diff --git a/packages/core/src/molecule/addMoleculeValidation.test.ts b/packages/core/src/molecule/addMoleculeValidation.test.ts index 400500f..fe2ed41 100644 --- a/packages/core/src/molecule/addMoleculeValidation.test.ts +++ b/packages/core/src/molecule/addMoleculeValidation.test.ts @@ -557,6 +557,101 @@ describe('addMoleculeValidation()', () => { }) }) }) + + describe('given unparsable molecule', () => { + let moleculeInfos: MoleculeInfo[] + let moleculesPropName: string | undefined + + beforeEach(async () => { + const globalParameters = { + molecules: ['a.pdb'] + } + const globalSchema: JSONSchema7 = { + type: 'object', + properties: { + molecules: { + type: 'array', + format: 'moleculefilepaths', + items: { + type: 'string' + } + } + } + } + const body = 'foo' + const file = + 'data:text/plain;name=a.pdb;base64,' + + Buffer.from(body).toString('base64') + const files = { + 'a.pdb': file + }; + [moleculeInfos, moleculesPropName] = await parseMolecules( + globalParameters, + globalSchema, + files + ) + }) + + describe('given array of object with array of scalar', () => { + it.each([ + ['residue', 'number'], + ['chain', 'string'] + ] as const)('should make items an array and not set enums for %s format', async (moleculeformat, moleculeType) => { + const propSchema: JSONSchema7WithMaxItemsFrom = { + type: 'array', + maxItemsFrom: 'molecules', + items: { + type: 'object', + properties: { + prop2: { + type: 'array', + items: { + type: moleculeType, + format: moleculeformat + } + } + } + } + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: propSchema + } + } + const actual = await addMoleculeValidation( + schema, + moleculeInfos, + moleculesPropName + ) + const expectedPropSchema: JSONSchema7WithMaxItemsFrom = { + type: 'array', + maxItemsFrom: 'molecules', + items: [ + { + type: 'object', + properties: { + prop2: { + type: 'array', + items: { + type: moleculeType, + format: moleculeformat + } + } + } + } + ] + } + const expected: JSONSchema7 = { + type: 'object', + properties: { + prop1: expectedPropSchema + } + } + expect(actual).toEqual(expected) + }) + }) + }) }) describe('addMoleculeUi()', () => { diff --git a/packages/core/src/molecule/addMoleculeValidation.ts b/packages/core/src/molecule/addMoleculeValidation.ts index 850c63c..69bde66 100644 --- a/packages/core/src/molecule/addMoleculeValidation.ts +++ b/packages/core/src/molecule/addMoleculeValidation.ts @@ -179,13 +179,15 @@ function walkSchemaForMoleculeFormats ( pv.items.format !== undefined && moleculeFormats.has(pv.items.format) ) { - if (pv.items.format === 'chain') { + if (pv.items.format === 'chain' && molinfo.chains.length > 0) { return [ pk, { ...pv, items: { ...pv.items, enum: molinfo.chains } } ] } - if (pv.items.format === 'residue') { + if (pv.items.format === 'residue' && + molinfo.residueSequenceNumbers.length > 0 + ) { return [ pk, { diff --git a/packages/haddock3_catalog/README.md b/packages/haddock3_catalog/README.md index fa6931a..244c58f 100644 --- a/packages/haddock3_catalog/README.md +++ b/packages/haddock3_catalog/README.md @@ -11,6 +11,8 @@ Run with # Reads modules from haddock3 in Python path ./generate_haddock3_catalog.py # Writes catalog files in public/catalog/ dir + +# TODO add command to check JSON schemas are valid. ``` Translations from haddock3 -> i-VRESSE workflow builder: diff --git a/packages/haddock3_catalog/generate_haddock3_catalog.py b/packages/haddock3_catalog/generate_haddock3_catalog.py index 3e4ea6f..404a248 100755 --- a/packages/haddock3_catalog/generate_haddock3_catalog.py +++ b/packages/haddock3_catalog/generate_haddock3_catalog.py @@ -326,6 +326,12 @@ def config2schema(config): prop['items'] = { "type": "number" } + elif k == 'ligand_chains': + prop['items'] = { + "type": "string", + "format": "chain" + } + prop['default'] = v['default'] else: raise ValueError(f"Don't know how to determine type of items of {v}") else: @@ -425,7 +431,9 @@ def process_level(level_fn: Path, level: str): broken_modules = { 'topocg', # Gives `AttributeError: module 'haddock.modules.topology.topocg' has no attribute 'HaddockModule'` error } - nodes = [process_module(module, category, level) for module, category in modules_category.items() if module not in broken_modules] + # TODO define module order like category order + # now they are sorted alphabetically + nodes = [process_module(module, category, level) for module, category in sorted(modules_category.items()) if module not in broken_modules] catalog = { "title": f"Haddock 3 on {level} level", diff --git a/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml b/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml index ea79aa4..34894f1 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml @@ -10,7 +10,7 @@ categories: description: HADDOCK3 actions referring to refinement. collapsed: false - name: scoring - description: HADDOCK3 modules to score modules. + description: HADDOCK3 modules to score models. collapsed: false - name: analysis description: HADDOCK3 modules related to model analysis. @@ -194,362 +194,269 @@ global: ui:group: clean tomlSchema: {} nodes: -- id: topoaa - category: topology - label: Create and manage CNS all-atom topology. - description: HADDOCK3 module to create CNS all-atom topologies. +- id: caprieval + category: analysis + label: Calculate CAPRI metrics. + description: HADDOCK3 module to calculate the CAPRI metrics. schema: type: object properties: - delenph: + 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: Keep or remove non-polar hydrogen atoms - description: If set to true, non-polar hydrogen atoms will be discarded to - save computing time - $comment: Since HADDOCK uses a united atom force field, the non-polar hydrogen - atoms can be in principle discarded. This saves computing time. However - this should not be done if you are defining distance restraints to specific - hydrogen atoms (e.g. when using NMR distance restraints). + 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 - mol: - title: Input 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 - format: chain - 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 - format: residue - 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 - format: residue - required: [] - additionalProperties: false - maxItemsFrom: molecules - required: [] - additionalProperties: false - uiSchema: - delenph: - ui:group: molecule - mol: - ui:indexable: true - ui:group: input molecules - tomlSchema: - mol: - indexed: true - items: - sectioned: true - properties: - hisd: - indexed: true - hise: - indexed: true -- id: mdscoring - category: scoring - label: MD scoring module. - description: HADDOCK3 module to perform energy minimization scoring. - schema: - type: object - properties: - ssdihed: - 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: - - 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' + 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 - elecflag: + lrmsd: 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. + 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_chains + parameter). Superposition and RMSD calculations are done on backbone heavy + atoms. 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 - enum: - - water - - dmso - required: [] - additionalProperties: false - uiSchema: - ssdihed: - ui:group: dihedral restraints - error_dih: - ui:group: dihedral restraints - dnarest_on: - ui:group: other restraints - elecflag: - ui:group: force field - tomlSchema: {} -- id: emscoring - category: scoring - label: EM scoring module. - description: HADDOCK3 module to perform energy minimization scoring. - schema: - type: object - properties: - elecflag: + ilrmsd: 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. + 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_chains parameter). type: boolean - required: [] - additionalProperties: false - uiSchema: - elecflag: - ui:group: force field - tomlSchema: {} -- id: mdref - category: refinement - label: Water refinement with CNS. - description: HADDOCK3 module for water refinement. - schema: - type: object - properties: - mol_shape: + 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: 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: 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: 1 + maxLength: 1 + format: chain + ligand_chains: + default: + - B + title: Ligand ChainIDs + description: Ligand ChainIDs to be considered for the RMSD calculations. + $comment: Ligand ChainIDs to be considered for the RMSD calculations. This + determines which chains will be treated as the ligand for the L-RMSD and + for I-L-RMSD. type: array - maxItemsFrom: molecules + minItems: 0 + maxItems: 100 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 - $comment: Filename of the ambiguous distance restraints file. By default 50% - of those restraints will be randomly discared. This can be changed/turned - off and is controlled by the randremoval and npart parameters. Note that - this file can contain both ambiguous and unambiguous restraints. - type: string - format: uri-reference - unambig_fname: - title: Unambiguous restraints filename - description: Filename of the unambiguous distance restraints file - $comment: Filename of the unambiguous distance restraints file. All restraints - in that file will be used. Note that this file can contain both ambiguous - and unambiguous restraints. - type: string - format: uri-reference - hbond_fname: - title: H-bond restraints filename - description: Filename of the hydrogen bond distance restraints file - $comment: Filename of the hydrogen bond distance restraints file. Note that - this file can contain any type of distance restraints. - type: string - format: uri-reference - dihe_fname: - title: Dihedral angle restraints filename - description: Filename of the Dihedral angle restraints file - $comment: Filename of the Dihedral angle restraints file. + type: string + format: chain + 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 - format: uri-reference - dihedrals_on: - default: false - title: Use dihedral angle restraints - description: Turns on dihedral angle restraints. - $comment: Turns on dihedral angle restraints. Those should be defined in the - dihe_fname file. + minLength: 0 + 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 - ssdihed: - 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. + 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: - - 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) + - structure + - sequence + lovoalign_exec: + 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: 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: 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 - 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, + 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_chains: + 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: clustfcc + category: analysis + label: Cluster modules with FCC. + description: HADDOCK3 module for clustering with FCC. + schema: + type: object + properties: + executable: type: string - minLength: 0 - maxLength: 100 - enum: - - water - - dmso + format: uri-reference + contact_distance_cutoff: + default: 5.0 + type: number + maximum: 9999 + minimum: -9999 + fraction_cutoff: + default: 0.6 + type: number + maximum: 9999 + minimum: -9999 + threshold: + default: 4 + type: number + maximum: 9999 + minimum: -9999 + strictness: + default: 0.75 + type: number + maximum: 9999 + minimum: -9999 required: [] additionalProperties: false uiSchema: - mol_shape: - ui:indexable: true - 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 - dihe_fname: + executable: ui:widget: file - ui:group: dihedral restraints - dihedrals_on: - ui:group: dihedral restraints - ssdihed: - ui:group: dihedral restraints - error_dih: - ui:group: dihedral restraints - dnarest_on: - ui:group: other restraints - elecflag: - ui:group: force field - tomlSchema: - mol_shape: - indexed: true -- id: flexref + tomlSchema: {} +- id: clustrmsd + category: analysis + label: RMSD clustering module. + description: HADDOCK3 module for clustering with RMSD. + schema: + type: object + properties: + threshold: + default: 4 + title: Clustering population threshold + description: Threshold employed to exclude clusters with less than this number + of members + $comment: Threshold employed to exclude clusters with less than this number + of members. When criterion is maxclust, this value is ignored. + type: number + maximum: 9999 + minimum: 1 + tolerance: + title: Numeric value for clustering + description: if criterion is maxclust, the number of desired clusters. if + criterion is distance, the value of cutoff cophenetic distance + $comment: if criterion is maxclust, the number of desired clusters. if criterion + is distance, the value of cutoff cophenetic distance + type: number + maximum: 9999 + minimum: 1 + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} +- id: emref category: refinement - label: Flexible refinement with CNS. - description: HADDOCK3 module for flexible refinement. + label: Energy minimization refinement with CNS. + description: HADDOCK3 module energy minimization refinement. schema: type: object properties: @@ -599,6 +506,16 @@ nodes: $comment: Turns on dihedral angle restraints. Those should be defined in the dihe_fname file. type: boolean + dihedrals_scale: + default: 200 + title: Force constant for dihedral angle restraints + description: Force constant applied to the dihedral angle restraints read + from dihe_fname. + $comment: Force constant applied to the dihedral angle restraints read from + dihe_fname. + type: number + maximum: 9999 + minimum: -9999 ssdihed: title: Define automatically backbone dihedral angle restraints description: If turned on, this option will automatically defined backbone @@ -644,16 +561,6 @@ nodes: $comment: Include electrostatics energy during the calculations. If set to false electrostatics will not be considered. type: boolean - sinter_rigid_final: - default: 0.001 - title: End rigid-body MD intermolecular interactions scaling factor. - description: End scaling factor for intermolecular interactions in the first - cooling stage. - $comment: End scaling factor applied to intermolecular interactions during - the first cooling stage of the simulated annealing protocol. - type: number - maximum: 1 - minimum: 1.0e-05 required: [] additionalProperties: false uiSchema: @@ -674,6 +581,8 @@ nodes: ui:group: dihedral restraints dihedrals_on: ui:group: dihedral restraints + dihedrals_scale: + ui:group: dihedral restraints ssdihed: ui:group: dihedral restraints error_dih: @@ -685,10 +594,49 @@ nodes: tomlSchema: mol_shape: indexed: true -- id: emref +- id: emscoring + category: scoring + label: EM scoring module. + description: HADDOCK3 module to perform energy minimization scoring. + schema: + type: object + properties: + 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 + required: [] + additionalProperties: false + uiSchema: + elecflag: + ui:group: force field + tomlSchema: {} +- id: exit + category: extras + label: Exit module + description: Stop the workflow when this module is reached. + schema: + type: object + properties: + message: + default: Stopping the workflow. + title: Exiting message. + description: The message to print when exiting. + $comment: The message to print when exiting. + type: string + minLength: 0 + maxLength: 1000 + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} +- id: flexref category: refinement - label: Energy minimization refinement with CNS. - description: HADDOCK3 module energy minimization refinement. + label: Flexible refinement with CNS. + description: HADDOCK3 module for flexible refinement. schema: type: object properties: @@ -738,16 +686,6 @@ nodes: $comment: Turns on dihedral angle restraints. Those should be defined in the dihe_fname file. type: boolean - dihedrals_scale: - default: 200 - title: Force constant for dihedral angle restraints - description: Force constant applied to the dihedral angle restraints read - from dihe_fname. - $comment: Force constant applied to the dihedral angle restraints read from - dihe_fname. - type: number - maximum: 9999 - minimum: -9999 ssdihed: title: Define automatically backbone dihedral angle restraints description: If turned on, this option will automatically defined backbone @@ -793,6 +731,16 @@ nodes: $comment: Include electrostatics energy during the calculations. If set to false electrostatics will not be considered. type: boolean + sinter_rigid_final: + default: 0.001 + title: End rigid-body MD intermolecular interactions scaling factor. + description: End scaling factor for intermolecular interactions in the first + cooling stage. + $comment: End scaling factor applied to intermolecular interactions during + the first cooling stage of the simulated annealing protocol. + type: number + maximum: 1 + minimum: 1.0e-05 required: [] additionalProperties: false uiSchema: @@ -813,8 +761,6 @@ nodes: ui:group: dihedral restraints dihedrals_on: ui:group: dihedral restraints - dihedrals_scale: - ui:group: dihedral restraints ssdihed: ui:group: dihedral restraints error_dih: @@ -826,379 +772,315 @@ nodes: tomlSchema: mol_shape: indexed: true -- id: seletopclusts - category: analysis - label: Select a top cluster module. - description: Haddock Module for 'seletopclusts'. - schema: - type: object - properties: - top_cluster: - default: 1000 - title: Number of clusters to consider - description: Number of clusters to consider (ranked by score) - $comment: Number of clusters to consider (ranked by score) - type: number - maximum: 99999 - minimum: 1 - top_models: - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: {} -- id: clustrmsd - category: analysis - label: RMSD clustering module. - description: HADDOCK3 module for clustering with RMSD. +- id: gdock + category: sampling + label: gdock integration sampling module. + description: HADDOCK3 gdock module. schema: type: object properties: - threshold: - default: 4 - title: Clustering population threshold - description: Threshold employed to exclude clusters with less than this number - of members - $comment: Threshold employed to exclude clusters with less than this number - of members. When criterion is maxclust, this value is ignored. - type: number - maximum: 9999 - minimum: 1 - tolerance: - title: Numeric value for clustering - description: if criterion is maxclust, the number of desired clusters. if - criterion is distance, the value of cutoff cophenetic distance - $comment: if criterion is maxclust, the number of desired clusters. if criterion - is distance, the value of cutoff cophenetic distance - type: number - maximum: 9999 - minimum: 1 + ambig_fname: + type: string + format: uri-reference required: [] additionalProperties: false - uiSchema: {} + uiSchema: + ambig_fname: + ui:widget: file tomlSchema: {} -- id: caprieval - category: analysis - label: Calculate CAPRI metrics. - description: HADDOCK3 module to calculate the CAPRI metrics. +- id: lightdock + category: sampling + label: LightDock integration sampling module. + description: HADDOCK3 Lightdock module. schema: 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." + glowworms: + default: 200 type: number - 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." + maximum: 9999 + minimum: -9999 + steps: + default: 100 type: number - maximum: 20.0 - minimum: 3.0 - receptor_chain: + maximum: 9999 + minimum: -9999 + swarms: + default: 400 + type: number + maximum: 9999 + minimum: -9999 + scoring: + default: fastdfire + type: string + minLength: 0 + maxLength: 100 + top: + default: 10 + type: number + maximum: 9999 + minimum: -9999 + receptor_chains: 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: 1 - maxLength: 1 + minLength: 0 + maxLength: 100 format: chain - 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. + receptor_active: type: string - minLength: 1 - maxLength: 1 - format: chain - 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. + minLength: 0 + maxLength: 100 + receptor_passive: type: string minLength: 0 - 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 + maxLength: 100 + ligand_chains: + default: B type: string minLength: 0 maxLength: 100 - enum: - - structure - - sequence - lovoalign_exec: - title: Location (path) of the LovoAlign executable - description: Location (path) of the LovoAlign executable. - $comment: Location (path) of the LovoAlign executable. + format: chain + ligand_active: type: string minLength: 0 - 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: rmsdmatrix - category: analysis - label: RMSD matrix module. - description: HADDOCK3 module for clustering with RMSD. - schema: - type: object - properties: - max_models: - default: 10000 - title: Maximum number of models to calculate RMSD matrix - description: If the number of models exceeds max_models the execution is blocked - $comment: If the number of models exceeds the few thousands, the calculation - of the RMSD matrix is computationally demanding, especially in terms of - CPU and disk space. - type: number - maximum: 20000 - minimum: 1 - resdic: - default: {} - title: List of residues - description: The residue numbers that should be used in the alignment and - in the RMSD calculation. - $comment: resdic_* is an expandable parameter. You can provide resdic_A, resdic_B, - resdic_C, etc, where the last capital letter is the chain identifier. - type: object - additionalProperties: - type: array - items: - type: number - format: residue - minItems: 0 - maxItems: 100 - uniqueItems: true - default: [] - propertyNames: - pattern: ^[A-Z]$ - format: chain - maxPropertiesFrom: molecules + maxLength: 100 + ligand_passive: + type: string + minLength: 0 + maxLength: 100 + noxt: + default: true + type: boolean + noh: + default: true + type: boolean + restraints: + default: false + type: boolean required: [] additionalProperties: false uiSchema: {} - tomlSchema: - resdic: - indexed: true -- id: clustfcc - category: analysis - label: Cluster modules with FCC. - description: HADDOCK3 module for clustering with FCC. + tomlSchema: {} +- id: mdref + category: refinement + label: Water refinement with CNS. + description: HADDOCK3 module for water refinement. schema: type: object properties: - executable: + mol_shape: + type: array + maxItemsFrom: molecules + 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 + $comment: Filename of the ambiguous distance restraints file. By default 50% + of those restraints will be randomly discared. This can be changed/turned + off and is controlled by the randremoval and npart parameters. Note that + this file can contain both ambiguous and unambiguous restraints. type: string format: uri-reference - contact_distance_cutoff: - default: 5.0 - type: number - maximum: 9999 - minimum: -9999 - fraction_cutoff: - default: 0.6 - type: number - maximum: 9999 - minimum: -9999 - threshold: - default: 4 - type: number - maximum: 9999 - minimum: -9999 - strictness: - default: 0.75 + unambig_fname: + title: Unambiguous restraints filename + description: Filename of the unambiguous distance restraints file + $comment: Filename of the unambiguous distance restraints file. All restraints + in that file will be used. Note that this file can contain both ambiguous + and unambiguous restraints. + type: string + format: uri-reference + hbond_fname: + title: H-bond restraints filename + description: Filename of the hydrogen bond distance restraints file + $comment: Filename of the hydrogen bond distance restraints file. Note that + this file can contain any type of distance restraints. + type: string + format: uri-reference + dihe_fname: + title: Dihedral angle restraints filename + description: Filename of the Dihedral angle restraints file + $comment: Filename of the Dihedral angle restraints file. + type: string + format: uri-reference + dihedrals_on: + default: false + title: Use dihedral angle restraints + description: Turns on dihedral angle restraints. + $comment: Turns on dihedral angle restraints. Those should be defined in the + dihe_fname file. + type: boolean + ssdihed: + 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: + - 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 + 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 + 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 + enum: + - water + - dmso required: [] additionalProperties: false uiSchema: - executable: + mol_shape: + ui:indexable: true + ui:group: molecule + ambig_fname: ui:widget: file - tomlSchema: {} -- id: seletop - category: analysis - label: Select a top models. - description: HADDOCK3 module to select top cluster/model. - schema: - type: object - properties: - select: - default: 200 - type: number - maximum: 9999 - minimum: -9999 - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: {} -- id: exit - category: extras - label: Exit module - description: Stop the workflow when this module is reached. + ui:group: distance restraints + unambig_fname: + ui:widget: file + ui:group: distance restraints + hbond_fname: + ui:widget: file + ui:group: distance restraints + dihe_fname: + ui:widget: file + ui:group: dihedral restraints + dihedrals_on: + ui:group: dihedral restraints + ssdihed: + ui:group: dihedral restraints + error_dih: + ui:group: dihedral restraints + dnarest_on: + ui:group: other restraints + elecflag: + ui:group: force field + tomlSchema: + mol_shape: + indexed: true +- id: mdscoring + category: scoring + label: MD scoring module. + description: HADDOCK3 module to perform energy minimization scoring. schema: type: object properties: - message: - default: Stopping the workflow. - title: Exiting message. - description: The message to print when exiting. - $comment: The message to print when exiting. + ssdihed: + 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: 1000 - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: {} -- id: gdock - category: sampling - label: gdock integration sampling module. - description: HADDOCK3 gdock module. - schema: - type: object - properties: - ambig_fname: + maxLength: 100 + enum: + - 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 + 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 + 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 - format: uri-reference + minLength: 0 + maxLength: 100 + enum: + - water + - dmso required: [] additionalProperties: false uiSchema: - ambig_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: rigidbody category: sampling @@ -1282,78 +1164,199 @@ nodes: tomlSchema: mol_shape: indexed: true -- id: lightdock - category: sampling - label: LightDock integration sampling module. - description: HADDOCK3 Lightdock module. +- id: rmsdmatrix + category: analysis + label: RMSD matrix module. + description: HADDOCK3 module for clustering with RMSD. schema: type: object properties: - glowworms: - default: 200 + max_models: + default: 10000 + title: Maximum number of models to calculate RMSD matrix + description: If the number of models exceeds max_models the execution is blocked + $comment: If the number of models exceeds the few thousands, the calculation + of the RMSD matrix is computationally demanding, especially in terms of + CPU and disk space. type: number - maximum: 9999 - minimum: -9999 - steps: - default: 100 + maximum: 20000 + minimum: 1 + resdic: + default: {} + title: List of residues + description: The residue numbers that should be used in the alignment and + in the RMSD calculation. + $comment: resdic_* is an expandable parameter. You can provide resdic_A, resdic_B, + resdic_C, etc, where the last capital letter is the chain identifier. + type: object + additionalProperties: + type: array + items: + type: number + format: residue + minItems: 0 + maxItems: 100 + uniqueItems: true + default: [] + propertyNames: + pattern: ^[A-Z]$ + format: chain + maxPropertiesFrom: molecules + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: + resdic: + indexed: true +- id: seletop + category: analysis + label: Select a top models. + description: HADDOCK3 module to select top cluster/model. + schema: + type: object + properties: + select: + default: 200 type: number maximum: 9999 minimum: -9999 - swarms: - default: 400 + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} +- id: seletopclusts + category: analysis + label: Select a top cluster module. + description: Haddock Module for 'seletopclusts'. + schema: + type: object + properties: + top_cluster: + default: 1000 + title: Number of clusters to consider + description: Number of clusters to consider (ranked by score) + $comment: Number of clusters to consider (ranked by score) type: number - maximum: 9999 - minimum: -9999 - scoring: - default: fastdfire - type: string - minLength: 0 - maxLength: 100 - top: - default: 10 + maximum: 99999 + minimum: 1 + top_models: type: number maximum: 9999 minimum: -9999 - receptor_chains: - default: A - type: string - minLength: 0 - maxLength: 100 - format: chain - receptor_active: - type: string - minLength: 0 - maxLength: 100 - receptor_passive: - type: string - minLength: 0 - maxLength: 100 - ligand_chains: - default: B - type: string - minLength: 0 - maxLength: 100 - format: chain - ligand_active: - type: string - minLength: 0 - maxLength: 100 - ligand_passive: - type: string - minLength: 0 - maxLength: 100 - noxt: - default: true - type: boolean - noh: - default: true - type: boolean - restraints: - default: false - type: boolean required: [] additionalProperties: false uiSchema: {} tomlSchema: {} +- id: topoaa + category: topology + label: Create and manage CNS all-atom topology. + description: HADDOCK3 module to create CNS all-atom topologies. + schema: + type: object + properties: + delenph: + default: true + title: Keep or remove non-polar hydrogen atoms + description: If set to true, non-polar hydrogen atoms will be discarded to + save computing time + $comment: Since HADDOCK uses a united atom force field, the non-polar hydrogen + atoms can be in principle discarded. This saves computing time. However + this should not be done if you are defining distance restraints to specific + hydrogen atoms (e.g. when using NMR distance restraints). + type: boolean + mol: + title: Input 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 + format: chain + 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 + format: residue + 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 + format: residue + required: [] + additionalProperties: false + maxItemsFrom: molecules + required: [] + additionalProperties: false + uiSchema: + delenph: + ui:group: molecule + mol: + ui:indexable: true + ui:group: input molecules + tomlSchema: + mol: + indexed: true + items: + sectioned: true + properties: + hisd: + indexed: true + hise: + indexed: true examples: docking-protein-ligand: /examples/docking-protein-ligand.zip diff --git a/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml b/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml index 2dba4c2..54f4484 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml @@ -10,7 +10,7 @@ categories: description: HADDOCK3 actions referring to refinement. collapsed: false - name: scoring - description: HADDOCK3 modules to score modules. + description: HADDOCK3 modules to score models. collapsed: false - name: analysis description: HADDOCK3 modules related to model analysis. @@ -206,666 +206,345 @@ global: ui:group: clean tomlSchema: {} nodes: -- id: topoaa - category: topology - label: Create and manage CNS all-atom topology. - description: HADDOCK3 module to create CNS all-atom topologies. +- id: caprieval + category: analysis + label: Calculate CAPRI metrics. + description: HADDOCK3 module to calculate the CAPRI metrics. schema: type: object properties: - autohis: + 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: Automatic HIS protonation state - description: 'The protonation state of histidine (+1: HIS or 0: HISD/HISE) - will be automatically set by HADDOCK' - $comment: 'If set to true, HADDOCK will automatically define the protonation - state of histidines ((+1: HIS or 0: HISD/HISE) by selecting the state leading - to the lowest electrostatic energy' + 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 - delenph: + fnat: default: true - title: Keep or remove non-polar hydrogen atoms - description: If set to true, non-polar hydrogen atoms will be discarded to - save computing time - $comment: Since HADDOCK uses a united atom force field, the non-polar hydrogen - atoms can be in principle discarded. This saves computing time. However - this should not be done if you are defining distance restraints to specific - hydrogen atoms (e.g. when using NMR distance restraints). + 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 - 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 - limit: + lrmsd: default: true - title: Limit the number of input molecules. - description: When TRUE, the topoaa module can accept any number of input molecules. - $comment: Enable/disable the limit of input molecules for the topoaa module. - Setting the limit to false is useful when the topoaa module is followed - by scoring modules such as emscoring, or other analysis modules. If topoaa - is used in the middle of the workflow this parameter has no effect. + 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_chains + parameter). Superposition and RMSD calculations are done on backbone heavy + atoms. 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 + 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_chains 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: 99 - minimum: 0 - mol: - title: Input 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. + 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: 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: 1 + maxLength: 1 + format: chain + ligand_chains: + default: + - B + title: Ligand ChainIDs + description: Ligand ChainIDs to be considered for the RMSD calculations. + $comment: Ligand ChainIDs to be considered for the RMSD calculations. This + determines which chains will be treated as the ligand for the L-RMSD and + for I-L-RMSD. type: array + minItems: 0 + maxItems: 100 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 - format: chain - 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 - format: residue - 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 - format: residue - required: [] - additionalProperties: false - maxItemsFrom: molecules - required: [] - additionalProperties: false - uiSchema: - autohis: - ui:group: molecule - delenph: - 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:indexable: true - ui:group: input molecules - tomlSchema: - mol: - indexed: true - items: - sectioned: true - properties: - hisd: - indexed: true - hise: - indexed: true -- id: mdscoring - category: scoring - label: MD 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: string + format: chain + 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: 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: + 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: 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_chains: + 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: clustfcc + category: analysis + label: Cluster modules with FCC. + description: HADDOCK3 module for clustering with FCC. + schema: + type: object + properties: + executable: + type: string + format: uri-reference + contact_distance_cutoff: + default: 5.0 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. + fraction_cutoff: + default: 0.6 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. + threshold: + default: 4 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. + strictness: + default: 0.75 type: number - maximum: 1000 - minimum: 0 - ssdihed: - 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. + maximum: 9999 + minimum: -9999 + required: [] + additionalProperties: false + uiSchema: + executable: + ui:widget: file + tomlSchema: {} +- id: clustrmsd + category: analysis + label: RMSD clustering module. + description: HADDOCK3 module for clustering with RMSD. + schema: + type: object + properties: + criterion: + default: maxclust + title: Criterion for fcluster + description: Criterion to be used to cut the dendrogram + $comment: if criterion is maxclust, the dendrogram is cut when a certain number + of clusters is formed. If criterion is distance, the dendrogram will be + cut based on the value of the cophenetic distance type: string minLength: 0 maxLength: 100 enum: - - 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 - 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 + - distance + - maxclust + linkage: + default: average + title: Linkage type + description: How to lump together clusters in hierarchical clustering + $comment: check out the full description at https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html type: string minLength: 0 - maxLength: 4 + maxLength: 100 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 - 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 - 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. + - average + - centroid + - complete + - median + - single + - ward + - weighted + threshold: + default: 4 + title: Clustering population threshold + description: Threshold employed to exclude clusters with less than this number + of members + $comment: Threshold employed to exclude clusters with less than this number + of members. When criterion is maxclust, this value is ignored. type: number - maximum: 10000 + maximum: 9999 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: 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: 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: 10000 - minimum: 0 tolerance: - default: 5 - 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 + title: Numeric value for clustering + description: if criterion is maxclust, the number of desired clusters. if + criterion is distance, the value of cutoff cophenetic distance + $comment: if criterion is maxclust, the number of desired clusters. if criterion + is distance, the value of cutoff cophenetic distance type: number - maximum: 99 - minimum: 0 + maximum: 9999 + minimum: 1 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 + uiSchema: {} tomlSchema: {} -- id: emscoring - category: scoring - label: EM scoring module. - description: HADDOCK3 module to perform energy minimization scoring. +- id: emref + category: refinement + label: Energy minimization refinement with CNS. + description: HADDOCK3 module energy minimization refinement. 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 + mol_fix_origin: + type: array + maxItemsFrom: molecules + 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 + maxItemsFrom: molecules + 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 + $comment: Filename of the ambiguous distance restraints file. By default 50% + of those restraints will be randomly discared. This can be changed/turned + off and is controlled by the randremoval and npart parameters. Note that + this file can contain both ambiguous and unambiguous restraints. 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 - 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: mdref - category: refinement - label: Water refinement with CNS. - description: HADDOCK3 module for water refinement. - schema: - type: object - properties: - mol_fix_origin: - type: array - maxItemsFrom: molecules - 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 - maxItemsFrom: molecules - 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 - $comment: Filename of the ambiguous distance restraints file. By default 50% - of those restraints will be randomly discared. This can be changed/turned - off and is controlled by the randremoval and npart parameters. Note that - this file can contain both ambiguous and unambiguous restraints. - type: string - format: uri-reference - previous_ambig: - default: false - title: Boolean condition on the previous ambiguous distance restraints file - description: Boolean condition on the previous ambiguous distance restraints - file. If true, use the the restraint information coming from the previous - CNS module. If False, don't use previous information. - $comment: Boolean condition on the ambiguous distance restraints file. If - true, use the restraint information coming from the previous CNS module, - as long as an ambig_fname is not defined for the current module. If False, - don't use previous information. - type: boolean - unambig_fname: - title: Unambiguous restraints filename - description: Filename of the unambiguous distance restraints file - $comment: Filename of the unambiguous distance restraints file. All restraints - in that file will be used. Note that this file can contain both ambiguous - and unambiguous restraints. + previous_ambig: + default: false + title: Boolean condition on the previous ambiguous distance restraints file + description: Boolean condition on the previous ambiguous distance restraints + file. If true, use the the restraint information coming from the previous + CNS module. If false, don't use previous information. + $comment: Boolean condition on the ambiguous distance restraints file. If + true, use the restraint information coming from the previous CNS module, + as long as an ambig_fname is not defined for the current module. If false, + don't use previous information. + type: boolean + unambig_fname: + title: Unambiguous restraints filename + description: Filename of the unambiguous distance restraints file + $comment: Filename of the unambiguous distance restraints file. All restraints + in that file will be used. Note that this file can contain both ambiguous + and unambiguous restraints. type: string format: uri-reference hbond_fname: @@ -944,47 +623,6 @@ nodes: type: number maximum: 1000 minimum: 0 - cmrest: - default: false - title: Center of mass restraints - description: Automatically defines distance restraints between the geometric - center of the various molecules. - $comment: When turned on, this option will automatically define center of - mass restraints between the various molecules. This allows HADDOCK to operate - in ab-initio mode in the absence of any other restraints. But those restraints - can also be combined with other restraints to ensure more compact solutions. - The distance restraints are defined between the geometrical centers of the - various molecules (calculated on CA atoms for proteins (BB in case of Martini - coarse-grained molecules) and N1 atoms for nucleic acids. For small ligands, - all atoms will be used to define the geometric center. The upper limit distance - is automatically calculated based on the dimension of the molecules (see - cmtight description). - type: boolean - cmtight: - default: true - title: Center of mass restraint tightness - description: Defines the upper distance limit based on the sum of the average - dimension of the two molecule, if cmtight=false all three dimensions are - used, if set to true the shortest two only are used, resulting in tighter - distance restraints. - $comment: This parameter controls how the upper limit distance is defined - for the center of mass restraints between molecules. Each molecule is oriented - along its principle components and the x,y and z dimensions are calculated. - If cmtight=true, the molecule distance (size) is set to the average of its - smallest two half dimensions. If cmtight=false, the molecule distance (size) - is set to the average of its three half dimensions.. In case of DNA or small - ligands the molecule distance (size) is set to 0. The effective upper distance - limit for the center or mass distance restraint is the sum of the two molecule - distances. - type: boolean - kcm: - default: 1.0 - title: Center of mass restraints force constant - description: Force constant applied to the center of mass restraints - $comment: Force constant applied to the center of mass restraints - type: number - maximum: 1000 - minimum: 0 dihe_fname: title: Dihedral angle restraints filename description: Filename of the Dihedral angle restraints file @@ -1006,8 +644,8 @@ nodes: $comment: Force constant applied to the dihedral angle restraints read from dihe_fname. type: number - maximum: 1000 - minimum: 0 + maximum: 9999 + minimum: -9999 ssdihed: title: Define automatically backbone dihedral angle restraints description: If turned on, this option will automatically defined backbone @@ -1034,8 +672,8 @@ nodes: option) $comment: Force constant for backbone dihedral angle restraints (ssdihed option) type: number - maximum: 1000 - minimum: 0 + maximum: 9999 + minimum: -9999 dnarest_on: default: false title: Restrain the DNA conformation @@ -1904,7 +1542,7 @@ nodes: function $comment: Weight of the intermolecular electrostatic energy in the scoring function. Note that this does not affect the electostatic energy during - the MD refinement. + the EM minimization. type: number maximum: 9999 minimum: -9999 @@ -1924,7 +1562,7 @@ nodes: 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 MD refinement. + the EM minimization. type: number maximum: 9999 minimum: -9999 @@ -1976,74 +1614,37 @@ nodes: 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 description: This paramater control how many times a model will be refined. - $comment: This paramater control how many times a model will be refined. + $comment: This paramater control how many times a model will be refined. For + EM refinement only it does not make sense to increase it unless random removal + of restraints is turned on. If not then the energy minimisation will lead + to the same final conformation. type: number - maximum: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 50000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 100000 minimum: 1 - 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 - 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. + $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 - 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: 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: 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: 10000 - minimum: 0 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 @@ -2641,12 +2242,6 @@ nodes: ui:group: distance restraints kcont: ui:group: distance restraints - cmrest: - ui:group: distance restraints - cmtight: - ui:group: distance restraints - kcm: - ui:group: distance restraints dihe_fname: ui:widget: file ui:group: dihedral restraints @@ -2736,13 +2331,9 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling - nemsteps: - ui:group: sampling - waterheatsteps: - ui:group: sampling - watersteps: + max_nmodels: ui:group: sampling - watercoolsteps: + nemsteps: ui:group: sampling tolerance: ui:group: module @@ -2879,6 +2470,190 @@ nodes: indexed: true items: flatten: true +- id: emscoring + category: scoring + label: EM 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 + 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: exit + category: extras + label: Exit module + description: Stop the workflow when this module is reached. + schema: + type: object + properties: + message: + default: Stopping the workflow. + title: Exiting message. + description: The message to print when exiting. + $comment: The message to print when exiting. + type: string + minLength: 0 + maxLength: 1000 + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} - id: flexref category: refinement label: Flexible refinement with CNS. @@ -4195,10 +3970,18 @@ nodes: sampling_factor: default: 1 title: Sampling factor for each starting model - description: This paramater control how many times a model will be refined. - $comment: This paramater control how many times a model will be refined. + description: This paramater controls how many times a model will be refined. + $comment: This paramater controls how many times a model will be refined. type: number - maximum: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 10000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 50000 minimum: 1 nemsteps: default: 200 @@ -4978,6 +4761,8 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling + max_nmodels: + ui:group: sampling nemsteps: ui:group: sampling mdsteps_rigid: @@ -5123,62 +4908,151 @@ nodes: indexed: true items: flatten: true -- id: emref - category: refinement - label: Energy minimization refinement with CNS. - description: HADDOCK3 module energy minimization refinement. +- id: gdock + category: sampling + label: gdock integration sampling module. + description: HADDOCK3 gdock module. schema: type: object properties: - mol_fix_origin: - type: array - maxItemsFrom: molecules - 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 - maxItemsFrom: molecules - 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 - $comment: Filename of the ambiguous distance restraints file. By default 50% - of those restraints will be randomly discared. This can be changed/turned - off and is controlled by the randremoval and npart parameters. Note that - this file can contain both ambiguous and unambiguous restraints. - type: string - format: uri-reference - previous_ambig: - default: false - title: Boolean condition on the previous ambiguous distance restraints file - description: Boolean condition on the previous ambiguous distance restraints - file. If true, use the the restraint information coming from the previous - CNS module. If false, don't use previous information. - $comment: Boolean condition on the ambiguous distance restraints file. If - true, use the restraint information coming from the previous CNS module, - as long as an ambig_fname is not defined for the current module. If false, - don't use previous information. - type: boolean - unambig_fname: - title: Unambiguous restraints filename - description: Filename of the unambiguous distance restraints file - $comment: Filename of the unambiguous distance restraints file. All restraints - in that file will be used. Note that this file can contain both ambiguous - and unambiguous restraints. type: string format: uri-reference - hbond_fname: - title: H-bond restraints filename - description: Filename of the hydrogen bond distance restraints file + required: [] + additionalProperties: false + uiSchema: + ambig_fname: + ui:widget: file + tomlSchema: {} +- id: lightdock + category: sampling + label: LightDock integration sampling module. + description: HADDOCK3 Lightdock module. + schema: + type: object + properties: + glowworms: + default: 200 + type: number + maximum: 9999 + minimum: -9999 + steps: + default: 100 + type: number + maximum: 9999 + minimum: -9999 + swarms: + default: 400 + type: number + maximum: 9999 + minimum: -9999 + scoring: + default: fastdfire + type: string + minLength: 0 + maxLength: 100 + top: + default: 10 + type: number + maximum: 9999 + minimum: -9999 + receptor_chains: + default: A + type: string + minLength: 0 + maxLength: 100 + format: chain + receptor_active: + type: string + minLength: 0 + maxLength: 100 + receptor_passive: + type: string + minLength: 0 + maxLength: 100 + ligand_chains: + default: B + type: string + minLength: 0 + maxLength: 100 + format: chain + ligand_active: + type: string + minLength: 0 + maxLength: 100 + ligand_passive: + type: string + minLength: 0 + maxLength: 100 + noxt: + default: true + type: boolean + noh: + default: true + type: boolean + restraints: + default: false + type: boolean + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} +- id: mdref + category: refinement + label: Water refinement with CNS. + description: HADDOCK3 module for water refinement. + schema: + type: object + properties: + mol_fix_origin: + type: array + maxItemsFrom: molecules + 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 + maxItemsFrom: molecules + 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 + $comment: Filename of the ambiguous distance restraints file. By default 50% + of those restraints will be randomly discared. This can be changed/turned + off and is controlled by the randremoval and npart parameters. Note that + this file can contain both ambiguous and unambiguous restraints. + type: string + format: uri-reference + previous_ambig: + default: false + title: Boolean condition on the previous ambiguous distance restraints file + description: Boolean condition on the previous ambiguous distance restraints + file. If true, use the the restraint information coming from the previous + CNS module. If false, don't use previous information. + $comment: Boolean condition on the ambiguous distance restraints file. If + true, use the restraint information coming from the previous CNS module, + as long as an ambig_fname is not defined for the current module. If False, + don't use previous information. + type: boolean + unambig_fname: + title: Unambiguous restraints filename + description: Filename of the unambiguous distance restraints file + $comment: Filename of the unambiguous distance restraints file. All restraints + in that file will be used. Note that this file can contain both ambiguous + and unambiguous restraints. + type: string + format: uri-reference + hbond_fname: + title: H-bond restraints filename + description: Filename of the hydrogen bond distance restraints file $comment: Filename of the hydrogen bond distance restraints file. Note that this file can contain any type of distance restraints. type: string @@ -5252,6 +5126,47 @@ nodes: type: number maximum: 1000 minimum: 0 + cmrest: + default: false + title: Center of mass restraints + description: Automatically defines distance restraints between the geometric + center of the various molecules. + $comment: When turned on, this option will automatically define center of + mass restraints between the various molecules. This allows HADDOCK to operate + in ab-initio mode in the absence of any other restraints. But those restraints + can also be combined with other restraints to ensure more compact solutions. + The distance restraints are defined between the geometrical centers of the + various molecules (calculated on CA atoms for proteins (BB in case of Martini + coarse-grained molecules) and N1 atoms for nucleic acids. For small ligands, + all atoms will be used to define the geometric center. The upper limit distance + is automatically calculated based on the dimension of the molecules (see + cmtight description). + type: boolean + cmtight: + default: true + title: Center of mass restraint tightness + description: Defines the upper distance limit based on the sum of the average + dimension of the two molecule, if cmtight=false all three dimensions are + used, if set to true the shortest two only are used, resulting in tighter + distance restraints. + $comment: This parameter controls how the upper limit distance is defined + for the center of mass restraints between molecules. Each molecule is oriented + along its principle components and the x,y and z dimensions are calculated. + If cmtight=true, the molecule distance (size) is set to the average of its + smallest two half dimensions. If cmtight=false, the molecule distance (size) + is set to the average of its three half dimensions.. In case of DNA or small + ligands the molecule distance (size) is set to 0. The effective upper distance + limit for the center or mass distance restraint is the sum of the two molecule + distances. + type: boolean + kcm: + default: 1.0 + title: Center of mass restraints force constant + description: Force constant applied to the center of mass restraints + $comment: Force constant applied to the center of mass restraints + type: number + maximum: 1000 + minimum: 0 dihe_fname: title: Dihedral angle restraints filename description: Filename of the Dihedral angle restraints file @@ -5273,8 +5188,8 @@ nodes: $comment: Force constant applied to the dihedral angle restraints read from dihe_fname. type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 ssdihed: title: Define automatically backbone dihedral angle restraints description: If turned on, this option will automatically defined backbone @@ -5301,8 +5216,8 @@ nodes: option) $comment: Force constant for backbone dihedral angle restraints (ssdihed option) type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 dnarest_on: default: false title: Restrain the DNA conformation @@ -6171,7 +6086,7 @@ nodes: 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. + the MD refinement. type: number maximum: 9999 minimum: -9999 @@ -6191,7 +6106,7 @@ nodes: 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. + the MD refinement. type: number maximum: 9999 minimum: -9999 @@ -6243,29 +6158,82 @@ nodes: 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 description: This paramater control how many times a model will be refined. - $comment: This paramater control how many times a model will be refined. For - EM refinement only it does not make sense to increase it unless random removal - of restraints is turned on. If not then the energy minimisation will lead - to the same final conformation. + $comment: This paramater control how many times a model will be refined. type: number - maximum: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 10000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 50000 minimum: 1 + 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 + 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. Note that the effective - number might be smaller if the minimisation converges earlier. + $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: 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: 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: 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: 10000 + minimum: 0 tolerance: - default: 0 + default: 5 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 @@ -6863,10 +6831,16 @@ nodes: ui:group: distance restraints kcont: ui:group: distance restraints - dihe_fname: - ui:widget: file - ui:group: dihedral restraints - dihedrals_on: + cmrest: + ui:group: distance restraints + cmtight: + ui:group: distance restraints + kcm: + ui:group: distance restraints + dihe_fname: + ui:widget: file + ui:group: dihedral restraints + dihedrals_on: ui:group: dihedral restraints dihedrals_scale: ui:group: dihedral restraints @@ -6952,8 +6926,16 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling + max_nmodels: + ui:group: sampling nemsteps: ui:group: sampling + waterheatsteps: + ui:group: sampling + watersteps: + ui:group: sampling + watercoolsteps: + ui:group: sampling tolerance: ui:group: module nseg1: @@ -7089,408 +7071,286 @@ nodes: indexed: true items: flatten: true -- id: seletopclusts - category: analysis - label: Select a top cluster module. - description: Haddock Module for 'seletopclusts'. +- id: mdscoring + category: scoring + label: MD scoring module. + description: HADDOCK3 module to perform energy minimization scoring. schema: type: object properties: - top_cluster: - default: 1000 - title: Number of clusters to consider - description: Number of clusters to consider (ranked by score) - $comment: Number of clusters to consider (ranked by score) + 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: 99999 - minimum: 1 - top_models: + 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 - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: {} -- id: clustrmsd - category: analysis - label: RMSD clustering module. - description: HADDOCK3 module for clustering with RMSD. - schema: - type: object - properties: - criterion: - default: maxclust - title: Criterion for fcluster - description: Criterion to be used to cut the dendrogram - $comment: if criterion is maxclust, the dendrogram is cut when a certain number - of clusters is formed. If criterion is distance, the dendrogram will be - cut based on the value of the cophenetic distance - type: string - minLength: 0 - maxLength: 100 - enum: - - distance - - maxclust - linkage: - default: average - title: Linkage type - description: How to lump together clusters in hierarchical clustering - $comment: check out the full description at https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html - type: string - minLength: 0 - maxLength: 100 - enum: - - average - - centroid - - complete - - median - - single - - ward - - weighted - threshold: - default: 4 - title: Clustering population threshold - description: Threshold employed to exclude clusters with less than this number - of members - $comment: Threshold employed to exclude clusters with less than this number - of members. When criterion is maxclust, this value is ignored. + 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: 1 - tolerance: - title: Numeric value for clustering - description: if criterion is maxclust, the number of desired clusters. if - criterion is distance, the value of cutoff cophenetic distance - $comment: if criterion is maxclust, the number of desired clusters. if criterion - is distance, the value of cutoff cophenetic distance + 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: 1 - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: {} -- id: caprieval - category: analysis - label: Calculate CAPRI metrics. - description: HADDOCK3 module to calculate the CAPRI metrics. - schema: - 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` + 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 - 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: 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." + 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: 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: 1 - maxLength: 1 - format: chain - 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: 1 - maxLength: 1 - format: chain - 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. + maximum: 1000 + minimum: 0 + ssdihed: + 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: 20 + maxLength: 100 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. + - 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 - 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 + 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 - minLength: 0 - maxLength: 100 - enum: - - structure - - sequence - lovoalign_exec: - title: Location (path) of the LovoAlign executable - description: Location (path) of the LovoAlign executable. - $comment: Location (path) of the LovoAlign executable. + 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: 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: rmsdmatrix - category: analysis - label: RMSD matrix module. - description: HADDOCK3 module for clustering with RMSD. - schema: - type: object - properties: - max_models: - default: 10000 - title: Maximum number of models to calculate RMSD matrix - description: If the number of models exceeds max_models the execution is blocked - $comment: If the number of models exceeds the few thousands, the calculation - of the RMSD matrix is computationally demanding, especially in terms of - CPU and disk space. + 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: 20000 + maximum: 78 minimum: 1 - resdic: - default: {} - title: List of residues - description: The residue numbers that should be used in the alignment and - in the RMSD calculation. - $comment: resdic_* is an expandable parameter. You can provide resdic_A, resdic_B, - resdic_C, etc, where the last capital letter is the chain identifier. - type: object - additionalProperties: - type: array - items: - type: number - format: residue - minItems: 0 - maxItems: 100 - uniqueItems: true - default: [] - propertyNames: - pattern: ^[A-Z]$ - format: chain - maxPropertiesFrom: molecules - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: - resdic: - indexed: true -- id: clustfcc - category: analysis - label: Cluster modules with FCC. - description: HADDOCK3 module for clustering with FCC. - schema: - type: object - properties: - executable: + 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 + 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 - format: uri-reference - contact_distance_cutoff: - default: 5.0 + minLength: 0 + maxLength: 100 + 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 - fraction_cutoff: - default: 0.6 + 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 - threshold: - default: 4 + 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 - strictness: - default: 0.75 + 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 - required: [] - additionalProperties: false - uiSchema: - executable: - ui:widget: file - tomlSchema: {} -- id: seletop - category: analysis - label: Select a top models. - description: HADDOCK3 module to select top cluster/model. - schema: - type: object - properties: - select: - default: 200 + maximum: 10000 + minimum: 0 + tolerance: + default: 5 + 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 - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: {} -- id: exit - category: extras - label: Exit module - description: Stop the workflow when this module is reached. - schema: - type: object - properties: - message: - default: Stopping the workflow. - title: Exiting message. - description: The message to print when exiting. - $comment: The message to print when exiting. - type: string - minLength: 0 - maxLength: 1000 - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: {} -- id: gdock - category: sampling - label: gdock integration sampling module. - description: HADDOCK3 gdock module. - schema: - type: object - properties: - ambig_fname: - type: string - format: uri-reference + maximum: 99 + minimum: 0 required: [] additionalProperties: false uiSchema: - ambig_fname: + 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: rigidbody category: sampling @@ -8892,80 +8752,253 @@ nodes: flatten: true ncs: indexed: true - items: - flatten: true -- id: lightdock - category: sampling - label: LightDock integration sampling module. - description: HADDOCK3 Lightdock module. + items: + flatten: true +- id: rmsdmatrix + category: analysis + label: RMSD matrix module. + description: HADDOCK3 module for clustering with RMSD. + schema: + type: object + properties: + max_models: + default: 10000 + title: Maximum number of models to calculate RMSD matrix + description: If the number of models exceeds max_models the execution is blocked + $comment: If the number of models exceeds the few thousands, the calculation + of the RMSD matrix is computationally demanding, especially in terms of + CPU and disk space. + type: number + maximum: 20000 + minimum: 1 + resdic: + default: {} + title: List of residues + description: The residue numbers that should be used in the alignment and + in the RMSD calculation. + $comment: resdic_* is an expandable parameter. You can provide resdic_A, resdic_B, + resdic_C, etc, where the last capital letter is the chain identifier. + type: object + additionalProperties: + type: array + items: + type: number + format: residue + minItems: 0 + maxItems: 100 + uniqueItems: true + default: [] + propertyNames: + pattern: ^[A-Z]$ + format: chain + maxPropertiesFrom: molecules + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: + resdic: + indexed: true +- id: seletop + category: analysis + label: Select a top models. + description: HADDOCK3 module to select top cluster/model. schema: type: object properties: - glowworms: + select: default: 200 type: number maximum: 9999 minimum: -9999 - steps: - default: 100 - type: number - maximum: 9999 - minimum: -9999 - swarms: - default: 400 + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} +- id: seletopclusts + category: analysis + label: Select a top cluster module. + description: Haddock Module for 'seletopclusts'. + schema: + type: object + properties: + top_cluster: + default: 1000 + title: Number of clusters to consider + description: Number of clusters to consider (ranked by score) + $comment: Number of clusters to consider (ranked by score) type: number - maximum: 9999 - minimum: -9999 - scoring: - default: fastdfire - type: string - minLength: 0 - maxLength: 100 - top: - default: 10 + maximum: 99999 + minimum: 1 + top_models: type: number maximum: 9999 minimum: -9999 - receptor_chains: - default: A - type: string - minLength: 0 - maxLength: 100 - format: chain - receptor_active: - type: string - minLength: 0 - maxLength: 100 - receptor_passive: - type: string - minLength: 0 - maxLength: 100 - ligand_chains: - default: B - type: string - minLength: 0 - maxLength: 100 - format: chain - ligand_active: - type: string - minLength: 0 - maxLength: 100 - ligand_passive: - type: string - minLength: 0 - maxLength: 100 - noxt: + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} +- id: topoaa + category: topology + label: Create and manage CNS all-atom topology. + description: HADDOCK3 module to create CNS all-atom topologies. + schema: + type: object + properties: + autohis: default: true + title: Automatic HIS protonation state + description: 'The protonation state of histidine (+1: HIS or 0: HISD/HISE) + will be automatically set by HADDOCK' + $comment: 'If set to true, HADDOCK will automatically define the protonation + state of histidines ((+1: HIS or 0: HISD/HISE) by selecting the state leading + to the lowest electrostatic energy' type: boolean - noh: + delenph: default: true + title: Keep or remove non-polar hydrogen atoms + description: If set to true, non-polar hydrogen atoms will be discarded to + save computing time + $comment: Since HADDOCK uses a united atom force field, the non-polar hydrogen + atoms can be in principle discarded. This saves computing time. However + this should not be done if you are defining distance restraints to specific + hydrogen atoms (e.g. when using NMR distance restraints). type: boolean - restraints: - default: false + 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 + limit: + default: true + title: Limit the number of input molecules. + description: When TRUE, the topoaa module can accept any number of input molecules. + $comment: Enable/disable the limit of input molecules for the topoaa module. + Setting the limit to false is useful when the topoaa module is followed + by scoring modules such as emscoring, or other analysis modules. If topoaa + is used in the middle of the workflow this parameter has no effect. 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 + mol: + title: Input 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 + format: chain + 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 + format: residue + 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 + format: residue + required: [] + additionalProperties: false + maxItemsFrom: molecules required: [] additionalProperties: false - uiSchema: {} - tomlSchema: {} + uiSchema: + autohis: + ui:group: molecule + delenph: + 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:indexable: true + ui:group: input molecules + tomlSchema: + mol: + indexed: true + items: + sectioned: true + properties: + hisd: + indexed: true + hise: + indexed: true examples: docking-protein-ligand: /examples/docking-protein-ligand.zip diff --git a/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml b/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml index e637ffb..a99f2b6 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml @@ -10,7 +10,7 @@ categories: description: HADDOCK3 actions referring to refinement. collapsed: false - name: scoring - description: HADDOCK3 modules to score modules. + description: HADDOCK3 modules to score models. collapsed: false - name: analysis description: HADDOCK3 modules related to model analysis. @@ -218,963 +218,515 @@ global: ui:group: clean tomlSchema: {} nodes: -- id: topoaa - category: topology - label: Create and manage CNS all-atom topology. - description: HADDOCK3 module to create CNS all-atom topologies. +- id: caprieval + category: analysis + label: Calculate CAPRI metrics. + description: HADDOCK3 module to calculate the CAPRI metrics. schema: type: object properties: - autohis: + 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: Automatic HIS protonation state - description: 'The protonation state of histidine (+1: HIS or 0: HISD/HISE) - will be automatically set by HADDOCK' - $comment: 'If set to true, HADDOCK will automatically define the protonation - state of histidines ((+1: HIS or 0: HISD/HISE) by selecting the state leading - to the lowest electrostatic energy' + 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 - delenph: + fnat: default: true - title: Keep or remove non-polar hydrogen atoms - description: If set to true, non-polar hydrogen atoms will be discarded to - save computing time - $comment: Since HADDOCK uses a united atom force field, the non-polar hydrogen - atoms can be in principle discarded. This saves computing time. However - this should not be done if you are defining distance restraints to specific - hydrogen atoms (e.g. when using NMR distance restraints). + 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 - 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). + 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_chains + 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_chains 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: 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: 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: 1 + maxLength: 1 + format: chain + ligand_chains: + default: + - B + title: Ligand ChainIDs + description: Ligand ChainIDs to be considered for the RMSD calculations. + $comment: Ligand ChainIDs to be considered for the RMSD calculations. This + determines which chains will be treated as the ligand for the L-RMSD and + for I-L-RMSD. + type: array + minItems: 0 + maxItems: 100 + items: + type: string + format: chain + 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: 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: - - verbose - - normal - - quiet - 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 - 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 + - structure + - sequence + lovoalign_exec: + title: Location (path) of the LovoAlign executable + description: Location (path) of the LovoAlign executable. + $comment: Location (path) of the LovoAlign executable. 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 + minLength: 0 + 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_chains: + 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: clustfcc + category: analysis + label: Cluster modules with FCC. + description: HADDOCK3 module for clustering with FCC. + schema: + type: object + properties: + executable: type: string format: uri-reference - limit: - default: true - title: Limit the number of input molecules. - description: When TRUE, the topoaa module can accept any number of input molecules. - $comment: Enable/disable the limit of input molecules for the topoaa module. - Setting the limit to false is useful when the topoaa module is followed - by scoring modules such as emscoring, or other analysis modules. If topoaa - is used in the middle of the workflow this parameter has no effect. - 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 - mol: - title: Input 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 - format: chain - 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 - format: residue - 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 - format: residue - required: [] - additionalProperties: false - maxItemsFrom: molecules - 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:indexable: true - ui:group: input molecules - tomlSchema: - mol: - indexed: true - items: - sectioned: true - properties: - hisd: - indexed: true - hise: - indexed: true -- id: mdscoring - category: scoring - label: MD 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. + contact_distance_cutoff: + default: 5.0 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. + fraction_cutoff: + default: 0.6 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. + threshold: + default: 4 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. + strictness: + default: 0.75 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: - 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. + required: [] + additionalProperties: false + uiSchema: + executable: + ui:widget: file + tomlSchema: {} +- id: clustrmsd + category: analysis + label: RMSD clustering module. + description: HADDOCK3 module for clustering with RMSD. + schema: + type: object + properties: + criterion: + default: maxclust + title: Criterion for fcluster + description: Criterion to be used to cut the dendrogram + $comment: if criterion is maxclust, the dendrogram is cut when a certain number + of clusters is formed. If criterion is distance, the dendrogram will be + cut based on the value of the cophenetic distance type: string minLength: 0 maxLength: 100 enum: - - 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 - 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 - 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, + - distance + - maxclust + linkage: + default: average + title: Linkage type + description: How to lump together clusters in hierarchical clustering + $comment: check out the full description at https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html type: string minLength: 0 maxLength: 100 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. + - average + - centroid + - complete + - median + - single + - ward + - weighted + threshold: + default: 4 + title: Clustering population threshold + description: Threshold employed to exclude clusters with less than this number + of members + $comment: Threshold employed to exclude clusters with less than this number + of members. When criterion is maxclust, this value is ignored. type: number - maximum: 10000 + maximum: 9999 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. + tolerance: + title: Numeric value for clustering + description: if criterion is maxclust, the number of desired clusters. if + criterion is distance, the value of cutoff cophenetic distance + $comment: if criterion is maxclust, the number of desired clusters. if criterion + is distance, the value of cutoff cophenetic distance type: number - 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. + maximum: 9999 + minimum: 1 + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} +- id: emref + category: refinement + label: Energy minimization refinement with CNS. + description: HADDOCK3 module energy minimization refinement. + schema: + type: object + properties: + mol_fix_origin: + type: array + maxItemsFrom: molecules + 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 + maxItemsFrom: molecules + 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 + $comment: Filename of the ambiguous distance restraints file. By default 50% + of those restraints will be randomly discared. This can be changed/turned + off and is controlled by the randremoval and npart parameters. Note that + this file can contain both ambiguous and unambiguous restraints. + type: string + format: uri-reference + previous_ambig: + default: false + title: Boolean condition on the previous ambiguous distance restraints file + description: Boolean condition on the previous ambiguous distance restraints + file. If true, use the the restraint information coming from the previous + CNS module. If false, don't use previous information. + $comment: Boolean condition on the ambiguous distance restraints file. If + true, use the restraint information coming from the previous CNS module, + as long as an ambig_fname is not defined for the current module. If false, + don't use previous information. + type: boolean + unambig_fname: + title: Unambiguous restraints filename + description: Filename of the unambiguous distance restraints file + $comment: Filename of the unambiguous distance restraints file. All restraints + in that file will be used. Note that this file can contain both ambiguous + and unambiguous restraints. + type: string + format: uri-reference + hbond_fname: + title: H-bond restraints filename + description: Filename of the hydrogen bond distance restraints file + $comment: Filename of the hydrogen bond distance restraints file. Note that + this file can contain any type of distance restraints. + type: string + format: uri-reference + amb_scale: + default: 50 + title: Force constant for ambiguous distance restraints + description: Force constant applied to the distance restraints defined in + ambig_fname. + $comment: Force constant applied to the distance restraints defined in ambig_fname. type: number - maximum: 10000 + maximum: 1000 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. + unamb_scale: + default: 50 + title: Force constant for unambiguous distance restraints + description: Force constant applied to the distance restraints defined in + unambig_fname. + $comment: Force constant applied to the distance restraints defined in unambig_fname. type: number - maximum: 100000 + maximum: 1000 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. + hbond_scale: + default: 50 + title: Force constant for hbonds distance restraints + description: Force constant applied to the distance restraints defined in + hbond_fname. + $comment: Force constant applied to the distance restraints defined in hbond_fname. type: number - maximum: 10000 + maximum: 1000 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 + randremoval: + default: true + title: Random removal of ambiguous restraints + description: If set to true (default) this will cause the random removal of + ambiguous restraints for each model generated. + $comment: If set to true (default) this will cause the random removal of ambiguous + restraints for each model generated. The fraction of restraints randomly + removed depends on the npart parameter which defines in how many sets the + restraints should be randomly split. The first set will be removed. The + fraction of randomly removed ambiguous restraints is thus 1/npart. + type: boolean + npart: + default: 2 + title: Number partitions for ambiguous restraints + description: Number of sets into which to randomly partition the ambiguous + restraints. + $comment: Number of sets into which to randomly partition the ambiguous restraints. + The fraction of restraints randomly removed depends on the npart parameter + which defines in how many sets the restraints should be randomly split. + The first set will be removed. The fraction of randomly removed ambiguous + restraints is thus 1/npart. type: number - maximum: 9999999999999999 - minimum: 0 - keepwater: + maximum: 20 + minimum: 1 + contactairs: 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. + 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 - tolerance: - default: 5 - 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 + 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: 99 + maximum: 1000 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). + dihe_fname: + title: Dihedral angle restraints filename + description: Filename of the Dihedral angle restraints file + $comment: Filename of the Dihedral angle restraints file. 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: emscoring - category: scoring - label: EM 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. + format: uri-reference + dihedrals_on: + default: false + title: Use dihedral angle restraints + description: Turns on dihedral angle restraints. + $comment: Turns on dihedral angle restraints. Those should be defined in the + dihe_fname file. + type: boolean + dihedrals_scale: + default: 200 + title: Force constant for dihedral angle restraints + description: Force constant applied to the dihedral angle restraints read + from dihe_fname. + $comment: Force constant applied to the dihedral angle restraints read from + dihe_fname. 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 + ssdihed: + 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: 4 + maxLength: 100 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. + - 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: 78 - minimum: 1 - dihedflag: - default: true + maximum: 9999 + minimum: -9999 + 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 - 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. + 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 - 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. + 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: 10000 - minimum: 1 - tolerance: + 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: 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 + 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: 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 - 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 - log_level: - ui:group: module - tomlSchema: {} -- id: mdref - category: refinement - label: Water refinement with CNS. - description: HADDOCK3 module for water refinement. - schema: - type: object - properties: - mol_fix_origin: - type: array - maxItemsFrom: molecules - 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 - maxItemsFrom: molecules - 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 - $comment: Filename of the ambiguous distance restraints file. By default 50% - of those restraints will be randomly discared. This can be changed/turned - off and is controlled by the randremoval and npart parameters. Note that - this file can contain both ambiguous and unambiguous restraints. - type: string - format: uri-reference - previous_ambig: - default: false - title: Boolean condition on the previous ambiguous distance restraints file - description: Boolean condition on the previous ambiguous distance restraints - file. If true, use the the restraint information coming from the previous - CNS module. If False, don't use previous information. - $comment: Boolean condition on the ambiguous distance restraints file. If - true, use the restraint information coming from the previous CNS module, - as long as an ambig_fname is not defined for the current module. If False, - don't use previous information. - type: boolean - unambig_fname: - title: Unambiguous restraints filename - description: Filename of the unambiguous distance restraints file - $comment: Filename of the unambiguous distance restraints file. All restraints - in that file will be used. Note that this file can contain both ambiguous - and unambiguous restraints. - type: string - format: uri-reference - hbond_fname: - title: H-bond restraints filename - description: Filename of the hydrogen bond distance restraints file - $comment: Filename of the hydrogen bond distance restraints file. Note that - this file can contain any type of distance restraints. - type: string - format: uri-reference - amb_scale: - default: 50 - title: Force constant for ambiguous distance restraints - description: Force constant applied to the distance restraints defined in - ambig_fname. - $comment: Force constant applied to the distance restraints defined in ambig_fname. - type: number - maximum: 1000 - minimum: 0 - unamb_scale: - default: 50 - title: Force constant for unambiguous distance restraints - description: Force constant applied to the distance restraints defined in - unambig_fname. - $comment: Force constant applied to the distance restraints defined in unambig_fname. - type: number - maximum: 1000 - minimum: 0 - hbond_scale: - default: 50 - title: Force constant for hbonds distance restraints - description: Force constant applied to the distance restraints defined in - hbond_fname. - $comment: Force constant applied to the distance restraints defined in hbond_fname. - type: number - maximum: 1000 - minimum: 0 - randremoval: - default: true - title: Random removal of ambiguous restraints - description: If set to true (default) this will cause the random removal of - ambiguous restraints for each model generated. - $comment: If set to true (default) this will cause the random removal of ambiguous - restraints for each model generated. The fraction of restraints randomly - removed depends on the npart parameter which defines in how many sets the - restraints should be randomly split. The first set will be removed. The - fraction of randomly removed ambiguous restraints is thus 1/npart. - type: boolean - npart: - default: 2 - title: Number partitions for ambiguous restraints - description: Number of sets into which to randomly partition the ambiguous - restraints. - $comment: Number of sets into which to randomly partition the ambiguous restraints. - The fraction of restraints randomly removed depends on the npart parameter - which defines in how many sets the restraints should be randomly split. - The first set will be removed. The fraction of randomly removed ambiguous - restraints is thus 1/npart. - type: number - maximum: 20 - minimum: 1 - 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 - cmrest: - default: false - title: Center of mass restraints - description: Automatically defines distance restraints between the geometric - center of the various molecules. - $comment: When turned on, this option will automatically define center of - mass restraints between the various molecules. This allows HADDOCK to operate - in ab-initio mode in the absence of any other restraints. But those restraints - can also be combined with other restraints to ensure more compact solutions. - The distance restraints are defined between the geometrical centers of the - various molecules (calculated on CA atoms for proteins (BB in case of Martini - coarse-grained molecules) and N1 atoms for nucleic acids. For small ligands, - all atoms will be used to define the geometric center. The upper limit distance - is automatically calculated based on the dimension of the molecules (see - cmtight description). - type: boolean - cmtight: - default: true - title: Center of mass restraint tightness - description: Defines the upper distance limit based on the sum of the average - dimension of the two molecule, if cmtight=false all three dimensions are - used, if set to true the shortest two only are used, resulting in tighter - distance restraints. - $comment: This parameter controls how the upper limit distance is defined - for the center of mass restraints between molecules. Each molecule is oriented - along its principle components and the x,y and z dimensions are calculated. - If cmtight=true, the molecule distance (size) is set to the average of its - smallest two half dimensions. If cmtight=false, the molecule distance (size) - is set to the average of its three half dimensions.. In case of DNA or small - ligands the molecule distance (size) is set to 0. The effective upper distance - limit for the center or mass distance restraint is the sum of the two molecule - distances. - type: boolean - kcm: - default: 1.0 - title: Center of mass restraints force constant - description: Force constant applied to the center of mass restraints - $comment: Force constant applied to the center of mass restraints - type: number - maximum: 1000 - minimum: 0 - dihe_fname: - title: Dihedral angle restraints filename - description: Filename of the Dihedral angle restraints file - $comment: Filename of the Dihedral angle restraints file. - type: string - format: uri-reference - dihedrals_on: - default: false - title: Use dihedral angle restraints - description: Turns on dihedral angle restraints. - $comment: Turns on dihedral angle restraints. Those should be defined in the - dihe_fname file. - type: boolean - dihedrals_scale: - default: 200 - title: Force constant for dihedral angle restraints - description: Force constant applied to the dihedral angle restraints read - from dihe_fname. - $comment: Force constant applied to the dihedral angle restraints read from - dihe_fname. - type: number - maximum: 1000 - minimum: 0 - ssdihed: - 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: - - 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 - 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 + maximum: 40 minimum: 0 c2sym: type: array @@ -2002,7 +1554,7 @@ nodes: function $comment: Weight of the intermolecular electrostatic energy in the scoring function. Note that this does not affect the electostatic energy during - the MD refinement. + the EM minimization. type: number maximum: 9999 minimum: -9999 @@ -2022,7 +1574,7 @@ nodes: 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 MD refinement. + the EM minimization. type: number maximum: 9999 minimum: -9999 @@ -2074,80 +1626,35 @@ nodes: 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 description: This paramater control how many times a model will be refined. - $comment: This paramater control how many times a model will be refined. + $comment: This paramater control how many times a model will be refined. For + EM refinement only it does not make sense to increase it unless random removal + of restraints is turned on. If not then the energy minimisation will lead + to the same final conformation. type: number - maximum: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 50000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 100000 minimum: 1 - 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 - 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. + $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 - 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: 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: 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: 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: 10000 - minimum: 0 iniseed: default: 917 title: Random seed @@ -2163,7 +1670,7 @@ nodes: $comment: Write water molecules if present to the output file. type: boolean 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 @@ -2176,7 +1683,7 @@ nodes: 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). + normal or quiet) type: string minLength: 0 maxLength: 100 @@ -2775,12 +2282,6 @@ nodes: ui:group: distance restraints kcont: ui:group: distance restraints - cmrest: - ui:group: distance restraints - cmtight: - ui:group: distance restraints - kcm: - ui:group: distance restraints dihe_fname: ui:widget: file ui:group: dihedral restraints @@ -2870,15 +2371,9 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling - nemsteps: - ui:group: sampling - timestep: - ui:group: sampling - waterheatsteps: - ui:group: sampling - watersteps: + max_nmodels: ui:group: sampling - watercoolsteps: + nemsteps: ui:group: sampling iniseed: ui:group: sampling @@ -3021,6 +2516,206 @@ nodes: indexed: true items: flatten: true +- id: emscoring + category: scoring + label: EM 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: + 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 + log_level: + ui:group: module + tomlSchema: {} +- id: exit + category: extras + label: Exit module + description: Stop the workflow when this module is reached. + schema: + type: object + properties: + message: + default: Stopping the workflow. + title: Exiting message. + description: The message to print when exiting. + $comment: The message to print when exiting. + type: string + minLength: 0 + maxLength: 1000 + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} - id: flexref category: refinement label: Flexible refinement with CNS. @@ -4337,10 +4032,18 @@ nodes: sampling_factor: default: 1 title: Sampling factor for each starting model - description: This paramater control how many times a model will be refined. - $comment: This paramater control how many times a model will be refined. + description: This paramater controls how many times a model will be refined. + $comment: This paramater controls how many times a model will be refined. type: number - maximum: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 10000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 50000 minimum: 1 nemsteps: default: 200 @@ -5299,6 +5002,8 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling + max_nmodels: + ui:group: sampling nemsteps: ui:group: sampling mdsteps_rigid: @@ -5478,10 +5183,99 @@ nodes: indexed: true items: flatten: true -- id: emref +- id: gdock + category: sampling + label: gdock integration sampling module. + description: HADDOCK3 gdock module. + schema: + type: object + properties: + ambig_fname: + type: string + format: uri-reference + required: [] + additionalProperties: false + uiSchema: + ambig_fname: + ui:widget: file + tomlSchema: {} +- id: lightdock + category: sampling + label: LightDock integration sampling module. + description: HADDOCK3 Lightdock module. + schema: + type: object + properties: + glowworms: + default: 200 + type: number + maximum: 9999 + minimum: -9999 + steps: + default: 100 + type: number + maximum: 9999 + minimum: -9999 + swarms: + default: 400 + type: number + maximum: 9999 + minimum: -9999 + scoring: + default: fastdfire + type: string + minLength: 0 + maxLength: 100 + top: + default: 10 + type: number + maximum: 9999 + minimum: -9999 + receptor_chains: + default: A + type: string + minLength: 0 + maxLength: 100 + format: chain + receptor_active: + type: string + minLength: 0 + maxLength: 100 + receptor_passive: + type: string + minLength: 0 + maxLength: 100 + ligand_chains: + default: B + type: string + minLength: 0 + maxLength: 100 + format: chain + ligand_active: + type: string + minLength: 0 + maxLength: 100 + ligand_passive: + type: string + minLength: 0 + maxLength: 100 + noxt: + default: true + type: boolean + noh: + default: true + type: boolean + restraints: + default: false + type: boolean + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} +- id: mdref category: refinement - label: Energy minimization refinement with CNS. - description: HADDOCK3 module energy minimization refinement. + label: Water refinement with CNS. + description: HADDOCK3 module for water refinement. schema: type: object properties: @@ -5520,7 +5314,7 @@ nodes: CNS module. If false, don't use previous information. $comment: Boolean condition on the ambiguous distance restraints file. If true, use the restraint information coming from the previous CNS module, - as long as an ambig_fname is not defined for the current module. If false, + as long as an ambig_fname is not defined for the current module. If False, don't use previous information. type: boolean unambig_fname: @@ -5607,6 +5401,47 @@ nodes: type: number maximum: 1000 minimum: 0 + cmrest: + default: false + title: Center of mass restraints + description: Automatically defines distance restraints between the geometric + center of the various molecules. + $comment: When turned on, this option will automatically define center of + mass restraints between the various molecules. This allows HADDOCK to operate + in ab-initio mode in the absence of any other restraints. But those restraints + can also be combined with other restraints to ensure more compact solutions. + The distance restraints are defined between the geometrical centers of the + various molecules (calculated on CA atoms for proteins (BB in case of Martini + coarse-grained molecules) and N1 atoms for nucleic acids. For small ligands, + all atoms will be used to define the geometric center. The upper limit distance + is automatically calculated based on the dimension of the molecules (see + cmtight description). + type: boolean + cmtight: + default: true + title: Center of mass restraint tightness + description: Defines the upper distance limit based on the sum of the average + dimension of the two molecule, if cmtight=false all three dimensions are + used, if set to true the shortest two only are used, resulting in tighter + distance restraints. + $comment: This parameter controls how the upper limit distance is defined + for the center of mass restraints between molecules. Each molecule is oriented + along its principle components and the x,y and z dimensions are calculated. + If cmtight=true, the molecule distance (size) is set to the average of its + smallest two half dimensions. If cmtight=false, the molecule distance (size) + is set to the average of its three half dimensions.. In case of DNA or small + ligands the molecule distance (size) is set to 0. The effective upper distance + limit for the center or mass distance restraint is the sum of the two molecule + distances. + type: boolean + kcm: + default: 1.0 + title: Center of mass restraints force constant + description: Force constant applied to the center of mass restraints + $comment: Force constant applied to the center of mass restraints + type: number + maximum: 1000 + minimum: 0 dihe_fname: title: Dihedral angle restraints filename description: Filename of the Dihedral angle restraints file @@ -5628,8 +5463,8 @@ nodes: $comment: Force constant applied to the dihedral angle restraints read from dihe_fname. type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 ssdihed: title: Define automatically backbone dihedral angle restraints description: If turned on, this option will automatically defined backbone @@ -5656,8 +5491,8 @@ nodes: option) $comment: Force constant for backbone dihedral angle restraints (ssdihed option) type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 dnarest_on: default: false title: Restrain the DNA conformation @@ -6526,7 +6361,7 @@ nodes: 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. + the MD refinement. type: number maximum: 9999 minimum: -9999 @@ -6546,7 +6381,7 @@ nodes: 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. + the MD refinement. type: number maximum: 9999 minimum: -9999 @@ -6598,27 +6433,88 @@ nodes: 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 description: This paramater control how many times a model will be refined. - $comment: This paramater control how many times a model will be refined. For - EM refinement only it does not make sense to increase it unless random removal - of restraints is turned on. If not then the energy minimisation will lead - to the same final conformation. + $comment: This paramater control how many times a model will be refined. type: number - maximum: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 10000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 50000 minimum: 1 + 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 + 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. Note that the effective - number might be smaller if the minimisation converges earlier. + $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: 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: 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: 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: 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: 10000 + minimum: 0 iniseed: default: 917 title: Random seed @@ -6634,7 +6530,7 @@ nodes: $comment: Write water molecules if present to the output file. type: boolean tolerance: - default: 0 + default: 5 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 @@ -6647,7 +6543,7 @@ nodes: 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) + normal or quiet). type: string minLength: 0 maxLength: 100 @@ -7246,6 +7142,12 @@ nodes: ui:group: distance restraints kcont: ui:group: distance restraints + cmrest: + ui:group: distance restraints + cmtight: + ui:group: distance restraints + kcm: + ui:group: distance restraints dihe_fname: ui:widget: file ui:group: dihedral restraints @@ -7335,8 +7237,18 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling + max_nmodels: + 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: @@ -7478,408 +7390,330 @@ nodes: indexed: true items: flatten: true -- id: seletopclusts - category: analysis - label: Select a top cluster module. - description: Haddock Module for 'seletopclusts'. +- id: mdscoring + category: scoring + label: MD scoring module. + description: HADDOCK3 module to perform energy minimization scoring. schema: type: object properties: - top_cluster: - default: 1000 - title: Number of clusters to consider - description: Number of clusters to consider (ranked by score) - $comment: Number of clusters to consider (ranked by score) + 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: 99999 - minimum: 1 - top_models: + 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 - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: {} -- id: clustrmsd - category: analysis - label: RMSD clustering module. - description: HADDOCK3 module for clustering with RMSD. - schema: - type: object - properties: - criterion: - default: maxclust - title: Criterion for fcluster - description: Criterion to be used to cut the dendrogram - $comment: if criterion is maxclust, the dendrogram is cut when a certain number - of clusters is formed. If criterion is distance, the dendrogram will be - cut based on the value of the cophenetic distance - type: string - minLength: 0 - maxLength: 100 - enum: - - distance - - maxclust - linkage: - default: average - title: Linkage type - description: How to lump together clusters in hierarchical clustering - $comment: check out the full description at https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html - type: string - minLength: 0 - maxLength: 100 - enum: - - average - - centroid - - complete - - median - - single - - ward - - weighted - threshold: - default: 4 - title: Clustering population threshold - description: Threshold employed to exclude clusters with less than this number - of members - $comment: Threshold employed to exclude clusters with less than this number - of members. When criterion is maxclust, this value is ignored. + 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: 1 - tolerance: - title: Numeric value for clustering - description: if criterion is maxclust, the number of desired clusters. if - criterion is distance, the value of cutoff cophenetic distance - $comment: if criterion is maxclust, the number of desired clusters. if criterion - is distance, the value of cutoff cophenetic distance + 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: 1 - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: {} -- id: caprieval - category: analysis - label: Calculate CAPRI metrics. - description: HADDOCK3 module to calculate the CAPRI metrics. - schema: - 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` + 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 - 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: 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." + 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: 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: 1 - maxLength: 1 - format: chain - 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: 1 - maxLength: 1 - format: chain - 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. + maximum: 1000 + minimum: 0 + ssdihed: + 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: 20 + maxLength: 100 enum: - - score - - irmsd - - lrmsd - - ilrmsd - - fnat - - dockq - sort_ascending: + - 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 + elecflag: default: true - title: Sort in ascending order - description: Sort in ascending order. - $comment: Sort in ascending order. + 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 - 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 + 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: - - structure - - sequence - lovoalign_exec: - 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: 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: rmsdmatrix - category: analysis - label: RMSD matrix module. - description: HADDOCK3 module for clustering with RMSD. - schema: - type: object - properties: - max_models: - default: 10000 - title: Maximum number of models to calculate RMSD matrix - description: If the number of models exceeds max_models the execution is blocked - $comment: If the number of models exceeds the few thousands, the calculation - of the RMSD matrix is computationally demanding, especially in terms of - CPU and disk space. + - 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: 20000 + maximum: 78 minimum: 1 - resdic: - default: {} - title: List of residues - description: The residue numbers that should be used in the alignment and - in the RMSD calculation. - $comment: resdic_* is an expandable parameter. You can provide resdic_A, resdic_B, - resdic_C, etc, where the last capital letter is the chain identifier. - type: object - additionalProperties: - type: array - items: - type: number - format: residue - minItems: 0 - maxItems: 100 - uniqueItems: true - default: [] - propertyNames: - pattern: ^[A-Z]$ - format: chain - maxPropertiesFrom: molecules - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: - resdic: - indexed: true -- id: clustfcc - category: analysis - label: Cluster modules with FCC. - description: HADDOCK3 module for clustering with FCC. - schema: - type: object - properties: - executable: + 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 + 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 - format: uri-reference - contact_distance_cutoff: - default: 5.0 + minLength: 0 + maxLength: 100 + 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 - fraction_cutoff: - default: 0.6 + 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 - threshold: - default: 4 + 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 - strictness: - default: 0.75 + 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 - required: [] - additionalProperties: false - uiSchema: - executable: - ui:widget: file - tomlSchema: {} -- id: seletop - category: analysis - label: Select a top models. - description: HADDOCK3 module to select top cluster/model. - schema: - type: object - properties: - select: - default: 200 + 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 - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: {} -- id: exit - category: extras - label: Exit module - description: Stop the workflow when this module is reached. - schema: - type: object - properties: - message: - default: Stopping the workflow. - title: Exiting message. - description: The message to print when exiting. - $comment: The message to print when exiting. + 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: 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: 5 + 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: 1000 - required: [] - additionalProperties: false - uiSchema: {} - tomlSchema: {} -- id: gdock - category: sampling - label: gdock integration sampling module. - description: HADDOCK3 gdock module. - schema: - type: object - properties: - ambig_fname: - type: string - format: uri-reference + maxLength: 100 + enum: + - verbose + - normal + - quiet required: [] additionalProperties: false uiSchema: - ambig_fname: + 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: rigidbody category: sampling @@ -9326,78 +9160,277 @@ nodes: indexed: true items: flatten: true -- id: lightdock - category: sampling - label: LightDock integration sampling module. - description: HADDOCK3 Lightdock module. +- id: rmsdmatrix + category: analysis + label: RMSD matrix module. + description: HADDOCK3 module for clustering with RMSD. + schema: + type: object + properties: + max_models: + default: 10000 + title: Maximum number of models to calculate RMSD matrix + description: If the number of models exceeds max_models the execution is blocked + $comment: If the number of models exceeds the few thousands, the calculation + of the RMSD matrix is computationally demanding, especially in terms of + CPU and disk space. + type: number + maximum: 20000 + minimum: 1 + resdic: + default: {} + title: List of residues + description: The residue numbers that should be used in the alignment and + in the RMSD calculation. + $comment: resdic_* is an expandable parameter. You can provide resdic_A, resdic_B, + resdic_C, etc, where the last capital letter is the chain identifier. + type: object + additionalProperties: + type: array + items: + type: number + format: residue + minItems: 0 + maxItems: 100 + uniqueItems: true + default: [] + propertyNames: + pattern: ^[A-Z]$ + format: chain + maxPropertiesFrom: molecules + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: + resdic: + indexed: true +- id: seletop + category: analysis + label: Select a top models. + description: HADDOCK3 module to select top cluster/model. schema: type: object properties: - glowworms: + select: default: 200 type: number maximum: 9999 minimum: -9999 - steps: - default: 100 + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} +- id: seletopclusts + category: analysis + label: Select a top cluster module. + description: Haddock Module for 'seletopclusts'. + schema: + type: object + properties: + top_cluster: + default: 1000 + title: Number of clusters to consider + description: Number of clusters to consider (ranked by score) + $comment: Number of clusters to consider (ranked by score) type: number - maximum: 9999 - minimum: -9999 - swarms: - default: 400 + maximum: 99999 + minimum: 1 + top_models: type: number maximum: 9999 minimum: -9999 - scoring: - default: fastdfire + required: [] + additionalProperties: false + uiSchema: {} + tomlSchema: {} +- id: topoaa + category: topology + label: Create and manage CNS all-atom topology. + description: HADDOCK3 module to create CNS all-atom topologies. + schema: + type: object + properties: + autohis: + default: true + title: Automatic HIS protonation state + description: 'The protonation state of histidine (+1: HIS or 0: HISD/HISE) + will be automatically set by HADDOCK' + $comment: 'If set to true, HADDOCK will automatically define the protonation + state of histidines ((+1: HIS or 0: HISD/HISE) by selecting the state leading + to the lowest electrostatic energy' + type: boolean + delenph: + default: true + title: Keep or remove non-polar hydrogen atoms + description: If set to true, non-polar hydrogen atoms will be discarded to + save computing time + $comment: Since HADDOCK uses a united atom force field, the non-polar hydrogen + atoms can be in principle discarded. This saves computing time. However + this should not be done if you are defining distance restraints to specific + hydrogen atoms (e.g. when using NMR distance restraints). + type: boolean + 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 - top: - default: 10 + enum: + - verbose + - normal + - quiet + 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 - receptor_chains: - default: A - type: string - minLength: 0 - maxLength: 100 - format: chain - receptor_active: - type: string - minLength: 0 - maxLength: 100 - receptor_passive: - type: string - minLength: 0 - maxLength: 100 - ligand_chains: - default: B - type: string - minLength: 0 - maxLength: 100 - format: chain - ligand_active: + maximum: 9999999999999999 + minimum: 0 + 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 - minLength: 0 - maxLength: 100 - ligand_passive: + 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 - minLength: 0 - maxLength: 100 - noxt: - default: true - type: boolean - noh: + format: uri-reference + limit: default: true + title: Limit the number of input molecules. + description: When TRUE, the topoaa module can accept any number of input molecules. + $comment: Enable/disable the limit of input molecules for the topoaa module. + Setting the limit to false is useful when the topoaa module is followed + by scoring modules such as emscoring, or other analysis modules. If topoaa + is used in the middle of the workflow this parameter has no effect. type: boolean - restraints: - default: false - 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 + mol: + title: Input 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 + format: chain + 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 + format: residue + 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 + format: residue + required: [] + additionalProperties: false + maxItemsFrom: molecules required: [] additionalProperties: false - uiSchema: {} - tomlSchema: {} + 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:indexable: true + ui:group: input molecules + tomlSchema: + mol: + indexed: true + items: + sectioned: true + properties: + hisd: + indexed: true + hise: + indexed: true examples: docking-protein-ligand: /examples/docking-protein-ligand.zip