: 0 - rair_sta_19_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints + w_elec: + default: 1.0 + title: Weight of the intermolecular electrostatic energy + description: Weight of the intermolecular electrostatic energy in the scoring + function + $comment: Weight of the intermolecular electrostatic energy in the scoring + function. Note that this does not affect the electostatic energy during + the rigidbody minimization. type: number maximum: 9999 minimum: -9999 - rair_end_19_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints + w_sym: + default: 0.1 + title: Weight of the symmetry restraint energy + description: Weight of the symmetry restraints energy in the scoring function + $comment: Weight of the symmetry restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. type: number maximum: 9999 - minimum: -9999 - nrair_20: - default: 0 - title: Number of segments from which to pick random restraints - description: Defines the number of segments for this molecule from which to - randomly define random interaction restraints. - $comment: Defines the number of segments for this molecule from which to randomly - define random interaction restraints. Only solvent accessible residues will - be considered. See also the ranair parameter. - type: number - maximum: 100 minimum: 0 - rair_sta_20_1: - title: Starting residue number - description: Starting residue number for segment from which to define random - interaction restraints - $comment: Starting residue number for segment from which to define random - interaction restraints - type: number - maximum: 9999 - minimum: -9999 - rair_end_20_1: - title: Ending residue number - description: Ending residue number for segment from which to define random - interaction restraints - $comment: Ending residue number for segment from which to define random interaction - restraints - type: number - maximum: 9999 - minimum: -9999 - surfrest: - default: false - title: Surface contact restraints - description: Surface contact restraints between molecules - $comment: Surface contact restraints between molecules. These are defined - as an ambiguous distance restraint between all CA,BB or N1 atoms of two - molecules (for small ligands all atoms are considered). The upper limit - is set to 7A (or 4.5A in case of small ligands). Note that this option is - computationally more expensive than the center of mass restraints (see cmrest). - type: boolean - ksurf: - default: 1.0 - title: Surface contact restraints force constant - description: Force constant applied to the surface contact restraints. - $comment: Force constant applied to the surface contact restraints. - type: number - maximum: 1000 - minimum: 0 - sampling: - default: 1000 - title: Number of models to generate - description: Number of rigidbody docking models to generate - $comment: Number of rigidbody docking models to generate - type: number - maximum: 50000 - minimum: 1 - crossdock: - default: true - title: Cross docking of starting ensembles - description: In case ensembles of starting structures are provided, if set - to true, takes all possible combinations for the docking. - $comment: This variable controls on starting models are combined in case ensembles - of starting structures are provided. If set to true, all possible combinations - of starting models will be used for the docking. If set to false, the first - model from molecule1 will be combined with the first model from molecule2 - and so on. - type: boolean - ntrials: - default: 5 - title: Number of internal docking trials - description: Number of internal docking trials. Only the best model will be - written to disk. - $comment: Number of internal docking trials. HADDOCK will repeat the docking - internally multiple times, ranking them internally and only writing the - best model to disk. - type: number - maximum: 100 - minimum: 1 - rotate180: - default: true - title: Sample 180-rotated solutions - description: If true, HADDOCK will rotate the molecule by 180 degree around - an axis perpendicular to the interface. - $comment: This parameter controls the sampling of 180 degree rotated solutions. - If set to true, HADDOCK will rotate the molecule by 180 degree around an - axis perpendicular to the interface. - type: boolean - randorien: - default: true - type: boolean - rigidtrans: - default: true - title: Allow translation during EM - description: Enables translation during rigidbody energy minimization - $comment: Enables translation during rigidbody energy minimization. If set - to false, only a rotational energy minimization will be performed. - type: boolean - iniseed: - default: 917 - title: Random seed - description: Random seed used in CNS to initialize the random seed function - $comment: Random seed used in CNS to initialize the random seed function - type: number - maximum: 9999999999999999 - minimum: 0 - keepwater: - default: false - title: Write water molecules to output file - description: Write water molecules if present to the output file. - $comment: Write water molecules if present to the output file. - type: boolean - inter_rigid: - default: 1.0 - title: Scaling of intermolecular interactions - description: Scaling of intermolecular interactions - $comment: Scaling of intermolecular interactions. This allows in particular - to scale down intermolecular interactions to reach buried sites (recommended - value for this is 0.01). If scaled-down do note that the van der Waals intermolecular - energy might be bad because of clashes. In that case it is best to also - set the weight of the van der Waals energy term to 0 (w_vdw). - type: number - maximum: 1 - minimum: 0 - tolerance: - default: 0 - title: Failure tolerance percentage - description: Percentage of allowed failures for a module to successfully complete - $comment: Percentage of allowed failures for a module to successfully complete - type: number - maximum: 99 - minimum: 0 - log_level: - default: verbose - title: Log level verbosity for CNS - description: Set the log level verbosity for CNS (minimal or verbose) - $comment: CNS, the computational engine used by HADDOCK can generate a lot - of output messages. This parameter controls the verbosity of CNS (minimal - or verbose) - type: string - minLength: 0 - maxLength: 100 - sym_on: - default: false - title: Symmetry restraints - description: Enables symmetry restraints - $comment: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 - supported) and the segments to which those apply must be defined. In addition - a custom symmetry restraint file can be supplied (symrest_fname). - type: boolean - ksym: - default: 10.0 - title: Force constant for symmetry restraints - description: Force constant for symmetry restraints - $comment: Force constant for symmetry restraints - type: number - maximum: 1000 - minimum: 0 - symtbl_fname: - title: Custom symmetry restraints filename - description: Filename of the custom symmetry restraints file - $comment: Filename of the custom symmetry restraints file. - type: string - format: uri-reference - numc2sym: - default: 0 - title: Number of C2 symmetry restraints - description: Defines the number of C2 symmetry restraints. - $comment: Defines the number of C2 symmetry restraints. For each, a pair of - segments on which the symmetry restraint is applied will have to be defined. - Those must all have the same length. - type: number - maximum: 40 - minimum: 0 - c2sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C2 symmetry segment - $comment: Residue number of first residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C2 symmetry segment - $comment: Residue number of last residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg1_1: - default: '' - title: Segment ID of first C2 segment - description: Segment ID of first C2 segment - $comment: Segment ID of first C2 segment - type: string - minLength: 0 - maxLength: 4 - c2sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C2 symmetry segment - $comment: Residue number of first residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C2 symmetry segment - $comment: Residue number of last residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg2_1: - default: '' - title: Segment ID of second C2 segment - description: Segment ID of second C2 segment - $comment: Segment ID of second C2 segment - type: string - minLength: 0 - maxLength: 4 - numc3sym: - default: 0 - title: Number of C3 symmetry restraints - description: Defines the number of C3 symmetry restraints. - $comment: Defines the number of C3 symmetry restraints. For each, three segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C3 symmetry segment - $comment: Residue number of first residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C3 symmetry segment - $comment: Residue number of last residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg1_1: - default: '' - title: Segment ID of first C3 segment - description: Segment ID of first C3 segment - $comment: Segment ID of first C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C3 symmetry segment - $comment: Residue number of first residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C3 symmetry segment - $comment: Residue number of last residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg2_1: - default: '' - title: Segment ID of second C3 segment - description: Segment ID of second C3 segment - $comment: Segment ID of second C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C3 symmetry segment - $comment: Residue number of first residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C3 symmetry segment - $comment: Residue number of last residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg3_1: - default: '' - title: Segment ID of third C3 segment - description: Segment ID of third C3 segment - $comment: Segment ID of third C3 segment - type: string - minLength: 0 - maxLength: 4 - numc4sym: - default: 0 - title: Number of C4 symmetry restraints - description: Defines the number of C4 symmetry restraints. - $comment: Defines the number of C4 symmetry restraints. For each, four segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c4sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C4 symmetry segment - $comment: Residue number of first residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C4 symmetry segment - $comment: Residue number of last residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg1_1: - default: '' - title: Segment ID of first C4 segment - description: Segment ID of first C4 segment - $comment: Segment ID of first C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C4 symmetry segment - $comment: Residue number of first residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C4 symmetry segment - $comment: Residue number of last residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg2_1: - default: '' - title: Segment ID of second C4 segment - description: Segment ID of second C4 segment - $comment: Segment ID of second C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C4 symmetry segment - $comment: Residue number of first residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C4 symmetry segment - $comment: Residue number of last residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg3_1: - default: '' - title: Segment ID of third C4 segment - description: Segment ID of third C4 segment - $comment: Segment ID of third C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C4 symmetry segment - $comment: Residue number of first residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C4 symmetry segment - $comment: Residue number of last residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg4_1: - default: '' - title: Segment ID of fourth C4 segment - description: Segment ID of fourth C4 segment - $comment: Segment ID of fourth C4 segment - type: string - minLength: 0 - maxLength: 4 - numc5sym: - default: 0 - title: Number of C5 symmetry restraints - description: Defines the number of C5 symmetry restraints. - $comment: Defines the number of C5 symmetry restraints. For each, five segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c5sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C5 symmetry segment - $comment: Residue number of first residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C5 symmetry segment - $comment: Residue number of last residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg1_1: - default: '' - title: Segment ID of first C5 segment - description: Segment ID of first C5 segment - $comment: Segment ID of first C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C5 symmetry segment - $comment: Residue number of first residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C5 symmetry segment - $comment: Residue number of last residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg2_1: - default: '' - title: Segment ID of second C5 segment - description: Segment ID of second C5 segment - $comment: Segment ID of second C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C5 symmetry segment - $comment: Residue number of first residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C5 symmetry segment - $comment: Residue number of last residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg3_1: - default: '' - title: Segment ID of third C5 segment - description: Segment ID of third C5 segment - $comment: Segment ID of third C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C5 symmetry segment - $comment: Residue number of first residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C5 symmetry segment - $comment: Residue number of last residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg4_1: - default: '' - title: Segment ID of fourth C5 segment - description: Segment ID of fourth C5 segment - $comment: Segment ID of fourth C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C5 symmetry segment - $comment: Residue number of first residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C5 symmetry segment - $comment: Residue number of last residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg5_1: - default: '' - title: Segment ID of fifth C5 segment - description: Segment ID of fifth C5 segment - $comment: Segment ID of fifth C5 segment - type: string - minLength: 0 - maxLength: 4 - numc6sym: - default: 0 - title: Number of C6 symmetry restraints - description: Defines the number of C6 symmetry restraints. - $comment: Defines the number of C6 symmetry restraints. For each, six segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c6sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C6 symmetry segment - $comment: Residue number of first residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C6 symmetry segment - $comment: Residue number of last residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg1_1: - default: '' - title: Segment ID of first C6 segment - description: Segment ID of first C6 segment - $comment: Segment ID of first C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C6 symmetry segment - $comment: Residue number of first residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C6 symmetry segment - $comment: Residue number of last residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg2_1: - default: '' - title: Segment ID of second C6 segment - description: Segment ID of second C6 segment - $comment: Segment ID of second C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C6 symmetry segment - $comment: Residue number of first residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C6 symmetry segment - $comment: Residue number of last residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg3_1: - default: '' - title: Segment ID of third C6 segment - description: Segment ID of third C6 segment - $comment: Segment ID of third C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C6 symmetry segment - $comment: Residue number of first residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C6 symmetry segment - $comment: Residue number of last residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg4_1: - default: '' - title: Segment ID of fourth C6 segment - description: Segment ID of fourth C6 segment - $comment: Segment ID of fourth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C6 symmetry segment - $comment: Residue number of first residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C6 symmetry segment - $comment: Residue number of last residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg5_1: - default: '' - title: Segment ID of fifth C6 segment - description: Segment ID of fifth C6 segment - $comment: Segment ID of fifth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta6_1: - title: Residue number of first residue - description: Residue number of first residue in the sixth C6 symmetry segment - $comment: Residue number of first residue in the sixth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end6_1: - title: Residue number of last residue - description: Residue number of last residue in the sixth C6 symmetry segment - $comment: Residue number of last residue in the sixth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg6_1: - default: '' - title: Segment ID of sixth C6 segment - description: Segment ID of sixth C6 segment - $comment: Segment ID of sixth C6 segment - type: string - minLength: 0 - maxLength: 4 - nums3sym: - default: 0 - title: Number of S3 symmetry restraints - description: Defines the number of S3 symmetry restraints. - $comment: Defines the number of S3 symmetry restraints. For each, three segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - s3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first S3 symmetry segment - $comment: Residue number of first residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first S3 symmetry segment - $comment: Residue number of last residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg1_1: - default: '' - title: Segment ID of first S3 segment - description: Segment ID of first S3 segment - $comment: Segment ID of first S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second S3 symmetry segment - $comment: Residue number of first residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second S3 symmetry segment - $comment: Residue number of last residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg2_1: - default: '' - title: Segment ID of second S3 segment - description: Segment ID of second S3 segment - $comment: Segment ID of second S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third S3 symmetry segment - $comment: Residue number of first residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third S3 symmetry segment - $comment: Residue number of last residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg3_1: - default: '' - title: Segment ID of third S3 segment - description: Segment ID of third S3 segment - $comment: Segment ID of third S3 segment - type: string - minLength: 0 - maxLength: 4 - ncs_on: - default: false - title: Non-crystallographic symmetry restraints - description: Non-crystallographic symmetry restraints to ensure two molecules - will have the same conformation. - $comment: Non-crystallographic symmetry restraints to ensure two molecules - will have the same conformation. This does not apply any symmetry between - the two molecules but rather defines restraints such as the RMSD between - those is 0. - type: boolean - kncs: - default: 1.0 - title: Force constant for non-crystallographic restraints - description: Force constant for non-crystallographic restraints - $comment: Force constant for non-crystallographic restraints - type: number - maximum: 1000 - minimum: 0 - numncs: - default: 0 - title: Number of non-crystallographic symmetry restraints - description: Number of non-crystallographic symmetry restraints (NCS). - $comment: Number of non-crystallographic symmetry restraints. For each pairs - of segments will have to be defined. Note that those must contain exactly - the same residues/atom combinations. - type: number - maximum: 100 - minimum: 0 - ncs_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first NCS segment - $comment: Residue number of first residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first NCS segment - $comment: Residue number of last residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg1_1: - default: '' - title: Segment ID of first NCS segment - description: Segment ID of first NCS segment - $comment: Segment ID of first NCS segment - type: string - minLength: 0 - maxLength: 100 - ncs_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second NCS segment - $comment: Residue number of first residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second NCS segment - $comment: Residue number of last residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg2_1: - default: '' - title: Segment ID of second NCS segment - description: Segment ID of second NCS segment - $comment: Segment ID of second NCS segment - type: string - minLength: 0 - maxLength: 100 - w_dist: - default: 0.01 - title: Weight of the distance restraint energy - description: Weight of the distance restraints energy in the scoring function - $comment: Weight of the distance restraints energy in the scoring function. - Note that this is different from the force constants used during the calculations. - type: number - maximum: 9999 - minimum: 0 - w_air: - default: 0.01 - title: Weight of the distance restraint energy - description: Weight of the distance restraints energy in the scoring function - $comment: Weight of the distance restraints energy in the scoring function. - Note that this is different from the force constants used during the calculations. - type: number - maximum: 9999 - minimum: 0 - w_bsa: - default: -0.01 - title: Weight of the buried surface area term - description: Weight of the buried surface area term in the scoring function - $comment: Weight of the buried surface area (BSA) term in the scoring function. - Note that the BSA is only used for scoring. - type: number - maximum: 9999 - minimum: -9999 - w_cdih: - default: 0.0 - title: Weight of the dihedral angle restraint energy - description: Weight of the dihedral angle restraints energy in the scoring - function - $comment: Weight of the dihedral angle restraints energy in the scoring function. - Note that this is different from the force constant used during the calculations. - type: number - maximum: 9999 - minimum: 0 - w_desolv: - default: 1.0 - title: Weight of the desolvation energy term - description: Weight of the desolvation energy term in the scoring function - $comment: Weight of the desolvation energy term in the scoring function. Note - that the desolvation energy is only used for scoring. - type: number - maximum: 9999 - minimum: -9999 - w_elec: - default: 1.0 - title: Weight of the intermolecular electrostatic energy - description: Weight of the intermolecular electrostatic energy in the scoring - function - $comment: Weight of the intermolecular electrostatic energy in the scoring - function. Note that this does not affect the electostatic energy during - the rigidbody minimization. - type: number - maximum: 9999 - minimum: -9999 - w_sym: - default: 0.1 - title: Weight of the symmetry restraint energy - description: Weight of the symmetry restraints energy in the scoring function - $comment: Weight of the symmetry restraints energy in the scoring function. - Note that this is different from the force constant used during the calculations. - type: number - maximum: 9999 - minimum: 0 - w_vdw: - default: 0.01 - title: Weight of the intermolecular van der Waals energy - description: Weight of the intermolecular van der Waals energy in the scoring - function - $comment: Weight of the intermolecular van der Waals energy in the scoring - function. Note that this does not affect the van der Waals energy during - the rigidbody minimization. + w_vdw: + default: 0.01 + title: Weight of the intermolecular van der Waals energy + description: Weight of the intermolecular van der Waals energy in the scoring + function + $comment: Weight of the intermolecular van der Waals energy in the scoring + function. Note that this does not affect the van der Waals energy during + the rigidbody minimization. type: number maximum: 9999 minimum: -9999 @@ -2162,232 +1596,40 @@ nodes: required: [] additionalProperties: false uiSchema: - mol_fix_origin_1: - ui:group: molecule - mol_fix_origin_2: - ui:group: molecule - mol_fix_origin_3: - ui:group: molecule - mol_fix_origin_4: - ui:group: molecule - mol_fix_origin_5: - ui:group: molecule - mol_fix_origin_6: - ui:group: molecule - mol_fix_origin_7: - ui:group: molecule - mol_fix_origin_8: - ui:group: molecule - mol_fix_origin_9: - ui:group: molecule - mol_fix_origin_10: - ui:group: molecule - mol_fix_origin_11: - ui:group: molecule - mol_fix_origin_12: - ui:group: molecule - mol_fix_origin_13: - ui:group: molecule - mol_fix_origin_14: - ui:group: molecule - mol_fix_origin_15: - ui:group: molecule - mol_fix_origin_16: - ui:group: molecule - mol_fix_origin_17: - ui:group: molecule - mol_fix_origin_18: - ui:group: molecule - mol_fix_origin_19: + mol_fix_origin: ui:group: molecule - mol_fix_origin_20: - ui:group: molecule - mol_shape_1: - ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: - ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: - ui:group: molecule - mol_shape_10: - ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file ui:group: distance restraints unambig_fname: ui:widget: file - ui:group: distance restraints - hbond_fname: - ui:widget: file - ui:group: distance restraints - amb_scale: - ui:group: distance restraints - unamb_scale: - ui:group: distance restraints - hbond_scale: - ui:group: distance restraints - randremoval: - ui:group: distance restraints - npart: - ui:group: distance restraints - cmrest: - ui:group: ab initio mode - cmtight: - ui:group: ab initio mode - kcm: - ui:group: ab initio mode - ranair: - ui:group: ab initio mode - nrair_1: - ui:group: ab initio mode - rair_sta_1_1: - ui:group: ab initio mode - rair_end_1_1: - ui:group: ab initio mode - nrair_2: - ui:group: ab initio mode - rair_sta_2_1: - ui:group: ab initio mode - rair_end_2_1: - ui:group: ab initio mode - nrair_3: - ui:group: ab initio mode - rair_sta_3_1: - ui:group: ab initio mode - rair_end_3_1: - ui:group: ab initio mode - nrair_4: - ui:group: ab initio mode - rair_sta_4_1: - ui:group: ab initio mode - rair_end_4_1: - ui:group: ab initio mode - nrair_5: - ui:group: ab initio mode - rair_sta_5_1: - ui:group: ab initio mode - rair_end_5_1: - ui:group: ab initio mode - nrair_6: - ui:group: ab initio mode - rair_sta_6_1: - ui:group: ab initio mode - rair_end_6_1: - ui:group: ab initio mode - nrair_7: - ui:group: ab initio mode - rair_sta_7_1: - ui:group: ab initio mode - rair_end_7_1: - ui:group: ab initio mode - nrair_8: - ui:group: ab initio mode - rair_sta_8_1: - ui:group: ab initio mode - rair_end_8_1: - ui:group: ab initio mode - nrair_9: - ui:group: ab initio mode - rair_sta_9_1: - ui:group: ab initio mode - rair_end_9_1: - ui:group: ab initio mode - nrair_10: - ui:group: ab initio mode - rair_sta_10_1: - ui:group: ab initio mode - rair_end_10_1: - ui:group: ab initio mode - nrair_11: - ui:group: ab initio mode - rair_sta_11_1: - ui:group: ab initio mode - rair_end_11_1: - ui:group: ab initio mode - nrair_12: - ui:group: ab initio mode - rair_sta_12_1: - ui:group: ab initio mode - rair_end_12_1: - ui:group: ab initio mode - nrair_13: - ui:group: ab initio mode - rair_sta_13_1: - ui:group: ab initio mode - rair_end_13_1: - ui:group: ab initio mode - nrair_14: - ui:group: ab initio mode - rair_sta_14_1: - ui:group: ab initio mode - rair_end_14_1: - ui:group: ab initio mode - nrair_15: - ui:group: ab initio mode - rair_sta_15_1: - ui:group: ab initio mode - rair_end_15_1: - ui:group: ab initio mode - nrair_16: - ui:group: ab initio mode - rair_sta_16_1: - ui:group: ab initio mode - rair_end_16_1: - ui:group: ab initio mode - nrair_17: - ui:group: ab initio mode - rair_sta_17_1: - ui:group: ab initio mode - rair_end_17_1: - ui:group: ab initio mode - nrair_18: - ui:group: ab initio mode - rair_sta_18_1: - ui:group: ab initio mode - rair_end_18_1: - ui:group: ab initio mode - nrair_19: + ui:group: distance restraints + hbond_fname: + ui:widget: file + ui:group: distance restraints + amb_scale: + ui:group: distance restraints + unamb_scale: + ui:group: distance restraints + hbond_scale: + ui:group: distance restraints + randremoval: + ui:group: distance restraints + npart: + ui:group: distance restraints + cmrest: ui:group: ab initio mode - rair_sta_19_1: + cmtight: ui:group: ab initio mode - rair_end_19_1: + kcm: ui:group: ab initio mode - nrair_20: + ranair: ui:group: ab initio mode - rair_sta_20_1: + nrair: ui:group: ab initio mode - rair_end_20_1: + rair: ui:group: ab initio mode surfrest: ui:group: ab initio mode @@ -2424,153 +1666,27 @@ nodes: ui:group: symmetry numc2sym: ui:group: symmetry - c2sym_sta1_1: - ui:group: symmetry - c2sym_end1_1: - ui:group: symmetry - c2sym_seg1_1: - ui:group: symmetry - c2sym_sta2_1: - ui:group: symmetry - c2sym_end2_1: - ui:group: symmetry - c2sym_seg2_1: + c2sym: ui:group: symmetry numc3sym: ui:group: symmetry - c3sym_sta1_1: - ui:group: symmetry - c3sym_end1_1: - ui:group: symmetry - c3sym_seg1_1: - ui:group: symmetry - c3sym_sta2_1: - ui:group: symmetry - c3sym_end2_1: - ui:group: symmetry - c3sym_seg2_1: - ui:group: symmetry - c3sym_sta3_1: - ui:group: symmetry - c3sym_end3_1: - ui:group: symmetry - c3sym_seg3_1: + c3sym: ui:group: symmetry numc4sym: ui:group: symmetry - c4sym_sta1_1: - ui:group: symmetry - c4sym_end1_1: - ui:group: symmetry - c4sym_seg1_1: - ui:group: symmetry - c4sym_sta2_1: - ui:group: symmetry - c4sym_end2_1: - ui:group: symmetry - c4sym_seg2_1: - ui:group: symmetry - c4sym_sta3_1: - ui:group: symmetry - c4sym_end3_1: - ui:group: symmetry - c4sym_seg3_1: - ui:group: symmetry - c4sym_sta4_1: - ui:group: symmetry - c4sym_end4_1: - ui:group: symmetry - c4sym_seg4_1: + c4sym: ui:group: symmetry numc5sym: ui:group: symmetry - c5sym_sta1_1: - ui:group: symmetry - c5sym_end1_1: - ui:group: symmetry - c5sym_seg1_1: - ui:group: symmetry - c5sym_sta2_1: - ui:group: symmetry - c5sym_end2_1: - ui:group: symmetry - c5sym_seg2_1: - ui:group: symmetry - c5sym_sta3_1: - ui:group: symmetry - c5sym_end3_1: - ui:group: symmetry - c5sym_seg3_1: - ui:group: symmetry - c5sym_sta4_1: - ui:group: symmetry - c5sym_end4_1: - ui:group: symmetry - c5sym_seg4_1: - ui:group: symmetry - c5sym_sta5_1: - ui:group: symmetry - c5sym_end5_1: - ui:group: symmetry - c5sym_seg5_1: + c5sym: ui:group: symmetry numc6sym: ui:group: symmetry - c6sym_sta1_1: - ui:group: symmetry - c6sym_end1_1: - ui:group: symmetry - c6sym_seg1_1: - ui:group: symmetry - c6sym_sta2_1: - ui:group: symmetry - c6sym_end2_1: - ui:group: symmetry - c6sym_seg2_1: - ui:group: symmetry - c6sym_sta3_1: - ui:group: symmetry - c6sym_end3_1: - ui:group: symmetry - c6sym_seg3_1: - ui:group: symmetry - c6sym_sta4_1: - ui:group: symmetry - c6sym_end4_1: - ui:group: symmetry - c6sym_seg4_1: - ui:group: symmetry - c6sym_sta5_1: - ui:group: symmetry - c6sym_end5_1: - ui:group: symmetry - c6sym_seg5_1: - ui:group: symmetry - c6sym_sta6_1: - ui:group: symmetry - c6sym_end6_1: - ui:group: symmetry - c6sym_seg6_1: + c6sym: ui:group: symmetry nums3sym: ui:group: symmetry - s3sym_sta1_1: - ui:group: symmetry - s3sym_end1_1: - ui:group: symmetry - s3sym_seg1_1: - ui:group: symmetry - s3sym_sta2_1: - ui:group: symmetry - s3sym_end2_1: - ui:group: symmetry - s3sym_seg2_1: - ui:group: symmetry - s3sym_sta3_1: - ui:group: symmetry - s3sym_end3_1: - ui:group: symmetry - s3sym_seg3_1: + s3sym: ui:group: symmetry ncs_on: ui:group: symmetry @@ -2578,17 +1694,7 @@ nodes: ui:group: symmetry numncs: ui:group: symmetry - ncs_sta1_1: - ui:group: symmetry - ncs_end1_1: - ui:group: symmetry - ncs_seg1_1: - ui:group: symmetry - ncs_sta2_1: - ui:group: symmetry - ncs_end2_1: - ui:group: symmetry - ncs_seg2_1: + ncs: ui:group: symmetry w_dist: ui:group: scoring @@ -2618,6 +1724,47 @@ nodes: ui:group: force field epsilon: ui:group: force field + tomlSchema: + mol_fix_origin: + indexed: true + mol_shape: + indexed: true + nrair: + indexed: true + rair: + indexed: true + items: + indexed: true + items: + flatten: true + c2sym: + indexed: true + items: + flatten: true + c3sym: + indexed: true + items: + flatten: true + c4sym: + indexed: true + items: + flatten: true + c5sym: + indexed: true + items: + flatten: true + c6sym: + indexed: true + items: + flatten: true + s3sym: + indexed: true + items: + flatten: true + ncs: + indexed: true + items: + flatten: true - id: lightdock category: sampling label: Run Lightdock as a HADDOCK3 module. @@ -2656,12 +1803,10 @@ nodes: minLength: 0 maxLength: 100 receptor_active: - default: '' type: string minLength: 0 maxLength: 100 receptor_passive: - default: '' type: string minLength: 0 maxLength: 100 @@ -2671,12 +1816,10 @@ nodes: minLength: 0 maxLength: 100 ligand_active: - default: '' type: string minLength: 0 maxLength: 100 ligand_passive: - default: '' type: string minLength: 0 maxLength: 100 @@ -2692,6 +1835,7 @@ nodes: required: [] additionalProperties: false uiSchema: {} + tomlSchema: {} - id: topoaa category: topology label: Create and manage CNS all-atom topology. @@ -2719,15 +1863,19 @@ nodes: hydrogen atoms (e.g. when using NMR distance restraints). type: boolean log_level: - default: verbose + default: quiet title: Log level verbosity for CNS - description: Set the log level verbosity for CNS (minimal or verbose) + description: Set the log level verbosity for CNS $comment: CNS, the computational engine used by HADDOCK can generate a lot - of output messages. This parameter controls the verbosity of CNS (minimal - or verbose) + of output messages. This parameter controls the verbosity of CNS (verbose, + normal or quiet). type: string minLength: 0 maxLength: 100 + enum: + - verbose + - normal + - quiet iniseed: default: 917 title: Random seed @@ -2763,1489 +1911,618 @@ nodes: type: number maximum: 99 minimum: 0 - mol1: - type: object - properties: - prot_segid: - default: A - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol2: - type: object - properties: - prot_segid: - default: B - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol3: - type: object - properties: - prot_segid: - default: C - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol4: - type: object - properties: - prot_segid: - default: D - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol5: - type: object - properties: - prot_segid: - default: E - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol6: - type: object - properties: - prot_segid: - default: F - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol7: - type: object - properties: - prot_segid: - default: G - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol8: - type: object - properties: - prot_segid: - default: H - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol9: - type: object - properties: - prot_segid: - default: I - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol10: - type: object - properties: - prot_segid: - default: J - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol11: - type: object - properties: - prot_segid: - default: K - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol12: - type: object - properties: - prot_segid: - default: L - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol13: - type: object - properties: - prot_segid: - default: M - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol14: - type: object - properties: - prot_segid: - default: N - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol15: - type: object - properties: - prot_segid: - default: O - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol16: - type: object - properties: - prot_segid: - default: P - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol17: - type: object - properties: - prot_segid: - default: Q - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol18: - type: object - properties: - prot_segid: - default: R - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol19: - type: object - properties: - prot_segid: - default: S - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - mol20: - type: object + mol: + title: Input molecule configuration + description: Specific molecule configuration + $comment: You can expand this parameter and associated sub-parameters to the + other input molecules. For example, if you input three molecules, you can + define mol1, mol2, and mol3 subparameters. Those not defined will be populated + with the defaults. + type: array + items: + type: object + properties: + prot_segid: + default: A + title: Segment ID + description: Segment ID assigned to this molecule + $comment: Segment ID assigned to this molecule in CNS. Used to distinguish + different molecules + type: string + minLength: 0 + maxLength: 4 + cyclicpept: + default: false + title: Cyclic peptide + description: Defines the molecule as a cyclic peptide + $comment: This option defines the molecule as a cyclic peptide and HADDOCK + will generate a peptide bond between the N- and C-ter provided those + are within 2A. This cutoff can be changed in the generate-topology.cns + script. + type: boolean + nhisd: + default: 0 + title: Number of HISD residue + description: Defines the number of HISD residues (neutral HIS with the + proton on the ND atom) residues when autohis=false + $comment: Defines the number of HISD residues (neutral HIS with the + proton on the ND atom) residues. The corresponding residue numbers + must be defined in the following parameter (hisd_1, hisd_2, ...). + Add as many as needed. Note that HIS is interpreted as a charged Histidine) + type: number + maximum: 9999 + minimum: 0 + hisd: + type: array + items: + title: HISD residue number + description: Residue number of the Histidine to be defined as HISD + $comment: Residue number of the Histidine to be defined as HISD + type: number + maximum: 9999 + minimum: -9999 + nhise: + default: 0 + title: Number of HISE residue + description: Defines the number of HISE residues (neutral HIS with the + proton on the NE atom) residues when autohis=false + $comment: Defines the number of HISE residues (neutral HIS with the + proton on the NE atom) residues. The corresponding residue numbers + must be defined in the following parameter (hise_1, hise_2, ...). + Add as many as needed. Note that HIS is interpreted as a charged Histidine) + type: number + maximum: 9999 + minimum: 0 + hise: + type: array + items: + title: HISE residue number + description: Residue number of the Histidine to be defined as HISE + $comment: Residue number of the Histidine to be defined as HISE + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false + required: [] + additionalProperties: false + uiSchema: + autohis: + ui:group: molecule + delenph: + ui:group: molecule + log_level: + ui:group: module + iniseed: + ui:group: molecule + ligand_param_fname: + ui:widget: file + ui:group: force field + ligand_top_fname: + ui:widget: file + ui:group: force field + tolerance: + ui:group: module + mol: + ui:group: input molecules + tomlSchema: + mol: + indexed: true + items: + sectioned: true properties: - prot_segid: - default: T - title: Segment ID - description: Segment ID assigned to this molecule - $comment: Segment ID assigned to this molecule in CNS. Used to distinguish - different molecules - type: string - minLength: 0 - maxLength: 4 - cyclicpept: - default: false - title: Cyclic peptide - description: Defines the molecule as a cyclic peptide - $comment: This option defines the molecule as a cyclic peptide and HADDOCK - will generate a peptide bond between the N- and C-ter provided those - are within 2A. This cutoff can be changed in the generate-topology.cns - script. - type: boolean - nhisd: - default: 0 - title: Number of HISD residue - description: Defines the number of HISD residues (neutral HIS with the - proton on the ND atom) residues when autohis=false - $comment: Defines the number of HISD residues (neutral HIS with the proton - on the ND atom) residues. The corresponding residue numbers must be - defined in the following parameter (hisd_1, hisd_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hisd_1: - title: HISD residue number - description: Residue number of the Histidine to be defined as HISD - $comment: Residue number of the Histidine to be defined as HISD - type: number - maximum: 9999 - minimum: -9999 - nhise: - default: 0 - title: Number of HISE residue - description: Defines the number of HISE residues (neutral HIS with the - proton on the NE atom) residues when autohis=false - $comment: Defines the number of HISE residues (neutral HIS with the proton - on the NE atom) residues. The corresponding residue numbers must be - defined in the following parameter (hise_1, hise_2, ...). Add as many - as needed. Note that HIS is interpreted as a charged Histidine) - type: number - maximum: 9999 - minimum: 0 - hise_1: - title: HISE residue number - description: Residue number of the Histidine to be defined as HISE - $comment: Residue number of the Histidine to be defined as HISE - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false + hisd: + indexed: true + hise: + indexed: true +- id: emscoring + category: scoring + label: HADDOCK3 scoring module. + description: HADDOCK3 module to perform energy minimization scoring. + schema: + type: object + properties: + w_bsa: + default: 0.0 + title: Weight of the buried surface area term + description: Weight of the buried surface area term in the scoring function + $comment: Weight of the buried surface area (BSA) term in the scoring function. + Note that the BSA is only used for scoring. + type: number + maximum: 9999 + minimum: -9999 + w_cdih: + default: 0.0 + title: Weight of the dihedral angle restraint energy + description: Weight of the dihedral angle restraints energy in the scoring + function + $comment: Weight of the dihedral angle restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. + type: number + maximum: 9999 + minimum: 0 + w_desolv: + default: 1.0 + title: Weight of the desolvation energy term + description: Weight of the desolvation energy term in the scoring function + $comment: Weight of the desolvation energy term in the scoring function. Note + that the desolvation energy is only used for scoring. + type: number + maximum: 9999 + minimum: -9999 + w_elec: + default: 0.2 + title: Weight of the intermolecular electrostatic energy + description: Weight of the intermolecular electrostatic energy in the scoring + function + $comment: Weight of the intermolecular electrostatic energy in the scoring + function. Note that this does not affect the electostatic energy during + the EM minimization. + type: number + maximum: 9999 + minimum: -9999 + w_vdw: + default: 1.0 + title: Weight of the intermolecular van der Waals energy + description: Weight of the intermolecular van der Waals energy in the scoring + function + $comment: Weight of the intermolecular van der Waals energy in the scoring + function. Note that this does not affect the van der Waals energy during + the EM minimization. + type: number + maximum: 9999 + minimum: -9999 + ligand_param_fname: + title: Custom ligand parameter file + description: Ligand parameter file in CNS format + $comment: Ligand parameter file in CNS format containing all force field parameters + (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported + by default by HADDOCK + type: string + format: uri-reference + ligand_top_fname: + title: Custom ligand topology file + description: Ligand topology file in CNS format + $comment: Ligand topology file in CNS format containing the ligand topologies + (atoms, masses, charges, bond definitions...) for any ligand not supported + by default by HADDOCK + type: string + format: uri-reference + elecflag: + default: true + title: Include electrostatics energy + description: Include electrostatics energy during the calculations. + $comment: Include electrostatics energy during the calculations. If set to + false electrostatics will not be considered. + type: boolean + dielec: + default: cdie + title: Constant (cdie) or distance-dependent dielectric (rdie) constant. + description: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. + $comment: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. A distance dependent dielectric + constant will effectively scale down the electrostatic energy by having + a 1/r**2 dependency instead of 1/r + type: string + minLength: 0 + maxLength: 4 + enum: + - cdie + - rdie + epsilon: + default: 1.0 + title: Dielectric constant + description: Dielectric constant for the electrostatic Coulomb energy term. + $comment: Dielectric constant for the electrostatic Coulomb energy term. + type: number + maximum: 78 + minimum: 1 + dihedflag: + default: true + type: boolean + individualize: + default: true + title: Individualise models + description: Treat each model in the PDB ensemble as a separate entity. + $comment: Treat each model in the PDB ensemble as a separate entity. This + means that for each a separate topology file will be generated. The models + in the ensemble can thus correspond to different molecules. + type: boolean + nemsteps: + default: 50 + title: Number of EM steps + description: Number of energy minimisation steps to perform. + $comment: Number of energy minimisation steps to perform. Note that the effective + number might be smaller if the minimisation converges earlier. + type: number + maximum: 10000 + minimum: 1 + tolerance: + default: 0 + title: Failure tolerance percentage + description: Percentage of allowed failures for a module to successfully complete + $comment: Percentage of allowed failures for a module to successfully complete + type: number + maximum: 99 + minimum: 0 + log_level: + default: quiet + title: Log level verbosity for CNS + description: Set the log level verbosity for CNS + $comment: CNS, the computational engine used by HADDOCK can generate a lot + of output messages. This parameter controls the verbosity of CNS (verbose, + normal or quiet) + type: string + minLength: 0 + maxLength: 100 + enum: + - verbose + - normal + - quiet required: [] additionalProperties: false uiSchema: - autohis: - ui:group: molecule - delenph: - ui:group: molecule - log_level: - ui:group: module - iniseed: - ui:group: molecule + w_bsa: + ui:group: scoring + w_cdih: + ui:group: scoring + w_desolv: + ui:group: scoring + w_elec: + ui:group: scoring + w_vdw: + ui:group: scoring ligand_param_fname: ui:widget: file ui:group: force field ligand_top_fname: ui:widget: file ui:group: force field + elecflag: + ui:group: force field + dielec: + ui:group: force field + epsilon: + ui:group: force field + dihedflag: + ui:group: force field + individualize: + ui:group: sampling + nemsteps: + ui:group: sampling tolerance: ui:group: module - mol1: - ui:field: collapsible - mol2: - ui:field: collapsible - mol3: - ui:field: collapsible - mol4: - ui:field: collapsible - mol5: - ui:field: collapsible - mol6: - ui:field: collapsible - mol7: - ui:field: collapsible - mol8: - ui:field: collapsible - mol9: - ui:field: collapsible - mol10: - ui:field: collapsible - mol11: - ui:field: collapsible - mol12: - ui:field: collapsible - mol13: - ui:field: collapsible - mol14: - ui:field: collapsible - mol15: - ui:field: collapsible - mol16: - ui:field: collapsible - mol17: - ui:field: collapsible - mol18: - ui:field: collapsible - mol19: - ui:field: collapsible - mol20: - ui:field: collapsible -- id: emscoring + log_level: + ui:group: module + tomlSchema: {} +- id: mdscoring category: scoring label: HADDOCK3 scoring module. description: HADDOCK3 module to perform energy minimization scoring. schema: type: object properties: - tolerance: - default: 5 + w_bsa: + default: 0.0 + title: Weight of the buried surface area term + description: Weight of the buried surface area term in the scoring function + $comment: Weight of the buried surface area (BSA) term in the scoring function. + Note that the BSA is only used for scoring. type: number maximum: 9999 minimum: -9999 - log_level: - default: verbose + w_cdih: + default: 0.0 + title: Weight of the dihedral angle restraint energy + description: Weight of the dihedral angle restraints energy in the scoring + function + $comment: Weight of the dihedral angle restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. + type: number + maximum: 9999 + minimum: 0 + w_desolv: + default: 1.0 + title: Weight of the desolvation energy term + description: Weight of the desolvation energy term in the scoring function + $comment: Weight of the desolvation energy term in the scoring function. Note + that the desolvation energy is only used for scoring. + type: number + maximum: 9999 + minimum: -9999 + w_elec: + default: 0.2 + title: Weight of the intermolecular electrostatic energy + description: Weight of the intermolecular electrostatic energy in the scoring + function + $comment: Weight of the intermolecular electrostatic energy in the scoring + function. Note that this does not affect the electostatic energy during + the EM minimization. + type: number + maximum: 9999 + minimum: -9999 + w_vdw: + default: 1.0 + title: Weight of the intermolecular van der Waals energy + description: Weight of the intermolecular van der Waals energy in the scoring + function + $comment: Weight of the intermolecular van der Waals energy in the scoring + function. Note that this does not affect the van der Waals energy during + the EM minimization. + type: number + maximum: 9999 + minimum: -9999 + contactairs: + default: false + title: Contact restraints + description: Contact restraints between molecules + $comment: Contact restraints between molecules. These are defined as ambiguous + distance restraint between each residue of a molecule and all residues of + the other molecules with 5A from that residue. This can be used to restraint + the contacts between the interfaces. Note that this can generate a large + number of ambiguous restraints and slow down the computations + type: boolean + kcont: + default: 1.0 + title: Contact restraints force constant + description: Force constant applied to the contact restraints. + $comment: Force constant applied to the contact restraints. + type: number + maximum: 1000 + minimum: 0 + ssdihed: + default: none + title: Define automatically backbone dihedral angle restraints + description: If turned on, this option will automatically defined backbone + dihedral angle restraints for the selected regions. + $comment: This option allows to utomatically defined backbone dihedral angle + restraints for the selected regions. The restraints will be defined for + the phi and psi backbone dihedral angles of amino acids, with the target + value taken from the measured angle in the input structure, and the error + bound defined by the error_dih parameter. Those restraints can be applied + to the entire structure (all), the alpha/beta secondary structure elements + (alphabeta) or only to the alpha helical regions (alpha). Those are automatically + detected based on the measured dihedral angle combinations. type: string minLength: 0 maxLength: 100 + enum: + - none + - all + - alpha + - alphabeta + error_dih: + default: 10 + title: Force constant for backbone dihedral angle restraints + description: Force constant for backbone dihedral angle restraints (ssdihed + option) + $comment: Force constant for backbone dihedral angle restraints (ssdihed option) + type: number + maximum: 1000 + minimum: 0 + dnarest_on: + default: false + title: Restrain the DNA conformation + description: Automatically creates restraints to maintain the conformation + of DNA/RNA + $comment: 'This option allows to restraint the conformation of nucleic acids + based on the values from the input structures. The following restraints + will be automatically defined: - single base planarity - sugar pucker - + phosphate backbone diherdral angle restraints - Watson-Crick base pairing' + type: boolean ligand_param_fname: + title: Custom ligand parameter file + description: Ligand parameter file in CNS format + $comment: Ligand parameter file in CNS format containing all force field parameters + (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported + by default by HADDOCK type: string format: uri-reference ligand_top_fname: + title: Custom ligand topology file + description: Ligand topology file in CNS format + $comment: Ligand topology file in CNS format containing the ligand topologies + (atoms, masses, charges, bond definitions...) for any ligand not supported + by default by HADDOCK type: string format: uri-reference - individualize: - default: true - type: boolean - nemsteps: - default: 40 - type: number - maximum: 9999 - minimum: -9999 elecflag: default: true + title: Include electrostatics energy + description: Include electrostatics energy during the calculations. + $comment: Include electrostatics energy during the calculations. If set to + false electrostatics will not be considered. type: boolean dielec: default: cdie + title: Constant (cdie) or distance-dependent dielectric (rdie) constant. + description: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. + $comment: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. A distance dependent dielectric + constant will effectively scale down the electrostatic energy by having + a 1/r**2 dependency instead of 1/r type: string minLength: 0 - maxLength: 100 + maxLength: 4 + enum: + - cdie + - rdie epsilon: default: 1.0 + title: Dielectric constant + description: Dielectric constant for the electrostatic Coulomb energy term. + $comment: Dielectric constant for the electrostatic Coulomb energy term. type: number - maximum: 9999 - minimum: -9999 + maximum: 78 + minimum: 1 dihedflag: default: true type: boolean - par_nonbonded: - default: OPLSX + individualize: + default: true + title: Individualise models + description: Treat each model in the PDB ensemble as a separate entity. + $comment: Treat each model in the PDB ensemble as a separate entity. This + means that for each a separate topology file will be generated. The models + in the ensemble can thus correspond to different molecules. + type: boolean + solvent: + default: water + title: Solvent + description: Solvent to use during the short MD refinement + $comment: Solvent to use during the short MD refinement. Water and DMSO are + supported. A solvent shelll is generated by shifting pre-equilibrated boxes + around the complex. For water an 8A water shell is generated and for DMSO + a 12.5A shell. For DMSO, type: string minLength: 0 maxLength: 100 - w_air: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_bsa: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_cdih: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_dani: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_deint: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_desolv: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - w_dist: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_elec: - default: 0.2 - type: number - maximum: 9999 - minimum: -9999 - w_lcc: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_rg: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_sani: - default: 0.0 - type: number - maximum: 9999 - minimum: -9999 - w_sym: - default: 0.0 + enum: + - water + - dmso + nemsteps: + default: 200 + title: Number of EM steps + description: Number of energy minimisation steps to perform. + $comment: Number of energy minimisation steps to perform in the various EM + stages of this refinement protocol. Note that the effective number might + be smaller if the minimisation converges earlier. type: number - maximum: 9999 - minimum: -9999 - w_vdw: - default: 1.0 + maximum: 10000 + minimum: 1 + timestep: + default: 0.002 + title: MD integrating time step + description: Integration time step for the molecular dynamics. + $comment: Integration time step for the molecular dynamics. type: number - maximum: 9999 - minimum: -9999 - w_vean: - default: 0.0 + maximum: 0.004 + minimum: 0.0005 + waterheatsteps: + default: 100 + title: Number of MD steps for the heating + description: Number of MD steps for the heating phase. + $comment: Number of MD steps for the heating phase. The heating consists of + three successive short molecular dynamics simluations at 100, 200 and 300 + Kelvin. type: number - maximum: 9999 - minimum: -9999 - w_xpcs: - default: 0.0 + maximum: 10000 + minimum: 0 + watersteps: + default: 1250 + title: Number of MD steps at 300K. + description: Number of MD steps for 300K simulation. + $comment: Number of MD steps for 300K simulation. This is the sampling state + of the refinement. type: number - maximum: 9999 - minimum: -9999 - w_xrdc: - default: 0.0 + maximum: 100000 + minimum: 0 + watercoolsteps: + default: 500 + title: Number of MD steps for the cooling + description: Number of MD steps for the cooling phase. + $comment: Number of MD steps for the cooling phase. The cooling consists of + three successive short molecular dynamics simluations at 300, 200 and 100 + Kelvin. type: number - maximum: 9999 - minimum: -9999 - w_zres: - default: 0.0 + maximum: 10000 + minimum: 0 + iniseed: + default: 917 + title: Random seed + description: Random seed used in CNS to initialize the random seed function + $comment: Random seed used in CNS to initialize the random seed function type: number - maximum: 9999 - minimum: -9999 - shape_1: - default: false - type: boolean - shape_2: - default: false - type: boolean - shape_3: - default: false - type: boolean - shape_4: - default: false - type: boolean - shape_5: - default: false - type: boolean - shape_6: - default: false - type: boolean - shape_7: - default: false - type: boolean - shape_8: - default: false - type: boolean - shape_9: - default: false - type: boolean - shape_10: - default: false - type: boolean - shape_11: - default: false - type: boolean - shape_12: - default: false - type: boolean - shape_13: - default: false - type: boolean - shape_14: - default: false - type: boolean - shape_15: - default: false - type: boolean - shape_16: - default: false - type: boolean - shape_17: - default: false - type: boolean - shape_18: - default: false - type: boolean - shape_19: - default: false - type: boolean - shape_20: + maximum: 9999999999999999 + minimum: 0 + keepwater: default: false + title: Write water molecules to output file + description: Write water molecules if present to the output file. + $comment: Write water molecules if present to the output file. type: boolean + tolerance: + default: 0 + title: Failure tolerance percentage + description: Percentage of allowed failures for a module to successfully complete + $comment: Percentage of allowed failures for a module to successfully complete + type: number + maximum: 99 + minimum: 0 + log_level: + default: quiet + title: Log level verbosity for CNS + description: Set the log level verbosity for CNS + $comment: CNS, the computational engine used by HADDOCK can generate a lot + of output messages. This parameter controls the verbosity of CNS (verbose, + normal or quiet). + type: string + minLength: 0 + maxLength: 100 + enum: + - verbose + - normal + - quiet required: [] additionalProperties: false uiSchema: + w_bsa: + ui:group: scoring + w_cdih: + ui:group: scoring + w_desolv: + ui:group: scoring + w_elec: + ui:group: scoring + w_vdw: + ui:group: scoring + contactairs: + ui:group: distance restraints + kcont: + ui:group: distance restraints + ssdihed: + ui:group: dihedral restraints + error_dih: + ui:group: dihedral restraints + dnarest_on: + ui:group: other restraints ligand_param_fname: ui:widget: file + ui:group: force field ligand_top_fname: ui:widget: file + ui:group: force field + elecflag: + ui:group: force field + dielec: + ui:group: force field + epsilon: + ui:group: force field + dihedflag: + ui:group: force field + individualize: + ui:group: sampling + nemsteps: + ui:group: sampling + timestep: + ui:group: sampling + waterheatsteps: + ui:group: sampling + watersteps: + ui:group: sampling + watercoolsteps: + ui:group: sampling + iniseed: + ui:group: sampling + keepwater: + ui:group: sampling + tolerance: + ui:group: module + log_level: + ui:group: module + tomlSchema: {} - id: flexref category: refinement label: HADDOCK3 module for flexible refinement. @@ -4253,246 +2530,22 @@ nodes: schema: type: object properties: - mol_fix_origin_1: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_2: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_3: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_4: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_5: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_6: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_7: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_8: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_9: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_10: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_11: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_12: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_13: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_14: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_15: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_16: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_17: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_18: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_19: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_20: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + mol_fix_origin: + type: array + items: + default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. + type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -4886,625 +2939,699 @@ nodes: default: -1.0 type: number maximum: 9999 - minimum: -9999 - masy_cool2: - default: -0.1 - type: number - maximum: 9999 - minimum: -9999 - masy_cool3: - default: -0.1 - type: number - maximum: 9999 - minimum: -9999 - asy_hot: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - asy_cool1: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - asy_cool2: - default: 0.1 - type: number - maximum: 9999 - minimum: -9999 - asy_cool3: - default: 0.1 - type: number - maximum: 9999 - minimum: -9999 - sym_on: - default: false - title: Symmetry restraints - description: Enables symmetry restraints - $comment: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 - supported) and the segments to which those apply must be defined. In addition - a custom symmetry restraint file can be supplied (symrest_fname). - type: boolean - ksym: - default: 10.0 - title: Force constant for symmetry restraints - description: Force constant for symmetry restraints - $comment: Force constant for symmetry restraints - type: number - maximum: 1000 - minimum: 0 - symtbl_fname: - title: Custom symmetry restraints filename - description: Filename of the custom symmetry restraints file - $comment: Filename of the custom symmetry restraints file. - type: string - format: uri-reference - numc2sym: - default: 0 - title: Number of C2 symmetry restraints - description: Defines the number of C2 symmetry restraints. - $comment: Defines the number of C2 symmetry restraints. For each, a pair of - segments on which the symmetry restraint is applied will have to be defined. - Those must all have the same length. - type: number - maximum: 40 - minimum: 0 - c2sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C2 symmetry segment - $comment: Residue number of first residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C2 symmetry segment - $comment: Residue number of last residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg1_1: - default: '' - title: Segment ID of first C2 segment - description: Segment ID of first C2 segment - $comment: Segment ID of first C2 segment - type: string - minLength: 0 - maxLength: 4 - c2sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C2 symmetry segment - $comment: Residue number of first residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C2 symmetry segment - $comment: Residue number of last residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg2_1: - default: '' - title: Segment ID of second C2 segment - description: Segment ID of second C2 segment - $comment: Segment ID of second C2 segment - type: string - minLength: 0 - maxLength: 4 - numc3sym: - default: 0 - title: Number of C3 symmetry restraints - description: Defines the number of C3 symmetry restraints. - $comment: Defines the number of C3 symmetry restraints. For each, three segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C3 symmetry segment - $comment: Residue number of first residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C3 symmetry segment - $comment: Residue number of last residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg1_1: - default: '' - title: Segment ID of first C3 segment - description: Segment ID of first C3 segment - $comment: Segment ID of first C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C3 symmetry segment - $comment: Residue number of first residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C3 symmetry segment - $comment: Residue number of last residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg2_1: - default: '' - title: Segment ID of second C3 segment - description: Segment ID of second C3 segment - $comment: Segment ID of second C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C3 symmetry segment - $comment: Residue number of first residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C3 symmetry segment - $comment: Residue number of last residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg3_1: - default: '' - title: Segment ID of third C3 segment - description: Segment ID of third C3 segment - $comment: Segment ID of third C3 segment - type: string - minLength: 0 - maxLength: 4 - numc4sym: - default: 0 - title: Number of C4 symmetry restraints - description: Defines the number of C4 symmetry restraints. - $comment: Defines the number of C4 symmetry restraints. For each, four segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c4sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C4 symmetry segment - $comment: Residue number of first residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C4 symmetry segment - $comment: Residue number of last residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg1_1: - default: '' - title: Segment ID of first C4 segment - description: Segment ID of first C4 segment - $comment: Segment ID of first C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C4 symmetry segment - $comment: Residue number of first residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C4 symmetry segment - $comment: Residue number of last residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg2_1: - default: '' - title: Segment ID of second C4 segment - description: Segment ID of second C4 segment - $comment: Segment ID of second C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C4 symmetry segment - $comment: Residue number of first residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C4 symmetry segment - $comment: Residue number of last residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg3_1: - default: '' - title: Segment ID of third C4 segment - description: Segment ID of third C4 segment - $comment: Segment ID of third C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C4 symmetry segment - $comment: Residue number of first residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C4 symmetry segment - $comment: Residue number of last residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg4_1: - default: '' - title: Segment ID of fourth C4 segment - description: Segment ID of fourth C4 segment - $comment: Segment ID of fourth C4 segment - type: string - minLength: 0 - maxLength: 4 - numc5sym: - default: 0 - title: Number of C5 symmetry restraints - description: Defines the number of C5 symmetry restraints. - $comment: Defines the number of C5 symmetry restraints. For each, five segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c5sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C5 symmetry segment - $comment: Residue number of first residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C5 symmetry segment - $comment: Residue number of last residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg1_1: - default: '' - title: Segment ID of first C5 segment - description: Segment ID of first C5 segment - $comment: Segment ID of first C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C5 symmetry segment - $comment: Residue number of first residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C5 symmetry segment - $comment: Residue number of last residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg2_1: - default: '' - title: Segment ID of second C5 segment - description: Segment ID of second C5 segment - $comment: Segment ID of second C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C5 symmetry segment - $comment: Residue number of first residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C5 symmetry segment - $comment: Residue number of last residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg3_1: - default: '' - title: Segment ID of third C5 segment - description: Segment ID of third C5 segment - $comment: Segment ID of third C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C5 symmetry segment - $comment: Residue number of first residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C5 symmetry segment - $comment: Residue number of last residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg4_1: - default: '' - title: Segment ID of fourth C5 segment - description: Segment ID of fourth C5 segment - $comment: Segment ID of fourth C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C5 symmetry segment - $comment: Residue number of first residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C5 symmetry segment - $comment: Residue number of last residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg5_1: - default: '' - title: Segment ID of fifth C5 segment - description: Segment ID of fifth C5 segment - $comment: Segment ID of fifth C5 segment - type: string - minLength: 0 - maxLength: 4 - numc6sym: - default: 0 - title: Number of C6 symmetry restraints - description: Defines the number of C6 symmetry restraints. - $comment: Defines the number of C6 symmetry restraints. For each, six segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c6sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C6 symmetry segment - $comment: Residue number of first residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C6 symmetry segment - $comment: Residue number of last residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg1_1: - default: '' - title: Segment ID of first C6 segment - description: Segment ID of first C6 segment - $comment: Segment ID of first C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C6 symmetry segment - $comment: Residue number of first residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C6 symmetry segment - $comment: Residue number of last residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg2_1: - default: '' - title: Segment ID of second C6 segment - description: Segment ID of second C6 segment - $comment: Segment ID of second C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C6 symmetry segment - $comment: Residue number of first residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C6 symmetry segment - $comment: Residue number of last residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg3_1: - default: '' - title: Segment ID of third C6 segment - description: Segment ID of third C6 segment - $comment: Segment ID of third C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C6 symmetry segment - $comment: Residue number of first residue in the fourth C6 symmetry segment + minimum: -9999 + masy_cool2: + default: -0.1 type: number maximum: 9999 minimum: -9999 - c6sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C6 symmetry segment - $comment: Residue number of last residue in the fourth C6 symmetry segment + masy_cool3: + default: -0.1 type: number maximum: 9999 minimum: -9999 - c6sym_seg4_1: - default: '' - title: Segment ID of fourth C6 segment - description: Segment ID of fourth C6 segment - $comment: Segment ID of fourth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C6 symmetry segment - $comment: Residue number of first residue in the fifth C6 symmetry segment + asy_hot: + default: 1.0 type: number maximum: 9999 minimum: -9999 - c6sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C6 symmetry segment - $comment: Residue number of last residue in the fifth C6 symmetry segment + asy_cool1: + default: 1.0 type: number maximum: 9999 minimum: -9999 - c6sym_seg5_1: - default: '' - title: Segment ID of fifth C6 segment - description: Segment ID of fifth C6 segment - $comment: Segment ID of fifth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta6_1: - title: Residue number of first residue - description: Residue number of first residue in the sixth C6 symmetry segment - $comment: Residue number of first residue in the sixth C6 symmetry segment + asy_cool2: + default: 0.1 type: number maximum: 9999 minimum: -9999 - c6sym_end6_1: - title: Residue number of last residue - description: Residue number of last residue in the sixth C6 symmetry segment - $comment: Residue number of last residue in the sixth C6 symmetry segment + asy_cool3: + default: 0.1 type: number maximum: 9999 minimum: -9999 - c6sym_seg6_1: - default: '' - title: Segment ID of sixth C6 segment - description: Segment ID of sixth C6 segment - $comment: Segment ID of sixth C6 segment + sym_on: + default: false + title: Symmetry restraints + description: Enables symmetry restraints + $comment: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 + supported) and the segments to which those apply must be defined. In addition + a custom symmetry restraint file can be supplied (symrest_fname). + type: boolean + ksym: + default: 10.0 + title: Force constant for symmetry restraints + description: Force constant for symmetry restraints + $comment: Force constant for symmetry restraints + type: number + maximum: 1000 + minimum: 0 + symtbl_fname: + title: Custom symmetry restraints filename + description: Filename of the custom symmetry restraints file + $comment: Filename of the custom symmetry restraints file. type: string - minLength: 0 - maxLength: 4 - nums3sym: + format: uri-reference + numc2sym: default: 0 - title: Number of S3 symmetry restraints - description: Defines the number of S3 symmetry restraints. - $comment: Defines the number of S3 symmetry restraints. For each, three segments + title: Number of C2 symmetry restraints + description: Defines the number of C2 symmetry restraints. + $comment: Defines the number of C2 symmetry restraints. For each, a pair of + segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + type: number + maximum: 40 + minimum: 0 + c2sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C2 symmetry + segment + $comment: Residue number of first residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C2 symmetry + segment + $comment: Residue number of last residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C2 segment + description: Segment ID of first C2 segment + $comment: Segment ID of first C2 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C2 symmetry + segment + $comment: Residue number of first residue in the second C2 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C2 symmetry + segment + $comment: Residue number of last residue in the second C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C2 segment + description: Segment ID of second C2 segment + $comment: Segment ID of second C2 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc3sym: + default: 0 + title: Number of C3 symmetry restraints + description: Defines the number of C3 symmetry restraints. + $comment: Defines the number of C3 symmetry restraints. For each, three segments on which the symmetry restraint is applied will have to be defined. Those must all have the same length. type: number maximum: 10 minimum: 0 - s3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first S3 symmetry segment - $comment: Residue number of first residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first S3 symmetry segment - $comment: Residue number of last residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg1_1: - default: '' - title: Segment ID of first S3 segment - description: Segment ID of first S3 segment - $comment: Segment ID of first S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second S3 symmetry segment - $comment: Residue number of first residue in the second S3 symmetry segment + c3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C3 symmetry + segment + $comment: Residue number of first residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C3 symmetry + segment + $comment: Residue number of last residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C3 segment + description: Segment ID of first C3 segment + $comment: Segment ID of first C3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C3 symmetry + segment + $comment: Residue number of first residue in the second C3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C3 symmetry + segment + $comment: Residue number of last residue in the second C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C3 segment + description: Segment ID of second C3 segment + $comment: Segment ID of second C3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C3 symmetry + segment + $comment: Residue number of first residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C3 symmetry + segment + $comment: Residue number of last residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C3 segment + description: Segment ID of third C3 segment + $comment: Segment ID of third C3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc4sym: + default: 0 + title: Number of C4 symmetry restraints + description: Defines the number of C4 symmetry restraints. + $comment: Defines the number of C4 symmetry restraints. For each, four segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - s3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second S3 symmetry segment - $comment: Residue number of last residue in the second S3 symmetry segment + maximum: 10 + minimum: 0 + c4sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C4 symmetry + segment + $comment: Residue number of first residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C4 symmetry + segment + $comment: Residue number of last residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C4 segment + description: Segment ID of first C4 segment + $comment: Segment ID of first C4 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C4 symmetry + segment + $comment: Residue number of first residue in the second C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C4 symmetry + segment + $comment: Residue number of last residue in the second C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C4 segment + description: Segment ID of second C4 segment + $comment: Segment ID of second C4 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C4 symmetry + segment + $comment: Residue number of first residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C4 symmetry + segment + $comment: Residue number of last residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C4 segment + description: Segment ID of third C4 segment + $comment: Segment ID of third C4 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C4 symmetry + segment + $comment: Residue number of first residue in the fourth C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C4 symmetry + segment + $comment: Residue number of last residue in the fourth C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C4 segment + description: Segment ID of fourth C4 segment + $comment: Segment ID of fourth C4 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc5sym: + default: 0 + title: Number of C5 symmetry restraints + description: Defines the number of C5 symmetry restraints. + $comment: Defines the number of C5 symmetry restraints. For each, five segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - s3sym_seg2_1: - default: '' - title: Segment ID of second S3 segment - description: Segment ID of second S3 segment - $comment: Segment ID of second S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third S3 symmetry segment - $comment: Residue number of first residue in the third S3 symmetry segment + maximum: 10 + minimum: 0 + c5sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C5 symmetry + segment + $comment: Residue number of first residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C5 symmetry + segment + $comment: Residue number of last residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C5 segment + description: Segment ID of first C5 segment + $comment: Segment ID of first C5 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C5 symmetry + segment + $comment: Residue number of first residue in the second C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C5 symmetry + segment + $comment: Residue number of last residue in the second C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C5 segment + description: Segment ID of second C5 segment + $comment: Segment ID of second C5 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C5 symmetry + segment + $comment: Residue number of first residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C5 symmetry + segment + $comment: Residue number of last residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C5 segment + description: Segment ID of third C5 segment + $comment: Segment ID of third C5 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C5 symmetry + segment + $comment: Residue number of first residue in the fourth C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C5 symmetry + segment + $comment: Residue number of last residue in the fourth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C5 segment + description: Segment ID of fourth C5 segment + $comment: Segment ID of fourth C5 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C5 symmetry + segment + $comment: Residue number of first residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C5 symmetry + segment + $comment: Residue number of last residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C5 segment + description: Segment ID of fifth C5 segment + $comment: Segment ID of fifth C5 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc6sym: + default: 0 + title: Number of C6 symmetry restraints + description: Defines the number of C6 symmetry restraints. + $comment: Defines the number of C6 symmetry restraints. For each, six segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - s3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third S3 symmetry segment - $comment: Residue number of last residue in the third S3 symmetry segment + maximum: 10 + minimum: 0 + c6sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C6 symmetry + segment + $comment: Residue number of first residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C6 symmetry + segment + $comment: Residue number of last residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C6 segment + description: Segment ID of first C6 segment + $comment: Segment ID of first C6 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C6 symmetry + segment + $comment: Residue number of first residue in the second C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C6 symmetry + segment + $comment: Residue number of last residue in the second C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C6 segment + description: Segment ID of second C6 segment + $comment: Segment ID of second C6 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C6 symmetry + segment + $comment: Residue number of first residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C6 symmetry + segment + $comment: Residue number of last residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C6 segment + description: Segment ID of third C6 segment + $comment: Segment ID of third C6 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C6 symmetry + segment + $comment: Residue number of first residue in the fourth C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C6 symmetry + segment + $comment: Residue number of last residue in the fourth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C6 segment + description: Segment ID of fourth C6 segment + $comment: Segment ID of fourth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C6 symmetry + segment + $comment: Residue number of first residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C6 symmetry + segment + $comment: Residue number of last residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C6 segment + description: Segment ID of fifth C6 segment + $comment: Segment ID of fifth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta6: + title: Residue number of first residue + description: Residue number of first residue in the sixth C6 symmetry + segment + $comment: Residue number of first residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end6: + title: Residue number of last residue + description: Residue number of last residue in the sixth C6 symmetry + segment + $comment: Residue number of last residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg6: + title: Segment ID of sixth C6 segment + description: Segment ID of sixth C6 segment + $comment: Segment ID of sixth C6 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + nums3sym: + default: 0 + title: Number of S3 symmetry restraints + description: Defines the number of S3 symmetry restraints. + $comment: Defines the number of S3 symmetry restraints. For each, three segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - s3sym_seg3_1: - default: '' - title: Segment ID of third S3 segment - description: Segment ID of third S3 segment - $comment: Segment ID of third S3 segment - type: string - minLength: 0 - maxLength: 4 + maximum: 10 + minimum: 0 + s3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first S3 symmetry + segment + $comment: Residue number of first residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first S3 symmetry + segment + $comment: Residue number of last residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first S3 segment + description: Segment ID of first S3 segment + $comment: Segment ID of first S3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second S3 symmetry + segment + $comment: Residue number of first residue in the second S3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second S3 symmetry + segment + $comment: Residue number of last residue in the second S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second S3 segment + description: Segment ID of second S3 segment + $comment: Segment ID of second S3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third S3 symmetry + segment + $comment: Residue number of first residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third S3 symmetry + segment + $comment: Residue number of last residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third S3 segment + description: Segment ID of third S3 segment + $comment: Segment ID of third S3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false ncs_on: default: false title: Non-crystallographic symmetry restraints @@ -5533,50 +3660,55 @@ nodes: type: number maximum: 100 minimum: 0 - ncs_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first NCS segment - $comment: Residue number of first residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first NCS segment - $comment: Residue number of last residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg1_1: - default: '' - title: Segment ID of first NCS segment - description: Segment ID of first NCS segment - $comment: Segment ID of first NCS segment - type: string - minLength: 0 - maxLength: 100 - ncs_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second NCS segment - $comment: Residue number of first residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second NCS segment - $comment: Residue number of last residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg2_1: - default: '' - title: Segment ID of second NCS segment - description: Segment ID of second NCS segment - $comment: Segment ID of second NCS segment - type: string - minLength: 0 - maxLength: 100 + ncs: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first NCS segment + $comment: Residue number of first residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first NCS segment + $comment: Residue number of last residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first NCS segment + description: Segment ID of first NCS segment + $comment: Segment ID of first NCS segment + type: string + minLength: 0 + maxLength: 100 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second NCS segment + $comment: Residue number of first residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second NCS segment + $comment: Residue number of last residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second NCS segment + description: Segment ID of second NCS segment + $comment: Segment ID of second NCS segment + type: string + minLength: 0 + maxLength: 100 + required: [] + additionalProperties: false w_air: default: 0.1 title: Weight of the distance restraint energy @@ -5940,15 +4072,19 @@ nodes: maximum: 99 minimum: 0 log_level: - default: verbose + default: quiet title: Log level verbosity for CNS - description: Set the log level verbosity for CNS (minimal or verbose) + description: Set the log level verbosity for CNS $comment: CNS, the computational engine used by HADDOCK can generate a lot - of output messages. This parameter controls the verbosity of CNS (minimal - or verbose) + of output messages. This parameter controls the verbosity of CNS (verbose, + normal or quiet). type: string minLength: 0 maxLength: 100 + enum: + - verbose + - normal + - quiet nseg1: default: -1 title: Number of semi-flexible segments @@ -5964,20 +4100,31 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_1_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 + seg: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the semi-flexible + segment. + $comment: Residue number defining the start of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: Ending residue number + description: Residue number defining the end of the semi-flexible + segment. + $comment: Residue number defining the end of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nseg2: default: -1 title: Number of semi-flexible segments @@ -5993,20 +4140,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_2_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg3: default: -1 title: Number of semi-flexible segments @@ -6022,20 +4155,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_3_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg4: default: -1 title: Number of semi-flexible segments @@ -6051,20 +4170,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_4_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg5: default: -1 title: Number of semi-flexible segments @@ -6080,20 +4185,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_5_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg6: default: -1 title: Number of semi-flexible segments @@ -6109,20 +4200,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_6_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg7: default: -1 title: Number of semi-flexible segments @@ -6138,20 +4215,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_7_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg8: default: -1 title: Number of semi-flexible segments @@ -6167,20 +4230,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_8_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg9: default: -1 title: Number of semi-flexible segments @@ -6196,20 +4245,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_9_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg10: default: -1 title: Number of semi-flexible segments @@ -6225,20 +4260,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_10_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg11: default: -1 title: Number of semi-flexible segments @@ -6254,20 +4275,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_11_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg12: default: -1 title: Number of semi-flexible segments @@ -6283,20 +4290,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_12_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg13: default: -1 title: Number of semi-flexible segments @@ -6312,20 +4305,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_13_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg14: default: -1 title: Number of semi-flexible segments @@ -6341,20 +4320,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_14_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg15: default: -1 title: Number of semi-flexible segments @@ -6370,20 +4335,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_15_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg16: default: -1 title: Number of semi-flexible segments @@ -6399,20 +4350,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_16_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg17: default: -1 title: Number of semi-flexible segments @@ -6428,20 +4365,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_17_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg18: default: -1 title: Number of semi-flexible segments @@ -6457,20 +4380,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_18_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg19: default: -1 title: Number of semi-flexible segments @@ -6486,20 +4395,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_19_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg20: default: -1 title: Number of semi-flexible segments @@ -6515,20 +4410,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_20_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle1: default: 0 title: Number of fully flexible segments @@ -6539,20 +4420,32 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_1_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 + fle: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the fully flexible + segment. + $comment: Residue number defining the start of the fully flexible + segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: End residue number + description: Residue number defining the end of the fully flexible + segment. + $comment: Residue number defining the end of the fully flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nfle2: default: 0 title: Number of fully flexible segments @@ -6563,20 +4456,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_2_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle3: default: 0 title: Number of fully flexible segments @@ -6587,20 +4466,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_3_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle4: default: 0 title: Number of fully flexible segments @@ -6611,20 +4476,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_4_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle5: default: 0 title: Number of fully flexible segments @@ -6635,20 +4486,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_5_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle6: default: 0 title: Number of fully flexible segments @@ -6659,20 +4496,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_6_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle7: default: 0 title: Number of fully flexible segments @@ -6683,20 +4506,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_7_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle8: default: 0 title: Number of fully flexible segments @@ -6707,20 +4516,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_8_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle9: default: 0 title: Number of fully flexible segments @@ -6731,20 +4526,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_9_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle10: default: 0 title: Number of fully flexible segments @@ -6755,20 +4536,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_10_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle11: default: 0 title: Number of fully flexible segments @@ -6779,20 +4546,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_11_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle12: default: 0 title: Number of fully flexible segments @@ -6803,20 +4556,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_12_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle13: default: 0 title: Number of fully flexible segments @@ -6827,20 +4566,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_13_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle14: default: 0 title: Number of fully flexible segments @@ -6851,20 +4576,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_14_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle15: default: 0 title: Number of fully flexible segments @@ -6875,20 +4586,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_15_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle16: default: 0 title: Number of fully flexible segments @@ -6899,20 +4596,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_16_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle17: default: 0 title: Number of fully flexible segments @@ -6923,20 +4606,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_17_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle18: default: 0 title: Number of fully flexible segments @@ -6947,20 +4616,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_18_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle19: default: 0 title: Number of fully flexible segments @@ -6971,20 +4626,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_19_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle20: default: 0 title: Number of fully flexible segments @@ -6995,102 +4636,12 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_20_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 required: [] additionalProperties: false uiSchema: - mol_fix_origin_1: - ui:group: molecule - mol_fix_origin_2: - ui:group: molecule - mol_fix_origin_3: - ui:group: molecule - mol_fix_origin_4: - ui:group: molecule - mol_fix_origin_5: - ui:group: molecule - mol_fix_origin_6: - ui:group: molecule - mol_fix_origin_7: - ui:group: molecule - mol_fix_origin_8: - ui:group: molecule - mol_fix_origin_9: - ui:group: molecule - mol_fix_origin_10: - ui:group: molecule - mol_fix_origin_11: - ui:group: molecule - mol_fix_origin_12: - ui:group: molecule - mol_fix_origin_13: - ui:group: molecule - mol_fix_origin_14: - ui:group: molecule - mol_fix_origin_15: - ui:group: molecule - mol_fix_origin_16: - ui:group: molecule - mol_fix_origin_17: - ui:group: molecule - mol_fix_origin_18: - ui:group: molecule - mol_fix_origin_19: - ui:group: molecule - mol_fix_origin_20: - ui:group: molecule - mol_shape_1: + mol_fix_origin: ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: - ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: - ui:group: molecule - mol_shape_10: - ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file @@ -7167,153 +4718,27 @@ nodes: ui:group: symmetry numc2sym: ui:group: symmetry - c2sym_sta1_1: - ui:group: symmetry - c2sym_end1_1: - ui:group: symmetry - c2sym_seg1_1: - ui:group: symmetry - c2sym_sta2_1: - ui:group: symmetry - c2sym_end2_1: - ui:group: symmetry - c2sym_seg2_1: + c2sym: ui:group: symmetry numc3sym: ui:group: symmetry - c3sym_sta1_1: - ui:group: symmetry - c3sym_end1_1: - ui:group: symmetry - c3sym_seg1_1: - ui:group: symmetry - c3sym_sta2_1: - ui:group: symmetry - c3sym_end2_1: - ui:group: symmetry - c3sym_seg2_1: - ui:group: symmetry - c3sym_sta3_1: - ui:group: symmetry - c3sym_end3_1: - ui:group: symmetry - c3sym_seg3_1: + c3sym: ui:group: symmetry numc4sym: ui:group: symmetry - c4sym_sta1_1: - ui:group: symmetry - c4sym_end1_1: - ui:group: symmetry - c4sym_seg1_1: - ui:group: symmetry - c4sym_sta2_1: - ui:group: symmetry - c4sym_end2_1: - ui:group: symmetry - c4sym_seg2_1: - ui:group: symmetry - c4sym_sta3_1: - ui:group: symmetry - c4sym_end3_1: - ui:group: symmetry - c4sym_seg3_1: - ui:group: symmetry - c4sym_sta4_1: - ui:group: symmetry - c4sym_end4_1: - ui:group: symmetry - c4sym_seg4_1: + c4sym: ui:group: symmetry numc5sym: ui:group: symmetry - c5sym_sta1_1: - ui:group: symmetry - c5sym_end1_1: - ui:group: symmetry - c5sym_seg1_1: - ui:group: symmetry - c5sym_sta2_1: - ui:group: symmetry - c5sym_end2_1: - ui:group: symmetry - c5sym_seg2_1: - ui:group: symmetry - c5sym_sta3_1: - ui:group: symmetry - c5sym_end3_1: - ui:group: symmetry - c5sym_seg3_1: - ui:group: symmetry - c5sym_sta4_1: - ui:group: symmetry - c5sym_end4_1: - ui:group: symmetry - c5sym_seg4_1: - ui:group: symmetry - c5sym_sta5_1: - ui:group: symmetry - c5sym_end5_1: - ui:group: symmetry - c5sym_seg5_1: + c5sym: ui:group: symmetry numc6sym: ui:group: symmetry - c6sym_sta1_1: - ui:group: symmetry - c6sym_end1_1: - ui:group: symmetry - c6sym_seg1_1: - ui:group: symmetry - c6sym_sta2_1: - ui:group: symmetry - c6sym_end2_1: - ui:group: symmetry - c6sym_seg2_1: - ui:group: symmetry - c6sym_sta3_1: - ui:group: symmetry - c6sym_end3_1: - ui:group: symmetry - c6sym_seg3_1: - ui:group: symmetry - c6sym_sta4_1: - ui:group: symmetry - c6sym_end4_1: - ui:group: symmetry - c6sym_seg4_1: - ui:group: symmetry - c6sym_sta5_1: - ui:group: symmetry - c6sym_end5_1: - ui:group: symmetry - c6sym_seg5_1: - ui:group: symmetry - c6sym_sta6_1: - ui:group: symmetry - c6sym_end6_1: - ui:group: symmetry - c6sym_seg6_1: + c6sym: ui:group: symmetry nums3sym: ui:group: symmetry - s3sym_sta1_1: - ui:group: symmetry - s3sym_end1_1: - ui:group: symmetry - s3sym_seg1_1: - ui:group: symmetry - s3sym_sta2_1: - ui:group: symmetry - s3sym_end2_1: - ui:group: symmetry - s3sym_seg2_1: - ui:group: symmetry - s3sym_sta3_1: - ui:group: symmetry - s3sym_end3_1: - ui:group: symmetry - s3sym_seg3_1: + s3sym: ui:group: symmetry ncs_on: ui:group: symmetry @@ -7321,17 +4746,7 @@ nodes: ui:group: symmetry numncs: ui:group: symmetry - ncs_sta1_1: - ui:group: symmetry - ncs_end1_1: - ui:group: symmetry - ncs_seg1_1: - ui:group: symmetry - ncs_sta2_1: - ui:group: symmetry - ncs_end2_1: - ui:group: symmetry - ncs_seg2_1: + ncs: ui:group: symmetry w_air: ui:group: scoring @@ -7359,6 +4774,8 @@ nodes: ui:group: force field epsilon: ui:group: force field + dihedflag: + ui:group: force field sampling_factor: ui:group: sampling nemsteps: @@ -7409,244 +4826,133 @@ nodes: ui:group: module nseg1: ui:group: flexibility - seg_sta_1_1: - ui:group: flexibility - seg_end_1_1: + seg: ui:group: flexibility nseg2: ui:group: flexibility - seg_sta_2_1: - ui:group: flexibility - seg_end_2_1: - ui:group: flexibility - nseg3: - ui:group: flexibility - seg_sta_3_1: - ui:group: flexibility - seg_end_3_1: - ui:group: flexibility - nseg4: - ui:group: flexibility - seg_sta_4_1: + nseg3: ui:group: flexibility - seg_end_4_1: + nseg4: ui:group: flexibility nseg5: ui:group: flexibility - seg_sta_5_1: - ui:group: flexibility - seg_end_5_1: - ui:group: flexibility nseg6: ui:group: flexibility - seg_sta_6_1: - ui:group: flexibility - seg_end_6_1: - ui:group: flexibility nseg7: ui:group: flexibility - seg_sta_7_1: - ui:group: flexibility - seg_end_7_1: - ui:group: flexibility nseg8: ui:group: flexibility - seg_sta_8_1: - ui:group: flexibility - seg_end_8_1: - ui:group: flexibility nseg9: ui:group: flexibility - seg_sta_9_1: - ui:group: flexibility - seg_end_9_1: - ui:group: flexibility nseg10: ui:group: flexibility - seg_sta_10_1: - ui:group: flexibility - seg_end_10_1: - ui:group: flexibility nseg11: ui:group: flexibility - seg_sta_11_1: - ui:group: flexibility - seg_end_11_1: - ui:group: flexibility nseg12: ui:group: flexibility - seg_sta_12_1: - ui:group: flexibility - seg_end_12_1: - ui:group: flexibility nseg13: ui:group: flexibility - seg_sta_13_1: - ui:group: flexibility - seg_end_13_1: - ui:group: flexibility nseg14: ui:group: flexibility - seg_sta_14_1: - ui:group: flexibility - seg_end_14_1: - ui:group: flexibility nseg15: ui:group: flexibility - seg_sta_15_1: - ui:group: flexibility - seg_end_15_1: - ui:group: flexibility nseg16: ui:group: flexibility - seg_sta_16_1: - ui:group: flexibility - seg_end_16_1: - ui:group: flexibility nseg17: ui:group: flexibility - seg_sta_17_1: - ui:group: flexibility - seg_end_17_1: - ui:group: flexibility nseg18: ui:group: flexibility - seg_sta_18_1: - ui:group: flexibility - seg_end_18_1: - ui:group: flexibility nseg19: ui:group: flexibility - seg_sta_19_1: - ui:group: flexibility - seg_end_19_1: - ui:group: flexibility nseg20: ui:group: flexibility - seg_sta_20_1: - ui:group: flexibility - seg_end_20_1: - ui:group: flexibility nfle1: ui:group: flexibility - fle_sta_1_1: - ui:group: flexibility - fle_end_1_1: + fle: ui:group: flexibility nfle2: ui:group: flexibility - fle_sta_2_1: - ui:group: flexibility - fle_end_2_1: - ui:group: flexibility nfle3: ui:group: flexibility - fle_sta_3_1: - ui:group: flexibility - fle_end_3_1: - ui:group: flexibility nfle4: ui:group: flexibility - fle_sta_4_1: - ui:group: flexibility - fle_end_4_1: - ui:group: flexibility nfle5: ui:group: flexibility - fle_sta_5_1: - ui:group: flexibility - fle_end_5_1: - ui:group: flexibility nfle6: ui:group: flexibility - fle_sta_6_1: - ui:group: flexibility - fle_end_6_1: - ui:group: flexibility nfle7: ui:group: flexibility - fle_sta_7_1: - ui:group: flexibility - fle_end_7_1: - ui:group: flexibility nfle8: ui:group: flexibility - fle_sta_8_1: - ui:group: flexibility - fle_end_8_1: - ui:group: flexibility nfle9: ui:group: flexibility - fle_sta_9_1: - ui:group: flexibility - fle_end_9_1: - ui:group: flexibility nfle10: ui:group: flexibility - fle_sta_10_1: - ui:group: flexibility - fle_end_10_1: - ui:group: flexibility nfle11: ui:group: flexibility - fle_sta_11_1: - ui:group: flexibility - fle_end_11_1: - ui:group: flexibility nfle12: ui:group: flexibility - fle_sta_12_1: - ui:group: flexibility - fle_end_12_1: - ui:group: flexibility nfle13: ui:group: flexibility - fle_sta_13_1: - ui:group: flexibility - fle_end_13_1: - ui:group: flexibility nfle14: ui:group: flexibility - fle_sta_14_1: - ui:group: flexibility - fle_end_14_1: - ui:group: flexibility nfle15: ui:group: flexibility - fle_sta_15_1: - ui:group: flexibility - fle_end_15_1: - ui:group: flexibility nfle16: ui:group: flexibility - fle_sta_16_1: - ui:group: flexibility - fle_end_16_1: - ui:group: flexibility nfle17: ui:group: flexibility - fle_sta_17_1: - ui:group: flexibility - fle_end_17_1: - ui:group: flexibility nfle18: ui:group: flexibility - fle_sta_18_1: - ui:group: flexibility - fle_end_18_1: - ui:group: flexibility nfle19: ui:group: flexibility - fle_sta_19_1: - ui:group: flexibility - fle_end_19_1: - ui:group: flexibility nfle20: ui:group: flexibility - fle_sta_20_1: - ui:group: flexibility - fle_end_20_1: - ui:group: flexibility + tomlSchema: + mol_fix_origin: + indexed: true + mol_shape: + indexed: true + c2sym: + indexed: true + items: + flatten: true + c3sym: + indexed: true + items: + flatten: true + c4sym: + indexed: true + items: + flatten: true + c5sym: + indexed: true + items: + flatten: true + c6sym: + indexed: true + items: + flatten: true + s3sym: + indexed: true + items: + flatten: true + ncs: + indexed: true + items: + flatten: true + seg: + indexed: true + items: + indexed: true + items: + flatten: true + fle: + indexed: true + items: + indexed: true + items: + flatten: true - id: mdref category: refinement label: HADDOCK3 module for water refinement. @@ -7654,246 +4960,22 @@ nodes: schema: type: object properties: - mol_fix_origin_1: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_2: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_3: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_4: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_5: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_6: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_7: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_8: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_9: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_10: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_11: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_12: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_13: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_14: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_15: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_16: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_17: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_18: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_19: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_20: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + mol_fix_origin: + type: array + items: + default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. + type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -8123,224 +5205,258 @@ nodes: type: number maximum: 40 minimum: 0 - c2sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C2 symmetry segment - $comment: Residue number of first residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C2 symmetry segment - $comment: Residue number of last residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg1_1: - default: '' - title: Segment ID of first C2 segment - description: Segment ID of first C2 segment - $comment: Segment ID of first C2 segment - type: string - minLength: 0 - maxLength: 4 - c2sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C2 symmetry segment - $comment: Residue number of first residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C2 symmetry segment - $comment: Residue number of last residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg2_1: - default: '' - title: Segment ID of second C2 segment - description: Segment ID of second C2 segment - $comment: Segment ID of second C2 segment - type: string - minLength: 0 - maxLength: 4 + c2sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C2 symmetry + segment + $comment: Residue number of first residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C2 symmetry + segment + $comment: Residue number of last residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C2 segment + description: Segment ID of first C2 segment + $comment: Segment ID of first C2 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C2 symmetry + segment + $comment: Residue number of first residue in the second C2 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C2 symmetry + segment + $comment: Residue number of last residue in the second C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C2 segment + description: Segment ID of second C2 segment + $comment: Segment ID of second C2 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc3sym: default: 0 title: Number of C3 symmetry restraints description: Defines the number of C3 symmetry restraints. $comment: Defines the number of C3 symmetry restraints. For each, three segments on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C3 symmetry segment - $comment: Residue number of first residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C3 symmetry segment - $comment: Residue number of last residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg1_1: - default: '' - title: Segment ID of first C3 segment - description: Segment ID of first C3 segment - $comment: Segment ID of first C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C3 symmetry segment - $comment: Residue number of first residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C3 symmetry segment - $comment: Residue number of last residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg2_1: - default: '' - title: Segment ID of second C3 segment - description: Segment ID of second C3 segment - $comment: Segment ID of second C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C3 symmetry segment - $comment: Residue number of first residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C3 symmetry segment - $comment: Residue number of last residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg3_1: - default: '' - title: Segment ID of third C3 segment - description: Segment ID of third C3 segment - $comment: Segment ID of third C3 segment - type: string - minLength: 0 - maxLength: 4 - numc4sym: - default: 0 - title: Number of C4 symmetry restraints - description: Defines the number of C4 symmetry restraints. - $comment: Defines the number of C4 symmetry restraints. For each, four segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c4sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C4 symmetry segment - $comment: Residue number of first residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C4 symmetry segment - $comment: Residue number of last residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg1_1: - default: '' - title: Segment ID of first C4 segment - description: Segment ID of first C4 segment - $comment: Segment ID of first C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C4 symmetry segment - $comment: Residue number of first residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C4 symmetry segment - $comment: Residue number of last residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg2_1: - default: '' - title: Segment ID of second C4 segment - description: Segment ID of second C4 segment - $comment: Segment ID of second C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C4 symmetry segment - $comment: Residue number of first residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C4 symmetry segment - $comment: Residue number of last residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg3_1: - default: '' - title: Segment ID of third C4 segment - description: Segment ID of third C4 segment - $comment: Segment ID of third C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C4 symmetry segment - $comment: Residue number of first residue in the fourth C4 symmetry segment + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - c4sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C4 symmetry segment - $comment: Residue number of last residue in the fourth C4 symmetry segment + maximum: 10 + minimum: 0 + c3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C3 symmetry + segment + $comment: Residue number of first residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C3 symmetry + segment + $comment: Residue number of last residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C3 segment + description: Segment ID of first C3 segment + $comment: Segment ID of first C3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C3 symmetry + segment + $comment: Residue number of first residue in the second C3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C3 symmetry + segment + $comment: Residue number of last residue in the second C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C3 segment + description: Segment ID of second C3 segment + $comment: Segment ID of second C3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C3 symmetry + segment + $comment: Residue number of first residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C3 symmetry + segment + $comment: Residue number of last residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C3 segment + description: Segment ID of third C3 segment + $comment: Segment ID of third C3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc4sym: + default: 0 + title: Number of C4 symmetry restraints + description: Defines the number of C4 symmetry restraints. + $comment: Defines the number of C4 symmetry restraints. For each, four segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - c4sym_seg4_1: - default: '' - title: Segment ID of fourth C4 segment - description: Segment ID of fourth C4 segment - $comment: Segment ID of fourth C4 segment - type: string - minLength: 0 - maxLength: 4 + maximum: 10 + minimum: 0 + c4sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C4 symmetry + segment + $comment: Residue number of first residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C4 symmetry + segment + $comment: Residue number of last residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C4 segment + description: Segment ID of first C4 segment + $comment: Segment ID of first C4 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C4 symmetry + segment + $comment: Residue number of first residue in the second C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C4 symmetry + segment + $comment: Residue number of last residue in the second C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C4 segment + description: Segment ID of second C4 segment + $comment: Segment ID of second C4 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C4 symmetry + segment + $comment: Residue number of first residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C4 symmetry + segment + $comment: Residue number of last residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C4 segment + description: Segment ID of third C4 segment + $comment: Segment ID of third C4 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C4 symmetry + segment + $comment: Residue number of first residue in the fourth C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C4 symmetry + segment + $comment: Residue number of last residue in the fourth C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C4 segment + description: Segment ID of fourth C4 segment + $comment: Segment ID of fourth C4 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc5sym: default: 0 title: Number of C5 symmetry restraints @@ -8351,116 +5467,130 @@ nodes: type: number maximum: 10 minimum: 0 - c5sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C5 symmetry segment - $comment: Residue number of first residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C5 symmetry segment - $comment: Residue number of last residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg1_1: - default: '' - title: Segment ID of first C5 segment - description: Segment ID of first C5 segment - $comment: Segment ID of first C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C5 symmetry segment - $comment: Residue number of first residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C5 symmetry segment - $comment: Residue number of last residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg2_1: - default: '' - title: Segment ID of second C5 segment - description: Segment ID of second C5 segment - $comment: Segment ID of second C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C5 symmetry segment - $comment: Residue number of first residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C5 symmetry segment - $comment: Residue number of last residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg3_1: - default: '' - title: Segment ID of third C5 segment - description: Segment ID of third C5 segment - $comment: Segment ID of third C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C5 symmetry segment - $comment: Residue number of first residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C5 symmetry segment - $comment: Residue number of last residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg4_1: - default: '' - title: Segment ID of fourth C5 segment - description: Segment ID of fourth C5 segment - $comment: Segment ID of fourth C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C5 symmetry segment - $comment: Residue number of first residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C5 symmetry segment - $comment: Residue number of last residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg5_1: - default: '' - title: Segment ID of fifth C5 segment - description: Segment ID of fifth C5 segment - $comment: Segment ID of fifth C5 segment - type: string - minLength: 0 - maxLength: 4 + c5sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C5 symmetry + segment + $comment: Residue number of first residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C5 symmetry + segment + $comment: Residue number of last residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C5 segment + description: Segment ID of first C5 segment + $comment: Segment ID of first C5 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C5 symmetry + segment + $comment: Residue number of first residue in the second C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C5 symmetry + segment + $comment: Residue number of last residue in the second C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C5 segment + description: Segment ID of second C5 segment + $comment: Segment ID of second C5 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C5 symmetry + segment + $comment: Residue number of first residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C5 symmetry + segment + $comment: Residue number of last residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C5 segment + description: Segment ID of third C5 segment + $comment: Segment ID of third C5 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C5 symmetry + segment + $comment: Residue number of first residue in the fourth C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C5 symmetry + segment + $comment: Residue number of last residue in the fourth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C5 segment + description: Segment ID of fourth C5 segment + $comment: Segment ID of fourth C5 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C5 symmetry + segment + $comment: Residue number of first residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C5 symmetry + segment + $comment: Residue number of last residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C5 segment + description: Segment ID of fifth C5 segment + $comment: Segment ID of fifth C5 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc6sym: default: 0 title: Number of C6 symmetry restraints @@ -8471,138 +5601,153 @@ nodes: type: number maximum: 10 minimum: 0 - c6sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C6 symmetry segment - $comment: Residue number of first residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C6 symmetry segment - $comment: Residue number of last residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg1_1: - default: '' - title: Segment ID of first C6 segment - description: Segment ID of first C6 segment - $comment: Segment ID of first C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C6 symmetry segment - $comment: Residue number of first residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C6 symmetry segment - $comment: Residue number of last residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg2_1: - default: '' - title: Segment ID of second C6 segment - description: Segment ID of second C6 segment - $comment: Segment ID of second C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C6 symmetry segment - $comment: Residue number of first residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C6 symmetry segment - $comment: Residue number of last residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg3_1: - default: '' - title: Segment ID of third C6 segment - description: Segment ID of third C6 segment - $comment: Segment ID of third C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C6 symmetry segment - $comment: Residue number of first residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C6 symmetry segment - $comment: Residue number of last residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg4_1: - default: '' - title: Segment ID of fourth C6 segment - description: Segment ID of fourth C6 segment - $comment: Segment ID of fourth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C6 symmetry segment - $comment: Residue number of first residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C6 symmetry segment - $comment: Residue number of last residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg5_1: - default: '' - title: Segment ID of fifth C6 segment - description: Segment ID of fifth C6 segment - $comment: Segment ID of fifth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta6_1: - title: Residue number of first residue - description: Residue number of first residue in the sixth C6 symmetry segment - $comment: Residue number of first residue in the sixth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end6_1: - title: Residue number of last residue - description: Residue number of last residue in the sixth C6 symmetry segment - $comment: Residue number of last residue in the sixth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg6_1: - default: '' - title: Segment ID of sixth C6 segment - description: Segment ID of sixth C6 segment - $comment: Segment ID of sixth C6 segment - type: string - minLength: 0 - maxLength: 4 + c6sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C6 symmetry + segment + $comment: Residue number of first residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C6 symmetry + segment + $comment: Residue number of last residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C6 segment + description: Segment ID of first C6 segment + $comment: Segment ID of first C6 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C6 symmetry + segment + $comment: Residue number of first residue in the second C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C6 symmetry + segment + $comment: Residue number of last residue in the second C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C6 segment + description: Segment ID of second C6 segment + $comment: Segment ID of second C6 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C6 symmetry + segment + $comment: Residue number of first residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C6 symmetry + segment + $comment: Residue number of last residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C6 segment + description: Segment ID of third C6 segment + $comment: Segment ID of third C6 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C6 symmetry + segment + $comment: Residue number of first residue in the fourth C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C6 symmetry + segment + $comment: Residue number of last residue in the fourth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C6 segment + description: Segment ID of fourth C6 segment + $comment: Segment ID of fourth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C6 symmetry + segment + $comment: Residue number of first residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C6 symmetry + segment + $comment: Residue number of last residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C6 segment + description: Segment ID of fifth C6 segment + $comment: Segment ID of fifth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta6: + title: Residue number of first residue + description: Residue number of first residue in the sixth C6 symmetry + segment + $comment: Residue number of first residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end6: + title: Residue number of last residue + description: Residue number of last residue in the sixth C6 symmetry + segment + $comment: Residue number of last residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg6: + title: Segment ID of sixth C6 segment + description: Segment ID of sixth C6 segment + $comment: Segment ID of sixth C6 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false nums3sym: default: 0 title: Number of S3 symmetry restraints @@ -8613,72 +5758,83 @@ nodes: type: number maximum: 10 minimum: 0 - s3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first S3 symmetry segment - $comment: Residue number of first residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first S3 symmetry segment - $comment: Residue number of last residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg1_1: - default: '' - title: Segment ID of first S3 segment - description: Segment ID of first S3 segment - $comment: Segment ID of first S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second S3 symmetry segment - $comment: Residue number of first residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second S3 symmetry segment - $comment: Residue number of last residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg2_1: - default: '' - title: Segment ID of second S3 segment - description: Segment ID of second S3 segment - $comment: Segment ID of second S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third S3 symmetry segment - $comment: Residue number of first residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third S3 symmetry segment - $comment: Residue number of last residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg3_1: - default: '' - title: Segment ID of third S3 segment - description: Segment ID of third S3 segment - $comment: Segment ID of third S3 segment - type: string - minLength: 0 - maxLength: 4 + s3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first S3 symmetry + segment + $comment: Residue number of first residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first S3 symmetry + segment + $comment: Residue number of last residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first S3 segment + description: Segment ID of first S3 segment + $comment: Segment ID of first S3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second S3 symmetry + segment + $comment: Residue number of first residue in the second S3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second S3 symmetry + segment + $comment: Residue number of last residue in the second S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second S3 segment + description: Segment ID of second S3 segment + $comment: Segment ID of second S3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third S3 symmetry + segment + $comment: Residue number of first residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third S3 symmetry + segment + $comment: Residue number of last residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third S3 segment + description: Segment ID of third S3 segment + $comment: Segment ID of third S3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false ncs_on: default: false title: Non-crystallographic symmetry restraints @@ -8707,50 +5863,55 @@ nodes: type: number maximum: 100 minimum: 0 - ncs_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first NCS segment - $comment: Residue number of first residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first NCS segment - $comment: Residue number of last residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg1_1: - default: '' - title: Segment ID of first NCS segment - description: Segment ID of first NCS segment - $comment: Segment ID of first NCS segment - type: string - minLength: 0 - maxLength: 100 - ncs_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second NCS segment - $comment: Residue number of first residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second NCS segment - $comment: Residue number of last residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg2_1: - default: '' - title: Segment ID of second NCS segment - description: Segment ID of second NCS segment - $comment: Segment ID of second NCS segment - type: string - minLength: 0 - maxLength: 100 + ncs: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first NCS segment + $comment: Residue number of first residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first NCS segment + $comment: Residue number of last residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first NCS segment + description: Segment ID of first NCS segment + $comment: Segment ID of first NCS segment + type: string + minLength: 0 + maxLength: 100 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second NCS segment + $comment: Residue number of first residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second NCS segment + $comment: Residue number of last residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second NCS segment + description: Segment ID of second NCS segment + $comment: Segment ID of second NCS segment + type: string + minLength: 0 + maxLength: 100 + required: [] + additionalProperties: false w_air: default: 0.1 title: Weight of the distance restraint energy @@ -8964,15 +6125,19 @@ nodes: maximum: 99 minimum: 0 log_level: - default: verbose + default: quiet title: Log level verbosity for CNS - description: Set the log level verbosity for CNS (minimal or verbose) + description: Set the log level verbosity for CNS $comment: CNS, the computational engine used by HADDOCK can generate a lot - of output messages. This parameter controls the verbosity of CNS (minimal - or verbose) + of output messages. This parameter controls the verbosity of CNS (verbose, + normal or quiet). type: string minLength: 0 maxLength: 100 + enum: + - verbose + - normal + - quiet nseg1: default: -1 title: Number of semi-flexible segments @@ -8988,20 +6153,31 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_1_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 + seg: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the semi-flexible + segment. + $comment: Residue number defining the start of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: Ending residue number + description: Residue number defining the end of the semi-flexible + segment. + $comment: Residue number defining the end of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nseg2: default: -1 title: Number of semi-flexible segments @@ -9017,20 +6193,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_2_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg3: default: -1 title: Number of semi-flexible segments @@ -9046,20 +6208,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_3_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg4: default: -1 title: Number of semi-flexible segments @@ -9075,20 +6223,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_4_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg5: default: -1 title: Number of semi-flexible segments @@ -9104,20 +6238,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_5_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg6: default: -1 title: Number of semi-flexible segments @@ -9133,20 +6253,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_6_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg7: default: -1 title: Number of semi-flexible segments @@ -9162,20 +6268,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_7_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg8: default: -1 title: Number of semi-flexible segments @@ -9191,20 +6283,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_8_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg9: default: -1 title: Number of semi-flexible segments @@ -9220,20 +6298,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_9_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg10: default: -1 title: Number of semi-flexible segments @@ -9249,20 +6313,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_10_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg11: default: -1 title: Number of semi-flexible segments @@ -9278,20 +6328,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_11_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg12: default: -1 title: Number of semi-flexible segments @@ -9307,20 +6343,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_12_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg13: default: -1 title: Number of semi-flexible segments @@ -9336,20 +6358,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_13_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg14: default: -1 title: Number of semi-flexible segments @@ -9365,20 +6373,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_14_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg15: default: -1 title: Number of semi-flexible segments @@ -9394,20 +6388,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_15_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg16: default: -1 title: Number of semi-flexible segments @@ -9423,20 +6403,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_16_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg17: default: -1 title: Number of semi-flexible segments @@ -9452,20 +6418,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_17_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg18: default: -1 title: Number of semi-flexible segments @@ -9481,20 +6433,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_18_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg19: default: -1 title: Number of semi-flexible segments @@ -9510,20 +6448,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_19_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg20: default: -1 title: Number of semi-flexible segments @@ -9539,20 +6463,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_20_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle1: default: 0 title: Number of fully flexible segments @@ -9563,20 +6473,32 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_1_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 + fle: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the fully flexible + segment. + $comment: Residue number defining the start of the fully flexible + segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: End residue number + description: Residue number defining the end of the fully flexible + segment. + $comment: Residue number defining the end of the fully flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nfle2: default: 0 title: Number of fully flexible segments @@ -9587,20 +6509,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_2_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle3: default: 0 title: Number of fully flexible segments @@ -9611,20 +6519,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_3_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle4: default: 0 title: Number of fully flexible segments @@ -9635,20 +6529,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_4_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle5: default: 0 title: Number of fully flexible segments @@ -9659,20 +6539,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_5_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle6: default: 0 title: Number of fully flexible segments @@ -9683,20 +6549,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_6_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle7: default: 0 title: Number of fully flexible segments @@ -9707,20 +6559,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_7_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle8: default: 0 title: Number of fully flexible segments @@ -9731,20 +6569,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_8_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle9: default: 0 title: Number of fully flexible segments @@ -9755,20 +6579,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_9_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle10: default: 0 title: Number of fully flexible segments @@ -9779,20 +6589,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_10_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle11: default: 0 title: Number of fully flexible segments @@ -9803,20 +6599,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_11_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle12: default: 0 title: Number of fully flexible segments @@ -9827,20 +6609,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_12_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle13: default: 0 title: Number of fully flexible segments @@ -9851,20 +6619,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_13_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle14: default: 0 title: Number of fully flexible segments @@ -9875,20 +6629,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_14_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle15: default: 0 title: Number of fully flexible segments @@ -9899,20 +6639,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_15_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle16: default: 0 title: Number of fully flexible segments @@ -9923,20 +6649,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_16_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle17: default: 0 title: Number of fully flexible segments @@ -9947,20 +6659,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_17_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle18: default: 0 title: Number of fully flexible segments @@ -9971,20 +6669,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_18_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle19: default: 0 title: Number of fully flexible segments @@ -9995,20 +6679,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_19_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle20: default: 0 title: Number of fully flexible segments @@ -10019,102 +6689,12 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_20_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 required: [] additionalProperties: false uiSchema: - mol_fix_origin_1: - ui:group: molecule - mol_fix_origin_2: - ui:group: molecule - mol_fix_origin_3: - ui:group: molecule - mol_fix_origin_4: - ui:group: molecule - mol_fix_origin_5: - ui:group: molecule - mol_fix_origin_6: - ui:group: molecule - mol_fix_origin_7: - ui:group: molecule - mol_fix_origin_8: - ui:group: molecule - mol_fix_origin_9: - ui:group: molecule - mol_fix_origin_10: - ui:group: molecule - mol_fix_origin_11: - ui:group: molecule - mol_fix_origin_12: - ui:group: molecule - mol_fix_origin_13: - ui:group: molecule - mol_fix_origin_14: - ui:group: molecule - mol_fix_origin_15: - ui:group: molecule - mol_fix_origin_16: - ui:group: molecule - mol_fix_origin_17: - ui:group: molecule - mol_fix_origin_18: - ui:group: molecule - mol_fix_origin_19: - ui:group: molecule - mol_fix_origin_20: - ui:group: molecule - mol_shape_1: - ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: - ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: + mol_fix_origin: ui:group: molecule - mol_shape_10: - ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file @@ -10150,170 +6730,44 @@ nodes: ui:group: dihedral restraints dihedrals_on: ui:group: dihedral restraints - dihedrals_scale: - ui:group: dihedral restraints - ssdihed: - ui:group: dihedral restraints - error_dih: - ui:group: dihedral restraints - dnarest_on: - ui:group: other restraints - sym_on: - ui:group: symmetry - ksym: - ui:group: symmetry - symtbl_fname: - ui:widget: file - ui:group: symmetry - numc2sym: - ui:group: symmetry - c2sym_sta1_1: - ui:group: symmetry - c2sym_end1_1: - ui:group: symmetry - c2sym_seg1_1: - ui:group: symmetry - c2sym_sta2_1: - ui:group: symmetry - c2sym_end2_1: - ui:group: symmetry - c2sym_seg2_1: - ui:group: symmetry - numc3sym: - ui:group: symmetry - c3sym_sta1_1: - ui:group: symmetry - c3sym_end1_1: - ui:group: symmetry - c3sym_seg1_1: - ui:group: symmetry - c3sym_sta2_1: - ui:group: symmetry - c3sym_end2_1: - ui:group: symmetry - c3sym_seg2_1: - ui:group: symmetry - c3sym_sta3_1: - ui:group: symmetry - c3sym_end3_1: - ui:group: symmetry - c3sym_seg3_1: - ui:group: symmetry - numc4sym: - ui:group: symmetry - c4sym_sta1_1: - ui:group: symmetry - c4sym_end1_1: - ui:group: symmetry - c4sym_seg1_1: - ui:group: symmetry - c4sym_sta2_1: - ui:group: symmetry - c4sym_end2_1: - ui:group: symmetry - c4sym_seg2_1: - ui:group: symmetry - c4sym_sta3_1: - ui:group: symmetry - c4sym_end3_1: - ui:group: symmetry - c4sym_seg3_1: - ui:group: symmetry - c4sym_sta4_1: - ui:group: symmetry - c4sym_end4_1: - ui:group: symmetry - c4sym_seg4_1: - ui:group: symmetry - numc5sym: - ui:group: symmetry - c5sym_sta1_1: - ui:group: symmetry - c5sym_end1_1: - ui:group: symmetry - c5sym_seg1_1: - ui:group: symmetry - c5sym_sta2_1: - ui:group: symmetry - c5sym_end2_1: + dihedrals_scale: + ui:group: dihedral restraints + ssdihed: + ui:group: dihedral restraints + error_dih: + ui:group: dihedral restraints + dnarest_on: + ui:group: other restraints + sym_on: ui:group: symmetry - c5sym_seg2_1: + ksym: ui:group: symmetry - c5sym_sta3_1: + symtbl_fname: + ui:widget: file ui:group: symmetry - c5sym_end3_1: + numc2sym: ui:group: symmetry - c5sym_seg3_1: + c2sym: ui:group: symmetry - c5sym_sta4_1: + numc3sym: ui:group: symmetry - c5sym_end4_1: + c3sym: ui:group: symmetry - c5sym_seg4_1: + numc4sym: ui:group: symmetry - c5sym_sta5_1: + c4sym: ui:group: symmetry - c5sym_end5_1: + numc5sym: ui:group: symmetry - c5sym_seg5_1: + c5sym: ui:group: symmetry numc6sym: ui:group: symmetry - c6sym_sta1_1: - ui:group: symmetry - c6sym_end1_1: - ui:group: symmetry - c6sym_seg1_1: - ui:group: symmetry - c6sym_sta2_1: - ui:group: symmetry - c6sym_end2_1: - ui:group: symmetry - c6sym_seg2_1: - ui:group: symmetry - c6sym_sta3_1: - ui:group: symmetry - c6sym_end3_1: - ui:group: symmetry - c6sym_seg3_1: - ui:group: symmetry - c6sym_sta4_1: - ui:group: symmetry - c6sym_end4_1: - ui:group: symmetry - c6sym_seg4_1: - ui:group: symmetry - c6sym_sta5_1: - ui:group: symmetry - c6sym_end5_1: - ui:group: symmetry - c6sym_seg5_1: - ui:group: symmetry - c6sym_sta6_1: - ui:group: symmetry - c6sym_end6_1: - ui:group: symmetry - c6sym_seg6_1: + c6sym: ui:group: symmetry nums3sym: ui:group: symmetry - s3sym_sta1_1: - ui:group: symmetry - s3sym_end1_1: - ui:group: symmetry - s3sym_seg1_1: - ui:group: symmetry - s3sym_sta2_1: - ui:group: symmetry - s3sym_end2_1: - ui:group: symmetry - s3sym_seg2_1: - ui:group: symmetry - s3sym_sta3_1: - ui:group: symmetry - s3sym_end3_1: - ui:group: symmetry - s3sym_seg3_1: + s3sym: ui:group: symmetry ncs_on: ui:group: symmetry @@ -10321,17 +6775,7 @@ nodes: ui:group: symmetry numncs: ui:group: symmetry - ncs_sta1_1: - ui:group: symmetry - ncs_end1_1: - ui:group: symmetry - ncs_seg1_1: - ui:group: symmetry - ncs_sta2_1: - ui:group: symmetry - ncs_end2_1: - ui:group: symmetry - ncs_seg2_1: + ncs: ui:group: symmetry w_air: ui:group: scoring @@ -10359,6 +6803,8 @@ nodes: ui:group: force field epsilon: ui:group: force field + dihedflag: + ui:group: force field sampling_factor: ui:group: sampling nemsteps: @@ -10381,491 +6827,156 @@ nodes: ui:group: module nseg1: ui:group: flexibility - seg_sta_1_1: - ui:group: flexibility - seg_end_1_1: + seg: ui:group: flexibility nseg2: ui:group: flexibility - seg_sta_2_1: - ui:group: flexibility - seg_end_2_1: - ui:group: flexibility nseg3: ui:group: flexibility - seg_sta_3_1: - ui:group: flexibility - seg_end_3_1: - ui:group: flexibility nseg4: ui:group: flexibility - seg_sta_4_1: - ui:group: flexibility - seg_end_4_1: - ui:group: flexibility nseg5: ui:group: flexibility - seg_sta_5_1: - ui:group: flexibility - seg_end_5_1: - ui:group: flexibility nseg6: ui:group: flexibility - seg_sta_6_1: - ui:group: flexibility - seg_end_6_1: - ui:group: flexibility nseg7: ui:group: flexibility - seg_sta_7_1: - ui:group: flexibility - seg_end_7_1: - ui:group: flexibility nseg8: ui:group: flexibility - seg_sta_8_1: - ui:group: flexibility - seg_end_8_1: - ui:group: flexibility nseg9: ui:group: flexibility - seg_sta_9_1: - ui:group: flexibility - seg_end_9_1: - ui:group: flexibility nseg10: ui:group: flexibility - seg_sta_10_1: - ui:group: flexibility - seg_end_10_1: - ui:group: flexibility nseg11: ui:group: flexibility - seg_sta_11_1: - ui:group: flexibility - seg_end_11_1: - ui:group: flexibility nseg12: ui:group: flexibility - seg_sta_12_1: - ui:group: flexibility - seg_end_12_1: - ui:group: flexibility nseg13: ui:group: flexibility - seg_sta_13_1: - ui:group: flexibility - seg_end_13_1: - ui:group: flexibility nseg14: ui:group: flexibility - seg_sta_14_1: - ui:group: flexibility - seg_end_14_1: - ui:group: flexibility nseg15: ui:group: flexibility - seg_sta_15_1: - ui:group: flexibility - seg_end_15_1: - ui:group: flexibility nseg16: ui:group: flexibility - seg_sta_16_1: - ui:group: flexibility - seg_end_16_1: - ui:group: flexibility nseg17: ui:group: flexibility - seg_sta_17_1: - ui:group: flexibility - seg_end_17_1: - ui:group: flexibility nseg18: ui:group: flexibility - seg_sta_18_1: - ui:group: flexibility - seg_end_18_1: - ui:group: flexibility nseg19: - ui:group: flexibility - seg_sta_19_1: - ui:group: flexibility - seg_end_19_1: - ui:group: flexibility - nseg20: - ui:group: flexibility - seg_sta_20_1: - ui:group: flexibility - seg_end_20_1: - ui:group: flexibility - nfle1: - ui:group: flexibility - fle_sta_1_1: - ui:group: flexibility - fle_end_1_1: - ui:group: flexibility - nfle2: - ui:group: flexibility - fle_sta_2_1: - ui:group: flexibility - fle_end_2_1: - ui:group: flexibility - nfle3: - ui:group: flexibility - fle_sta_3_1: - ui:group: flexibility - fle_end_3_1: - ui:group: flexibility - nfle4: - ui:group: flexibility - fle_sta_4_1: - ui:group: flexibility - fle_end_4_1: - ui:group: flexibility - nfle5: - ui:group: flexibility - fle_sta_5_1: - ui:group: flexibility - fle_end_5_1: - ui:group: flexibility - nfle6: - ui:group: flexibility - fle_sta_6_1: - ui:group: flexibility - fle_end_6_1: - ui:group: flexibility - nfle7: - ui:group: flexibility - fle_sta_7_1: - ui:group: flexibility - fle_end_7_1: - ui:group: flexibility - nfle8: - ui:group: flexibility - fle_sta_8_1: - ui:group: flexibility - fle_end_8_1: - ui:group: flexibility - nfle9: - ui:group: flexibility - fle_sta_9_1: - ui:group: flexibility - fle_end_9_1: - ui:group: flexibility - nfle10: - ui:group: flexibility - fle_sta_10_1: - ui:group: flexibility - fle_end_10_1: - ui:group: flexibility - nfle11: - ui:group: flexibility - fle_sta_11_1: - ui:group: flexibility - fle_end_11_1: - ui:group: flexibility - nfle12: - ui:group: flexibility - fle_sta_12_1: - ui:group: flexibility - fle_end_12_1: - ui:group: flexibility - nfle13: - ui:group: flexibility - fle_sta_13_1: - ui:group: flexibility - fle_end_13_1: - ui:group: flexibility - nfle14: - ui:group: flexibility - fle_sta_14_1: - ui:group: flexibility - fle_end_14_1: - ui:group: flexibility - nfle15: - ui:group: flexibility - fle_sta_15_1: - ui:group: flexibility - fle_end_15_1: - ui:group: flexibility - nfle16: - ui:group: flexibility - fle_sta_16_1: - ui:group: flexibility - fle_end_16_1: - ui:group: flexibility - nfle17: - ui:group: flexibility - fle_sta_17_1: - ui:group: flexibility - fle_end_17_1: - ui:group: flexibility - nfle18: - ui:group: flexibility - fle_sta_18_1: - ui:group: flexibility - fle_end_18_1: - ui:group: flexibility - nfle19: - ui:group: flexibility - fle_sta_19_1: - ui:group: flexibility - fle_end_19_1: - ui:group: flexibility - nfle20: - ui:group: flexibility - fle_sta_20_1: - ui:group: flexibility - fle_end_20_1: - ui:group: flexibility -- id: emref - category: refinement - label: HADDOCK3 module for energy minimization refinement. - description: HADDOCK3 module energy minimization refinement. - schema: - type: object - properties: - mol_fix_origin_1: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_2: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_3: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_4: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_5: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_6: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_7: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_8: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_9: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_10: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_11: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_12: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_13: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_14: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_15: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_16: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_17: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_18: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_19: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_fix_origin_20: - default: false - title: Fix molecule - description: Fixes the molecule in its original position. - $comment: Fixes the molecule in its original position. - type: boolean - mol_shape_1: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_2: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_3: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_4: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_5: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_6: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_7: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_8: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_9: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_10: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_11: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_12: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_13: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_14: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_15: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_16: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_17: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_18: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_19: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean - mol_shape_20: - default: false - title: Is the molecule a shape? - description: Defines a molecule as a shape. - $comment: Defines a molecule as a shape, which is a collection of beads. - type: boolean + ui:group: flexibility + nseg20: + ui:group: flexibility + nfle1: + ui:group: flexibility + fle: + ui:group: flexibility + nfle2: + ui:group: flexibility + nfle3: + ui:group: flexibility + nfle4: + ui:group: flexibility + nfle5: + ui:group: flexibility + nfle6: + ui:group: flexibility + nfle7: + ui:group: flexibility + nfle8: + ui:group: flexibility + nfle9: + ui:group: flexibility + nfle10: + ui:group: flexibility + nfle11: + ui:group: flexibility + nfle12: + ui:group: flexibility + nfle13: + ui:group: flexibility + nfle14: + ui:group: flexibility + nfle15: + ui:group: flexibility + nfle16: + ui:group: flexibility + nfle17: + ui:group: flexibility + nfle18: + ui:group: flexibility + nfle19: + ui:group: flexibility + nfle20: + ui:group: flexibility + tomlSchema: + mol_fix_origin: + indexed: true + mol_shape: + indexed: true + c2sym: + indexed: true + items: + flatten: true + c3sym: + indexed: true + items: + flatten: true + c4sym: + indexed: true + items: + flatten: true + c5sym: + indexed: true + items: + flatten: true + c6sym: + indexed: true + items: + flatten: true + s3sym: + indexed: true + items: + flatten: true + ncs: + indexed: true + items: + flatten: true + seg: + indexed: true + items: + indexed: true + items: + flatten: true + fle: + indexed: true + items: + indexed: true + items: + flatten: true +- id: emref + category: refinement + label: HADDOCK3 module for energy minimization refinement. + description: HADDOCK3 module energy minimization refinement. + schema: + type: object + properties: + mol_fix_origin: + type: array + items: + default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. + type: boolean + mol_shape: + type: array + items: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean ambig_fname: title: Ambiguous distance restraints filename description: Filename of the ambiguous distance restraints file @@ -11054,50 +7165,60 @@ nodes: type: number maximum: 40 minimum: 0 - c2sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C2 symmetry segment - $comment: Residue number of first residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C2 symmetry segment - $comment: Residue number of last residue in the first C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg1_1: - default: '' - title: Segment ID of first C2 segment - description: Segment ID of first C2 segment - $comment: Segment ID of first C2 segment - type: string - minLength: 0 - maxLength: 4 - c2sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C2 symmetry segment - $comment: Residue number of first residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C2 symmetry segment - $comment: Residue number of last residue in the second C2 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg2_1: - default: '' - title: Segment ID of second C2 segment - description: Segment ID of second C2 segment - $comment: Segment ID of second C2 segment - type: string - minLength: 0 - maxLength: 4 + c2sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C2 symmetry + segment + $comment: Residue number of first residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C2 symmetry + segment + $comment: Residue number of last residue in the first C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C2 segment + description: Segment ID of first C2 segment + $comment: Segment ID of first C2 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C2 symmetry + segment + $comment: Residue number of first residue in the second C2 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C2 symmetry + segment + $comment: Residue number of last residue in the second C2 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C2 segment + description: Segment ID of second C2 segment + $comment: Segment ID of second C2 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc3sym: default: 0 title: Number of C3 symmetry restraints @@ -11108,72 +7229,83 @@ nodes: type: number maximum: 10 minimum: 0 - c3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C3 symmetry segment - $comment: Residue number of first residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C3 symmetry segment - $comment: Residue number of last residue in the first C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg1_1: - default: '' - title: Segment ID of first C3 segment - description: Segment ID of first C3 segment - $comment: Segment ID of first C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C3 symmetry segment - $comment: Residue number of first residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C3 symmetry segment - $comment: Residue number of last residue in the second C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg2_1: - default: '' - title: Segment ID of second C3 segment - description: Segment ID of second C3 segment - $comment: Segment ID of second C3 segment - type: string - minLength: 0 - maxLength: 4 - c3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C3 symmetry segment - $comment: Residue number of first residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C3 symmetry segment - $comment: Residue number of last residue in the third C3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg3_1: - default: '' - title: Segment ID of third C3 segment - description: Segment ID of third C3 segment - $comment: Segment ID of third C3 segment - type: string - minLength: 0 - maxLength: 4 + c3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C3 symmetry + segment + $comment: Residue number of first residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C3 symmetry + segment + $comment: Residue number of last residue in the first C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C3 segment + description: Segment ID of first C3 segment + $comment: Segment ID of first C3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C3 symmetry + segment + $comment: Residue number of first residue in the second C3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C3 symmetry + segment + $comment: Residue number of last residue in the second C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C3 segment + description: Segment ID of second C3 segment + $comment: Segment ID of second C3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C3 symmetry + segment + $comment: Residue number of first residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C3 symmetry + segment + $comment: Residue number of last residue in the third C3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C3 segment + description: Segment ID of third C3 segment + $comment: Segment ID of third C3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc4sym: default: 0 title: Number of C4 symmetry restraints @@ -11184,94 +7316,107 @@ nodes: type: number maximum: 10 minimum: 0 - c4sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C4 symmetry segment - $comment: Residue number of first residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C4 symmetry segment - $comment: Residue number of last residue in the first C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg1_1: - default: '' - title: Segment ID of first C4 segment - description: Segment ID of first C4 segment - $comment: Segment ID of first C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C4 symmetry segment - $comment: Residue number of first residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C4 symmetry segment - $comment: Residue number of last residue in the second C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg2_1: - default: '' - title: Segment ID of second C4 segment - description: Segment ID of second C4 segment - $comment: Segment ID of second C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C4 symmetry segment - $comment: Residue number of first residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C4 symmetry segment - $comment: Residue number of last residue in the third C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg3_1: - default: '' - title: Segment ID of third C4 segment - description: Segment ID of third C4 segment - $comment: Segment ID of third C4 segment - type: string - minLength: 0 - maxLength: 4 - c4sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C4 symmetry segment - $comment: Residue number of first residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C4 symmetry segment - $comment: Residue number of last residue in the fourth C4 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg4_1: - default: '' - title: Segment ID of fourth C4 segment - description: Segment ID of fourth C4 segment - $comment: Segment ID of fourth C4 segment - type: string - minLength: 0 - maxLength: 4 + c4sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C4 symmetry + segment + $comment: Residue number of first residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C4 symmetry + segment + $comment: Residue number of last residue in the first C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C4 segment + description: Segment ID of first C4 segment + $comment: Segment ID of first C4 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C4 symmetry + segment + $comment: Residue number of first residue in the second C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C4 symmetry + segment + $comment: Residue number of last residue in the second C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C4 segment + description: Segment ID of second C4 segment + $comment: Segment ID of second C4 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C4 symmetry + segment + $comment: Residue number of first residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C4 symmetry + segment + $comment: Residue number of last residue in the third C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C4 segment + description: Segment ID of third C4 segment + $comment: Segment ID of third C4 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C4 symmetry + segment + $comment: Residue number of first residue in the fourth C4 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C4 symmetry + segment + $comment: Residue number of last residue in the fourth C4 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C4 segment + description: Segment ID of fourth C4 segment + $comment: Segment ID of fourth C4 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false numc5sym: default: 0 title: Number of C5 symmetry restraints @@ -11280,260 +7425,289 @@ nodes: on which the symmetry restraint is applied will have to be defined. Those must all have the same length. type: number - maximum: 10 - minimum: 0 - c5sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C5 symmetry segment - $comment: Residue number of first residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C5 symmetry segment - $comment: Residue number of last residue in the first C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg1_1: - default: '' - title: Segment ID of first C5 segment - description: Segment ID of first C5 segment - $comment: Segment ID of first C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C5 symmetry segment - $comment: Residue number of first residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C5 symmetry segment - $comment: Residue number of last residue in the second C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg2_1: - default: '' - title: Segment ID of second C5 segment - description: Segment ID of second C5 segment - $comment: Segment ID of second C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C5 symmetry segment - $comment: Residue number of first residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C5 symmetry segment - $comment: Residue number of last residue in the third C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg3_1: - default: '' - title: Segment ID of third C5 segment - description: Segment ID of third C5 segment - $comment: Segment ID of third C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C5 symmetry segment - $comment: Residue number of first residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C5 symmetry segment - $comment: Residue number of last residue in the fourth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg4_1: - default: '' - title: Segment ID of fourth C5 segment - description: Segment ID of fourth C5 segment - $comment: Segment ID of fourth C5 segment - type: string - minLength: 0 - maxLength: 4 - c5sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C5 symmetry segment - $comment: Residue number of first residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C5 symmetry segment - $comment: Residue number of last residue in the fifth C5 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg5_1: - default: '' - title: Segment ID of fifth C5 segment - description: Segment ID of fifth C5 segment - $comment: Segment ID of fifth C5 segment - type: string - minLength: 0 - maxLength: 4 - numc6sym: - default: 0 - title: Number of C6 symmetry restraints - description: Defines the number of C6 symmetry restraints. - $comment: Defines the number of C6 symmetry restraints. For each, six segments - on which the symmetry restraint is applied will have to be defined. Those - must all have the same length. - type: number - maximum: 10 - minimum: 0 - c6sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first C6 symmetry segment - $comment: Residue number of first residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first C6 symmetry segment - $comment: Residue number of last residue in the first C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg1_1: - default: '' - title: Segment ID of first C6 segment - description: Segment ID of first C6 segment - $comment: Segment ID of first C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second C6 symmetry segment - $comment: Residue number of first residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second C6 symmetry segment - $comment: Residue number of last residue in the second C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg2_1: - default: '' - title: Segment ID of second C6 segment - description: Segment ID of second C6 segment - $comment: Segment ID of second C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third C6 symmetry segment - $comment: Residue number of first residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third C6 symmetry segment - $comment: Residue number of last residue in the third C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg3_1: - default: '' - title: Segment ID of third C6 segment - description: Segment ID of third C6 segment - $comment: Segment ID of third C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta4_1: - title: Residue number of first residue - description: Residue number of first residue in the fourth C6 symmetry segment - $comment: Residue number of first residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end4_1: - title: Residue number of last residue - description: Residue number of last residue in the fourth C6 symmetry segment - $comment: Residue number of last residue in the fourth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg4_1: - default: '' - title: Segment ID of fourth C6 segment - description: Segment ID of fourth C6 segment - $comment: Segment ID of fourth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta5_1: - title: Residue number of first residue - description: Residue number of first residue in the fifth C6 symmetry segment - $comment: Residue number of first residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end5_1: - title: Residue number of last residue - description: Residue number of last residue in the fifth C6 symmetry segment - $comment: Residue number of last residue in the fifth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg5_1: - default: '' - title: Segment ID of fifth C6 segment - description: Segment ID of fifth C6 segment - $comment: Segment ID of fifth C6 segment - type: string - minLength: 0 - maxLength: 4 - c6sym_sta6_1: - title: Residue number of first residue - description: Residue number of first residue in the sixth C6 symmetry segment - $comment: Residue number of first residue in the sixth C6 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - c6sym_end6_1: - title: Residue number of last residue - description: Residue number of last residue in the sixth C6 symmetry segment - $comment: Residue number of last residue in the sixth C6 symmetry segment + maximum: 10 + minimum: 0 + c5sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C5 symmetry + segment + $comment: Residue number of first residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C5 symmetry + segment + $comment: Residue number of last residue in the first C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C5 segment + description: Segment ID of first C5 segment + $comment: Segment ID of first C5 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C5 symmetry + segment + $comment: Residue number of first residue in the second C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C5 symmetry + segment + $comment: Residue number of last residue in the second C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C5 segment + description: Segment ID of second C5 segment + $comment: Segment ID of second C5 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C5 symmetry + segment + $comment: Residue number of first residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C5 symmetry + segment + $comment: Residue number of last residue in the third C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C5 segment + description: Segment ID of third C5 segment + $comment: Segment ID of third C5 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C5 symmetry + segment + $comment: Residue number of first residue in the fourth C5 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C5 symmetry + segment + $comment: Residue number of last residue in the fourth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C5 segment + description: Segment ID of fourth C5 segment + $comment: Segment ID of fourth C5 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C5 symmetry + segment + $comment: Residue number of first residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C5 symmetry + segment + $comment: Residue number of last residue in the fifth C5 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C5 segment + description: Segment ID of fifth C5 segment + $comment: Segment ID of fifth C5 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false + numc6sym: + default: 0 + title: Number of C6 symmetry restraints + description: Defines the number of C6 symmetry restraints. + $comment: Defines the number of C6 symmetry restraints. For each, six segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - c6sym_seg6_1: - default: '' - title: Segment ID of sixth C6 segment - description: Segment ID of sixth C6 segment - $comment: Segment ID of sixth C6 segment - type: string - minLength: 0 - maxLength: 4 + maximum: 10 + minimum: 0 + c6sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first C6 symmetry + segment + $comment: Residue number of first residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first C6 symmetry + segment + $comment: Residue number of last residue in the first C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first C6 segment + description: Segment ID of first C6 segment + $comment: Segment ID of first C6 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second C6 symmetry + segment + $comment: Residue number of first residue in the second C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second C6 symmetry + segment + $comment: Residue number of last residue in the second C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second C6 segment + description: Segment ID of second C6 segment + $comment: Segment ID of second C6 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third C6 symmetry + segment + $comment: Residue number of first residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third C6 symmetry + segment + $comment: Residue number of last residue in the third C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third C6 segment + description: Segment ID of third C6 segment + $comment: Segment ID of third C6 segment + type: string + minLength: 0 + maxLength: 4 + sta4: + title: Residue number of first residue + description: Residue number of first residue in the fourth C6 symmetry + segment + $comment: Residue number of first residue in the fourth C6 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end4: + title: Residue number of last residue + description: Residue number of last residue in the fourth C6 symmetry + segment + $comment: Residue number of last residue in the fourth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg4: + title: Segment ID of fourth C6 segment + description: Segment ID of fourth C6 segment + $comment: Segment ID of fourth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta5: + title: Residue number of first residue + description: Residue number of first residue in the fifth C6 symmetry + segment + $comment: Residue number of first residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end5: + title: Residue number of last residue + description: Residue number of last residue in the fifth C6 symmetry + segment + $comment: Residue number of last residue in the fifth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg5: + title: Segment ID of fifth C6 segment + description: Segment ID of fifth C6 segment + $comment: Segment ID of fifth C6 segment + type: string + minLength: 0 + maxLength: 4 + sta6: + title: Residue number of first residue + description: Residue number of first residue in the sixth C6 symmetry + segment + $comment: Residue number of first residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end6: + title: Residue number of last residue + description: Residue number of last residue in the sixth C6 symmetry + segment + $comment: Residue number of last residue in the sixth C6 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg6: + title: Segment ID of sixth C6 segment + description: Segment ID of sixth C6 segment + $comment: Segment ID of sixth C6 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false nums3sym: default: 0 title: Number of S3 symmetry restraints @@ -11544,72 +7718,83 @@ nodes: type: number maximum: 10 minimum: 0 - s3sym_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first S3 symmetry segment - $comment: Residue number of first residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first S3 symmetry segment - $comment: Residue number of last residue in the first S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg1_1: - default: '' - title: Segment ID of first S3 segment - description: Segment ID of first S3 segment - $comment: Segment ID of first S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second S3 symmetry segment - $comment: Residue number of first residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second S3 symmetry segment - $comment: Residue number of last residue in the second S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg2_1: - default: '' - title: Segment ID of second S3 segment - description: Segment ID of second S3 segment - $comment: Segment ID of second S3 segment - type: string - minLength: 0 - maxLength: 4 - s3sym_sta3_1: - title: Residue number of first residue - description: Residue number of first residue in the third S3 symmetry segment - $comment: Residue number of first residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_end3_1: - title: Residue number of last residue - description: Residue number of last residue in the third S3 symmetry segment - $comment: Residue number of last residue in the third S3 symmetry segment - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg3_1: - default: '' - title: Segment ID of third S3 segment - description: Segment ID of third S3 segment - $comment: Segment ID of third S3 segment - type: string - minLength: 0 - maxLength: 4 + s3sym: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first S3 symmetry + segment + $comment: Residue number of first residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first S3 symmetry + segment + $comment: Residue number of last residue in the first S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first S3 segment + description: Segment ID of first S3 segment + $comment: Segment ID of first S3 segment + type: string + minLength: 0 + maxLength: 4 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second S3 symmetry + segment + $comment: Residue number of first residue in the second S3 symmetry + segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second S3 symmetry + segment + $comment: Residue number of last residue in the second S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second S3 segment + description: Segment ID of second S3 segment + $comment: Segment ID of second S3 segment + type: string + minLength: 0 + maxLength: 4 + sta3: + title: Residue number of first residue + description: Residue number of first residue in the third S3 symmetry + segment + $comment: Residue number of first residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + end3: + title: Residue number of last residue + description: Residue number of last residue in the third S3 symmetry + segment + $comment: Residue number of last residue in the third S3 symmetry segment + type: number + maximum: 9999 + minimum: -9999 + seg3: + title: Segment ID of third S3 segment + description: Segment ID of third S3 segment + $comment: Segment ID of third S3 segment + type: string + minLength: 0 + maxLength: 4 + required: [] + additionalProperties: false ncs_on: default: false title: Non-crystallographic symmetry restraints @@ -11638,50 +7823,55 @@ nodes: type: number maximum: 100 minimum: 0 - ncs_sta1_1: - title: Residue number of first residue - description: Residue number of first residue in the first NCS segment - $comment: Residue number of first residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end1_1: - title: Residue number of last residue - description: Residue number of last residue in the first NCS segment - $comment: Residue number of last residue in the first NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg1_1: - default: '' - title: Segment ID of first NCS segment - description: Segment ID of first NCS segment - $comment: Segment ID of first NCS segment - type: string - minLength: 0 - maxLength: 100 - ncs_sta2_1: - title: Residue number of first residue - description: Residue number of first residue in the second NCS segment - $comment: Residue number of first residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_end2_1: - title: Residue number of last residue - description: Residue number of last residue in the second NCS segment - $comment: Residue number of last residue in the second NCS segment - type: number - maximum: 9999 - minimum: -9999 - ncs_seg2_1: - default: '' - title: Segment ID of second NCS segment - description: Segment ID of second NCS segment - $comment: Segment ID of second NCS segment - type: string - minLength: 0 - maxLength: 100 + ncs: + type: array + items: + type: object + properties: + sta1: + title: Residue number of first residue + description: Residue number of first residue in the first NCS segment + $comment: Residue number of first residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + end1: + title: Residue number of last residue + description: Residue number of last residue in the first NCS segment + $comment: Residue number of last residue in the first NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg1: + title: Segment ID of first NCS segment + description: Segment ID of first NCS segment + $comment: Segment ID of first NCS segment + type: string + minLength: 0 + maxLength: 100 + sta2: + title: Residue number of first residue + description: Residue number of first residue in the second NCS segment + $comment: Residue number of first residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + end2: + title: Residue number of last residue + description: Residue number of last residue in the second NCS segment + $comment: Residue number of last residue in the second NCS segment + type: number + maximum: 9999 + minimum: -9999 + seg2: + title: Segment ID of second NCS segment + description: Segment ID of second NCS segment + $comment: Segment ID of second NCS segment + type: string + minLength: 0 + maxLength: 100 + required: [] + additionalProperties: false w_air: default: 0.1 title: Weight of the distance restraint energy @@ -11850,15 +8040,19 @@ nodes: maximum: 99 minimum: 0 log_level: - default: verbose + default: quiet title: Log level verbosity for CNS - description: Set the log level verbosity for CNS (minimal or verbose) + description: Set the log level verbosity for CNS $comment: CNS, the computational engine used by HADDOCK can generate a lot - of output messages. This parameter controls the verbosity of CNS (minimal - or verbose) + of output messages. This parameter controls the verbosity of CNS (verbose, + normal or quiet) type: string minLength: 0 maxLength: 100 + enum: + - verbose + - normal + - quiet nseg1: default: -1 title: Number of semi-flexible segments @@ -11874,20 +8068,31 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_1_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 + seg: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the semi-flexible + segment. + $comment: Residue number defining the start of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: Ending residue number + description: Residue number defining the end of the semi-flexible + segment. + $comment: Residue number defining the end of the semi-flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nseg2: default: -1 title: Number of semi-flexible segments @@ -11903,20 +8108,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_2_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg3: default: -1 title: Number of semi-flexible segments @@ -11932,20 +8123,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_3_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg4: default: -1 title: Number of semi-flexible segments @@ -11961,20 +8138,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_4_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg5: default: -1 title: Number of semi-flexible segments @@ -11990,20 +8153,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_5_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg6: default: -1 title: Number of semi-flexible segments @@ -12019,20 +8168,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_6_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg7: default: -1 title: Number of semi-flexible segments @@ -12048,20 +8183,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_7_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg8: default: -1 title: Number of semi-flexible segments @@ -12077,20 +8198,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_8_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg9: default: -1 title: Number of semi-flexible segments @@ -12106,20 +8213,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_9_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg10: default: -1 title: Number of semi-flexible segments @@ -12135,20 +8228,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_10_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg11: default: -1 title: Number of semi-flexible segments @@ -12164,20 +8243,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_11_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg12: default: -1 title: Number of semi-flexible segments @@ -12193,20 +8258,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_12_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg13: default: -1 title: Number of semi-flexible segments @@ -12222,20 +8273,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_13_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg14: default: -1 title: Number of semi-flexible segments @@ -12251,20 +8288,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_14_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg15: default: -1 title: Number of semi-flexible segments @@ -12280,20 +8303,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_15_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg16: default: -1 title: Number of semi-flexible segments @@ -12309,20 +8318,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_16_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg17: default: -1 title: Number of semi-flexible segments @@ -12338,20 +8333,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_17_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg18: default: -1 title: Number of semi-flexible segments @@ -12367,20 +8348,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_18_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg19: default: -1 title: Number of semi-flexible segments @@ -12396,20 +8363,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_19_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nseg20: default: -1 title: Number of semi-flexible segments @@ -12425,20 +8378,6 @@ nodes: type: number maximum: 1000 minimum: -1 - seg_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the semi-flexible segment. - $comment: Residue number defining the start of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 - seg_end_20_1: - title: Ending residue number - description: Residue number defining the end of the semi-flexible segment. - $comment: Residue number defining the end of the semi-flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle1: default: 0 title: Number of fully flexible segments @@ -12449,20 +8388,32 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_1_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_1_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 + fle: + type: array + items: + type: array + items: + type: object + properties: + sta: + title: Starting residue number + description: Residue number defining the start of the fully flexible + segment. + $comment: Residue number defining the start of the fully flexible + segment. + type: number + maximum: 9999 + minimum: -9999 + end: + title: End residue number + description: Residue number defining the end of the fully flexible + segment. + $comment: Residue number defining the end of the fully flexible segment. + type: number + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false nfle2: default: 0 title: Number of fully flexible segments @@ -12473,20 +8424,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_2_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_2_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle3: default: 0 title: Number of fully flexible segments @@ -12497,20 +8434,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_3_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_3_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle4: default: 0 title: Number of fully flexible segments @@ -12521,20 +8444,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_4_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_4_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle5: default: 0 title: Number of fully flexible segments @@ -12545,20 +8454,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_5_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_5_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle6: default: 0 title: Number of fully flexible segments @@ -12569,20 +8464,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_6_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_6_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle7: default: 0 title: Number of fully flexible segments @@ -12593,20 +8474,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_7_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_7_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle8: default: 0 title: Number of fully flexible segments @@ -12617,20 +8484,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_8_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_8_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle9: default: 0 title: Number of fully flexible segments @@ -12641,20 +8494,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_9_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_9_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle10: default: 0 title: Number of fully flexible segments @@ -12665,20 +8504,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_10_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_10_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle11: default: 0 title: Number of fully flexible segments @@ -12689,20 +8514,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_11_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_11_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle12: default: 0 title: Number of fully flexible segments @@ -12713,20 +8524,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_12_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_12_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle13: default: 0 title: Number of fully flexible segments @@ -12737,20 +8534,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_13_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_13_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle14: default: 0 title: Number of fully flexible segments @@ -12761,20 +8544,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_14_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_14_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle15: default: 0 title: Number of fully flexible segments @@ -12785,20 +8554,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_15_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_15_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle16: default: 0 title: Number of fully flexible segments @@ -12809,20 +8564,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_16_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_16_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle17: default: 0 title: Number of fully flexible segments @@ -12833,20 +8574,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_17_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_17_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle18: default: 0 title: Number of fully flexible segments @@ -12857,20 +8584,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_18_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_18_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle19: default: 0 title: Number of fully flexible segments @@ -12881,20 +8594,6 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_19_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_19_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 nfle20: default: 0 title: Number of fully flexible segments @@ -12905,102 +8604,12 @@ nodes: type: number maximum: 1000 minimum: 0 - fle_sta_20_1: - title: Starting residue number - description: Residue number defining the start of the fully flexible segment. - $comment: Residue number defining the start of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 - fle_end_20_1: - title: End residue number - description: Residue number defining the end of the fully flexible segment. - $comment: Residue number defining the end of the fully flexible segment. - type: number - maximum: 9999 - minimum: -9999 required: [] additionalProperties: false uiSchema: - mol_fix_origin_1: - ui:group: molecule - mol_fix_origin_2: - ui:group: molecule - mol_fix_origin_3: - ui:group: molecule - mol_fix_origin_4: - ui:group: molecule - mol_fix_origin_5: + mol_fix_origin: ui:group: molecule - mol_fix_origin_6: - ui:group: molecule - mol_fix_origin_7: - ui:group: molecule - mol_fix_origin_8: - ui:group: molecule - mol_fix_origin_9: - ui:group: molecule - mol_fix_origin_10: - ui:group: molecule - mol_fix_origin_11: - ui:group: molecule - mol_fix_origin_12: - ui:group: molecule - mol_fix_origin_13: - ui:group: molecule - mol_fix_origin_14: - ui:group: molecule - mol_fix_origin_15: - ui:group: molecule - mol_fix_origin_16: - ui:group: molecule - mol_fix_origin_17: - ui:group: molecule - mol_fix_origin_18: - ui:group: molecule - mol_fix_origin_19: - ui:group: molecule - mol_fix_origin_20: - ui:group: molecule - mol_shape_1: - ui:group: molecule - mol_shape_2: - ui:group: molecule - mol_shape_3: - ui:group: molecule - mol_shape_4: - ui:group: molecule - mol_shape_5: - ui:group: molecule - mol_shape_6: - ui:group: molecule - mol_shape_7: - ui:group: molecule - mol_shape_8: - ui:group: molecule - mol_shape_9: - ui:group: molecule - mol_shape_10: - ui:group: molecule - mol_shape_11: - ui:group: molecule - mol_shape_12: - ui:group: molecule - mol_shape_13: - ui:group: molecule - mol_shape_14: - ui:group: molecule - mol_shape_15: - ui:group: molecule - mol_shape_16: - ui:group: molecule - mol_shape_17: - ui:group: molecule - mol_shape_18: - ui:group: molecule - mol_shape_19: - ui:group: molecule - mol_shape_20: + mol_shape: ui:group: molecule ambig_fname: ui:widget: file @@ -13047,153 +8656,27 @@ nodes: ui:group: symmetry numc2sym: ui:group: symmetry - c2sym_sta1_1: - ui:group: symmetry - c2sym_end1_1: - ui:group: symmetry - c2sym_seg1_1: - ui:group: symmetry - c2sym_sta2_1: - ui:group: symmetry - c2sym_end2_1: - ui:group: symmetry - c2sym_seg2_1: + c2sym: ui:group: symmetry numc3sym: ui:group: symmetry - c3sym_sta1_1: - ui:group: symmetry - c3sym_end1_1: - ui:group: symmetry - c3sym_seg1_1: - ui:group: symmetry - c3sym_sta2_1: - ui:group: symmetry - c3sym_end2_1: - ui:group: symmetry - c3sym_seg2_1: - ui:group: symmetry - c3sym_sta3_1: - ui:group: symmetry - c3sym_end3_1: - ui:group: symmetry - c3sym_seg3_1: + c3sym: ui:group: symmetry numc4sym: ui:group: symmetry - c4sym_sta1_1: - ui:group: symmetry - c4sym_end1_1: - ui:group: symmetry - c4sym_seg1_1: - ui:group: symmetry - c4sym_sta2_1: - ui:group: symmetry - c4sym_end2_1: - ui:group: symmetry - c4sym_seg2_1: - ui:group: symmetry - c4sym_sta3_1: - ui:group: symmetry - c4sym_end3_1: - ui:group: symmetry - c4sym_seg3_1: - ui:group: symmetry - c4sym_sta4_1: - ui:group: symmetry - c4sym_end4_1: - ui:group: symmetry - c4sym_seg4_1: + c4sym: ui:group: symmetry numc5sym: ui:group: symmetry - c5sym_sta1_1: - ui:group: symmetry - c5sym_end1_1: - ui:group: symmetry - c5sym_seg1_1: - ui:group: symmetry - c5sym_sta2_1: - ui:group: symmetry - c5sym_end2_1: - ui:group: symmetry - c5sym_seg2_1: - ui:group: symmetry - c5sym_sta3_1: - ui:group: symmetry - c5sym_end3_1: - ui:group: symmetry - c5sym_seg3_1: - ui:group: symmetry - c5sym_sta4_1: - ui:group: symmetry - c5sym_end4_1: - ui:group: symmetry - c5sym_seg4_1: - ui:group: symmetry - c5sym_sta5_1: - ui:group: symmetry - c5sym_end5_1: - ui:group: symmetry - c5sym_seg5_1: + c5sym: ui:group: symmetry numc6sym: ui:group: symmetry - c6sym_sta1_1: - ui:group: symmetry - c6sym_end1_1: - ui:group: symmetry - c6sym_seg1_1: - ui:group: symmetry - c6sym_sta2_1: - ui:group: symmetry - c6sym_end2_1: - ui:group: symmetry - c6sym_seg2_1: - ui:group: symmetry - c6sym_sta3_1: - ui:group: symmetry - c6sym_end3_1: - ui:group: symmetry - c6sym_seg3_1: - ui:group: symmetry - c6sym_sta4_1: - ui:group: symmetry - c6sym_end4_1: - ui:group: symmetry - c6sym_seg4_1: - ui:group: symmetry - c6sym_sta5_1: - ui:group: symmetry - c6sym_end5_1: - ui:group: symmetry - c6sym_seg5_1: - ui:group: symmetry - c6sym_sta6_1: - ui:group: symmetry - c6sym_end6_1: - ui:group: symmetry - c6sym_seg6_1: + c6sym: ui:group: symmetry nums3sym: ui:group: symmetry - s3sym_sta1_1: - ui:group: symmetry - s3sym_end1_1: - ui:group: symmetry - s3sym_seg1_1: - ui:group: symmetry - s3sym_sta2_1: - ui:group: symmetry - s3sym_end2_1: - ui:group: symmetry - s3sym_seg2_1: - ui:group: symmetry - s3sym_sta3_1: - ui:group: symmetry - s3sym_end3_1: - ui:group: symmetry - s3sym_seg3_1: + s3sym: ui:group: symmetry ncs_on: ui:group: symmetry @@ -13201,17 +8684,7 @@ nodes: ui:group: symmetry numncs: ui:group: symmetry - ncs_sta1_1: - ui:group: symmetry - ncs_end1_1: - ui:group: symmetry - ncs_seg1_1: - ui:group: symmetry - ncs_sta2_1: - ui:group: symmetry - ncs_end2_1: - ui:group: symmetry - ncs_seg2_1: + ncs: ui:group: symmetry w_air: ui:group: scoring @@ -13239,6 +8712,8 @@ nodes: ui:group: force field epsilon: ui:group: force field + dihedflag: + ui:group: force field sampling: ui:group: sampling sampling_factor: @@ -13255,243 +8730,132 @@ nodes: ui:group: module nseg1: ui:group: flexibility - seg_sta_1_1: - ui:group: flexibility - seg_end_1_1: + seg: ui:group: flexibility nseg2: ui:group: flexibility - seg_sta_2_1: - ui:group: flexibility - seg_end_2_1: - ui:group: flexibility nseg3: ui:group: flexibility - seg_sta_3_1: - ui:group: flexibility - seg_end_3_1: - ui:group: flexibility nseg4: ui:group: flexibility - seg_sta_4_1: - ui:group: flexibility - seg_end_4_1: - ui:group: flexibility nseg5: ui:group: flexibility - seg_sta_5_1: - ui:group: flexibility - seg_end_5_1: - ui:group: flexibility nseg6: ui:group: flexibility - seg_sta_6_1: - ui:group: flexibility - seg_end_6_1: - ui:group: flexibility nseg7: ui:group: flexibility - seg_sta_7_1: - ui:group: flexibility - seg_end_7_1: - ui:group: flexibility nseg8: ui:group: flexibility - seg_sta_8_1: - ui:group: flexibility - seg_end_8_1: - ui:group: flexibility nseg9: ui:group: flexibility - seg_sta_9_1: - ui:group: flexibility - seg_end_9_1: - ui:group: flexibility nseg10: ui:group: flexibility - seg_sta_10_1: - ui:group: flexibility - seg_end_10_1: - ui:group: flexibility nseg11: ui:group: flexibility - seg_sta_11_1: - ui:group: flexibility - seg_end_11_1: - ui:group: flexibility nseg12: ui:group: flexibility - seg_sta_12_1: - ui:group: flexibility - seg_end_12_1: - ui:group: flexibility nseg13: ui:group: flexibility - seg_sta_13_1: - ui:group: flexibility - seg_end_13_1: - ui:group: flexibility nseg14: ui:group: flexibility - seg_sta_14_1: - ui:group: flexibility - seg_end_14_1: - ui:group: flexibility nseg15: ui:group: flexibility - seg_sta_15_1: - ui:group: flexibility - seg_end_15_1: - ui:group: flexibility nseg16: ui:group: flexibility - seg_sta_16_1: - ui:group: flexibility - seg_end_16_1: - ui:group: flexibility nseg17: ui:group: flexibility - seg_sta_17_1: - ui:group: flexibility - seg_end_17_1: - ui:group: flexibility nseg18: ui:group: flexibility - seg_sta_18_1: - ui:group: flexibility - seg_end_18_1: - ui:group: flexibility nseg19: ui:group: flexibility - seg_sta_19_1: - ui:group: flexibility - seg_end_19_1: - ui:group: flexibility nseg20: ui:group: flexibility - seg_sta_20_1: - ui:group: flexibility - seg_end_20_1: - ui:group: flexibility nfle1: ui:group: flexibility - fle_sta_1_1: - ui:group: flexibility - fle_end_1_1: + fle: ui:group: flexibility nfle2: ui:group: flexibility - fle_sta_2_1: - ui:group: flexibility - fle_end_2_1: - ui:group: flexibility nfle3: ui:group: flexibility - fle_sta_3_1: - ui:group: flexibility - fle_end_3_1: - ui:group: flexibility nfle4: ui:group: flexibility - fle_sta_4_1: - ui:group: flexibility - fle_end_4_1: - ui:group: flexibility nfle5: ui:group: flexibility - fle_sta_5_1: - ui:group: flexibility - fle_end_5_1: - ui:group: flexibility nfle6: ui:group: flexibility - fle_sta_6_1: - ui:group: flexibility - fle_end_6_1: - ui:group: flexibility nfle7: ui:group: flexibility - fle_sta_7_1: - ui:group: flexibility - fle_end_7_1: - ui:group: flexibility nfle8: ui:group: flexibility - fle_sta_8_1: - ui:group: flexibility - fle_end_8_1: - ui:group: flexibility nfle9: ui:group: flexibility - fle_sta_9_1: - ui:group: flexibility - fle_end_9_1: - ui:group: flexibility nfle10: ui:group: flexibility - fle_sta_10_1: - ui:group: flexibility - fle_end_10_1: - ui:group: flexibility nfle11: ui:group: flexibility - fle_sta_11_1: - ui:group: flexibility - fle_end_11_1: - ui:group: flexibility nfle12: ui:group: flexibility - fle_sta_12_1: - ui:group: flexibility - fle_end_12_1: - ui:group: flexibility nfle13: ui:group: flexibility - fle_sta_13_1: - ui:group: flexibility - fle_end_13_1: - ui:group: flexibility nfle14: ui:group: flexibility - fle_sta_14_1: - ui:group: flexibility - fle_end_14_1: - ui:group: flexibility nfle15: ui:group: flexibility - fle_sta_15_1: - ui:group: flexibility - fle_end_15_1: - ui:group: flexibility nfle16: ui:group: flexibility - fle_sta_16_1: - ui:group: flexibility - fle_end_16_1: - ui:group: flexibility nfle17: ui:group: flexibility - fle_sta_17_1: - ui:group: flexibility - fle_end_17_1: - ui:group: flexibility nfle18: ui:group: flexibility - fle_sta_18_1: - ui:group: flexibility - fle_end_18_1: - ui:group: flexibility nfle19: ui:group: flexibility - fle_sta_19_1: - ui:group: flexibility - fle_end_19_1: - ui:group: flexibility nfle20: ui:group: flexibility - fle_sta_20_1: - ui:group: flexibility - fle_end_20_1: - ui:group: flexibility + tomlSchema: + mol_fix_origin: + indexed: true + mol_shape: + indexed: true + c2sym: + indexed: true + items: + flatten: true + c3sym: + indexed: true + items: + flatten: true + c4sym: + indexed: true + items: + flatten: true + c5sym: + indexed: true + items: + flatten: true + c6sym: + indexed: true + items: + flatten: true + s3sym: + indexed: true + items: + flatten: true + ncs: + indexed: true + items: + flatten: true + seg: + indexed: true + items: + indexed: true + items: + flatten: true + fle: + indexed: true + items: + indexed: true + items: + flatten: true examples: docking-protein-ligand: /examples/docking-protein-ligand.zip diff --git a/util/generate_haddock3_catalog.py b/util/generate_haddock3_catalog.py index a4ec783a..86a775ad 100755 --- a/util/generate_haddock3_catalog.py +++ b/util/generate_haddock3_catalog.py @@ -33,10 +33,11 @@ * maxchars -> maxLength * minitems -> minItems * maxitems -> maxItems - * accept -> ui:options={accept} + * accept -> ui:options={accept: ','.join(...)} * choices -> enum * explevel -> each explevel gets generated into own catalog * group -> ui:group in ui schema + * expandable (*_1) -> arrays and objects + tomlschema TODO move script outside workflow-builder repo as this repo should be generic and not have any haddock specific scripts """ @@ -47,11 +48,12 @@ import logging from math import isnan from pathlib import Path +import re import sys from yaml import dump, load, Loader from haddock.modules import modules_category -from haddock import config_expert_levels +from haddock import config_expert_levels, _hidden_level def argparser_builder(): parser = argparse.ArgumentParser() @@ -59,18 +61,90 @@ def argparser_builder(): parser.add_argument('--root_url', type=Path, default='/catalog') return parser +def collapse_expandable(config): + """ + The haddock3 defaults.yaml files define complex shape inside the parameter name. + The workflow builder uses type:array, type:object from JSON schema to define complex data types. + + The method converts the shape in parameter name into a shortened parameter name and a shape + 1. arrays of scalars (X_1 -> X:[1]), + 2. arrays of objects (X_Y_1 -> X:[{Y}]), + 3. array of arrays of scalars (X_1_1 -> X:[[1]]) and + 4. array of arrays of object (X_Y_1_1 -> X:[[{Y}]]) + + """ + array_of_scalar = r'(\w+)_1' + array_of_object = r'(\w+)_(\w+)_1' + array_of_array_of_scalar = r'(\w+)_1_1' + array_of_array_of_object = r'(\w+)_(\w+)_1_1' + skip = r'\w+?(_\d\d?)(_\d\d?)?' + must_be_array_of_scalar = {'mol_fix_origin_1', 'mol_shape_1'} + new_config = {} + for k, v in config.items(): + logging.info(f'Processing var: {k}') + if (match := re.match(skip, k)) and not (match.groups()[0] == '_1' and (match.groups()[1] in {None,'_1'})): + logging.info(f'SKipping {k} as their schema will be captured by first index.') + continue + # TODO nice to store maxitems with type:array + # for example rair_end_20_1 -> outer array should have maxitems:20 + # for example int_20_20 -> both array should have maxitems:20 + elif match := re.match(array_of_array_of_object, k): + p, n = match.groups() + if p not in new_config: + new_config[p] = {'dim': 2, 'properties': {}, 'type': 'list'} + new_config[p]['properties'][n] = v + if 'group' in v: + # Move group from nested prop to outer array + new_config[p]['group'] = v['group'] + del v['group'] + elif match := re.match(array_of_array_of_scalar, k): + p, = match.groups() + new_config[p] = { + 'type': 'list', + 'dim': 2, + 'items': v + } + if 'group' in v: + new_config[p]['group'] = v['group'] + del v['group'] + elif (match := re.match(array_of_object, k)) and k not in must_be_array_of_scalar: + p, n = match.groups() + if p not in new_config: + new_config[p] = {'dim': 1, 'properties': {}, 'type': 'list'} + new_config[p]['properties'][n] = v + if 'group' in v: + new_config[p]['group'] = v['group'] + del v['group'] + elif match := re.match(array_of_scalar, k): + p, = match.groups() + new_config[p] = { + 'type': 'list', + 'dim': 1, + 'items': v + } + if 'group' in v: + new_config[p]['group'] = v['group'] + del v['group'] + else: + new_config[k] = v + + return new_config + def config2schema(config): """Translate haddock3 config file of a module to JSON schema""" properties = {} uiSchema = {} + tomlSchema = {} required = [] - for k, v in config.items(): + collapsed_config = collapse_expandable(config) + for k, v in collapsed_config.items(): prop = {} prop_ui = {} + prop_toml = {} if 'default' in v: prop["default"] = v['default'] - else: + elif 'type' in v and v['type'] != 'list': # If there is no default then user must supply a value so prop is required required.append(k) if 'title' in v and v['title'] != 'No title yet': @@ -84,16 +158,29 @@ def config2schema(config): # TODO instead of removing group and explevel from mol1.prot_segid dict do proper filtering and support group recursivly config2 = { k2:{ - k3:v3 for k3,v3 in v2.items() if k3 != 'group' and k3 != 'explevel' - } for k2,v2 in v.items() if k2 != 'explevel' + k3:v3 for k3,v3 in v2.items() if k3 not in {'group','explevel'} + } for k2,v2 in v.items() if k2 not in {'explevel', 'title', 'short', 'long', 'group'} + } + schemas = config2schema(collapse_expandable(config2)) + prop.update({ + 'type': 'array', + 'items': schemas['schema'], + }) + + if schemas['uiSchema']: + prop_ui['items'] = schemas['uiSchema'] + + prop_toml = { + 'indexed': True, + 'items': { + 'sectioned': True + } } - schema_uiSchema = config2schema(config2) - prop = schema_uiSchema['schema'] - prop_ui = { 'ui:field': 'collapsible'} - if schema_uiSchema['uiSchema']: - prop_ui.update(schema_uiSchema['uiSchema']) - # molXX in topaa are not required - required.pop() + if schemas['tomlSchema']: + prop_toml['items']['properties'] = schemas['tomlSchema'] + # Rename as parameter is array and does not need extra index + if k == 'mol1': + k = 'mol' elif v['type'] == 'boolean': prop['type'] = "boolean" elif v['type'] in {'float', 'integer'}: @@ -103,7 +190,7 @@ def config2schema(config): if 'min' in v: prop['minimum'] = v['min'] if 'default' in v and isnan(v['default']): - # TODO handle nan's more gracefully + # TODO handle nan's more gracefully, instead of now just deleting it del prop['default'] elif v['type'] == 'file': prop['type'] = 'string' @@ -120,7 +207,7 @@ def config2schema(config): } if 'accept' in v: - prop_ui["ui:options"] = { "accept": v['accept']} + prop_ui["ui:options"] = { "accept": ",".join(v['accept'])} elif v['type'] == 'dir': prop['type'] = 'string' prop['format'] = 'uri-reference' @@ -135,41 +222,103 @@ def config2schema(config): prop['maxLength'] = v['maxchars'] if 'choices' in v: prop['enum'] = v['choices'] + if v['default'] == '': + del prop['default'] elif v['type'] == 'list': prop['type'] = "array" if 'minitems' in v: prop['minItems'] = v['minitems'] if 'maxitems' in v: prop['maxItems'] = v['maxitems'] - if 'itemtype' in v: - obj = {'a' : {'type': v['itemtype']}} # config2schema requires object - if 'accept' in v: - obj['a']['accept'] = v['accept'] - schema_uiSchema = config2schema(obj) - prop['items'] = schema_uiSchema['schema']['properties']['a'] - if schema_uiSchema['uiSchema'] and schema_uiSchema['uiSchema']['a']: - prop_ui = { - "items": schema_uiSchema['uiSchema']['a'] + if 'properties' in v: + obj_schemas = config2schema(v['properties']) + if v['dim'] == 1: + prop['items'] = obj_schemas['schema'] + if obj_schemas['uiSchema']: + prop_ui = { + "items": obj_schemas['uiSchema'] + } + prop_toml = { + 'indexed': True, + 'items': { + 'flatten': True + } + } + elif v['dim'] == 2: + prop['items'] = { + 'type': 'array', + 'items': obj_schemas['schema'] } + if obj_schemas['uiSchema']: + prop_ui = { + "items": { + 'items': obj_schemas['uiSchema'] + } + } + prop_toml = { + 'indexed': True, + 'items': { + 'indexed': True, + 'items': { + 'flatten': True + } + } + } + else: + raise Exception('Unknown dim') elif 'items' in v: - obj = {'a' : v['items']} # config2schema requires object - schema_uiSchema = config2schema(obj) - prop['items'] = schema_uiSchema['schema']['properties']['a'] - if schema_uiSchema['uiSchema'] and schema_uiSchema['uiSchema']['a']: - prop_ui = { - "items": schema_uiSchema['uiSchema']['a'] + obj_schemas = config2schema({'a': v['items']}) + if v['dim'] == 1: + prop['items'] = obj_schemas['schema']['properties']['a'] + if 'a' in obj_schemas['uiSchema']: + prop_ui = { + "items": obj_schemas['uiSchema']['a'] + } + prop_toml = { + 'indexed': True + } + elif v['dim'] == 2: + prop['items'] = { + 'type': 'array', + 'items': obj_schemas['schema']['properties']['a'] } - elif len(v['default']) and (isinstance(v['default'][0], int) or isinstance(v['default'][0], float)): + if 'a' in obj_schemas['uiSchema']: + prop_ui = { + "items": { + 'items': obj_schemas['uiSchema']['a'] + } + } + prop_toml = { + 'indexed': True, + 'items': { + 'indexed': True + } + } + else: + raise Exception(f'Invalid value of dim in {v=}') + elif k == 'molecules': + # TODO dont hardcode item type and ui for global.molecules, but use itemtype defined in haddock3 # Use default value to determine type of items in array/list prop['items'] = { - "type": "number" + "type": "string", + "format": "uri-reference" } - else: - # TODO dont fallback to number, for example seletopclusts:top_cluster + prop_ui = { + 'items': { + 'ui:widget': 'file', + 'ui:options': { + # Make comma seperated string, see https://developer.mozilla.org/en-US/docs/Web/HTML/Element/input/file#accept + 'accept': ",".join(v['accept']) + } + } + } + elif k == 'top_cluster': + # TODO dont hardcode item type for seletopclusts:top_cluster, but use items:type defined in haddock3 prop['items'] = { "type": "number" } - # raise ValueError(f"Don't know how to determine type of items of {v}") + else: + raise ValueError(f"Don't know how to determine type of items of {v}") else: raise ValueError(f"Don't know what to do with {k}:{v}") properties[k] = prop @@ -177,6 +326,8 @@ def config2schema(config): prop_ui['ui:group'] = v['group'] if prop_ui: uiSchema[k] = prop_ui + if prop_toml: + tomlSchema[k] = prop_toml schema = { "type": "object", "properties": properties, @@ -185,7 +336,8 @@ def config2schema(config): } return { "schema": schema, - "uiSchema": uiSchema + "uiSchema": uiSchema, + "tomlSchema": tomlSchema, } def filter_on_level(config, level): @@ -195,9 +347,10 @@ def filter_on_level(config, level): valid_levels.add(l) if l == level: break - return {k: v for k, v in config.items() if v['explevel'] in valid_levels} + return {k: v for k, v in config.items() if v['explevel'] in valid_levels and not v['explevel'] == _hidden_level} def process_module(module_name, category, level): + logging.warning(f'Processing module: {module_name}') package = f'haddock.modules.{category}.{module_name}' module = importlib.import_module(package) cls = module.HaddockModule @@ -205,15 +358,16 @@ def process_module(module_name, category, level): config = load(f, Loader=Loader) config4level = filter_on_level(config, level) - schema_uiSchema = config2schema(config4level) + schemas = config2schema(config4level) # TODO add $schema and $id to schema return { "id": module_name, "category": category, "label": module.__doc__, "description": cls.__doc__, - "schema": schema_uiSchema['schema'], - "uiSchema": schema_uiSchema['uiSchema'] + "schema": schemas['schema'], + "uiSchema": schemas['uiSchema'], + "tomlSchema": schemas['tomlSchema'], } def process_category(category): @@ -227,41 +381,25 @@ def process_category(category): def get_category_order(): return importlib.import_module('haddock.modules').category_hierarchy + def process_global(level): package = 'haddock.modules' module = importlib.import_module(package) with open(module.modules_defaults_path) as f: optional_global_parameters = load(f, Loader=Loader) - config = REQUIRED_GLOBAL_PARAMETERS | optional_global_parameters + gmodule = importlib.import_module('haddock.gear.parameters') + with open(gmodule.MANDATORY_YAML) as f: + mandatory_parameters = load(f, Loader=Loader) + config = mandatory_parameters | optional_global_parameters config4level = filter_on_level(config, level) - schema_uiSchema = config2schema(config4level) + schemas = config2schema(config4level) # TODO add $schema and $id to schema return { - "schema": schema_uiSchema['schema'], - "uiSchema": schema_uiSchema['uiSchema'] - } - - -# TODO retrieve required global config from haddock3 code -REQUIRED_GLOBAL_PARAMETERS = { - 'molecules': { - 'type': 'list', - 'itemtype': 'file', - 'accept': '.pdb', - 'minitems': 1, - 'maxitems': 20, - 'title': 'Molecules', - 'group': '', - 'explevel': 'easy' - }, - 'run_dir': { - 'type': 'dir', - 'title': 'Run directory', - 'group': '', - 'explevel': 'easy' + "schema": schemas['schema'], + "uiSchema": schemas['uiSchema'], + "tomlSchema": schemas['tomlSchema'], } -} def process_level(level_fn: Path, level: str): category_list = get_category_order() @@ -306,4 +444,4 @@ def main(argv=sys.argv[1:]): if __name__ == '__main__': - sys.exit(main()) \ No newline at end of file + sys.exit(main())