From 2c52ba81a57bc2f5f3f7fb0d2d77c23521777fec Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Tue, 1 Mar 2022 11:30:31 +0100 Subject: [PATCH 1/7] Regenerate catalog from https://github.com/haddocking/haddock3/commit/0707193707820306a2fbeb241d7100b51735db80 --- public/catalog/haddock3.easy.yaml | 3010 ++------------ public/catalog/haddock3.expert.yaml | 5663 ++++++++++++++------------ public/catalog/haddock3.guru.yaml | 5748 +++++++++++++++------------ 3 files changed, 6856 insertions(+), 7565 deletions(-) diff --git a/public/catalog/haddock3.easy.yaml b/public/catalog/haddock3.easy.yaml index f115813b..831ea531 100644 --- a/public/catalog/haddock3.easy.yaml +++ b/public/catalog/haddock3.easy.yaml @@ -304,121 +304,121 @@ nodes: schema: type: object properties: - shape_1: + mol_shape_1: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_2: + mol_shape_2: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_3: + mol_shape_3: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_4: + mol_shape_4: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_5: + mol_shape_5: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_6: + mol_shape_6: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_7: + mol_shape_7: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_8: + mol_shape_8: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_9: + mol_shape_9: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_10: + mol_shape_10: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_11: + mol_shape_11: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_12: + mol_shape_12: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_13: + mol_shape_13: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_14: + mol_shape_14: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_15: + mol_shape_15: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_16: + mol_shape_16: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_17: + mol_shape_17: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_18: + mol_shape_18: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_19: + mol_shape_19: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_20: + mol_shape_20: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. @@ -469,45 +469,45 @@ nodes: required: [] additionalProperties: false uiSchema: - shape_1: + mol_shape_1: ui:group: molecule - shape_2: + mol_shape_2: ui:group: molecule - shape_3: + mol_shape_3: ui:group: molecule - shape_4: + mol_shape_4: ui:group: molecule - shape_5: + mol_shape_5: ui:group: molecule - shape_6: + mol_shape_6: ui:group: molecule - shape_7: + mol_shape_7: ui:group: molecule - shape_8: + mol_shape_8: ui:group: molecule - shape_9: + mol_shape_9: ui:group: molecule - shape_10: + mol_shape_10: ui:group: molecule - shape_11: + mol_shape_11: ui:group: molecule - shape_12: + mol_shape_12: ui:group: molecule - shape_13: + mol_shape_13: ui:group: molecule - shape_14: + mol_shape_14: ui:group: molecule - shape_15: + mol_shape_15: ui:group: molecule - shape_16: + mol_shape_16: ui:group: molecule - shape_17: + mol_shape_17: ui:group: molecule - shape_18: + mol_shape_18: ui:group: molecule - shape_19: + mol_shape_19: ui:group: molecule - shape_20: + mol_shape_20: ui:group: molecule ambig_fname: ui:widget: file @@ -2094,2538 +2094,365 @@ nodes: schema: type: object properties: - tolerance: - default: 5 - type: number - maximum: 9999 - minimum: -9999 - log_level: - default: verbose - type: string - minLength: 0 - maxLength: 100 + mol_shape_1: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_2: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_3: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_4: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_5: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_6: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_7: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_8: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_9: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_10: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_11: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_12: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_13: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_14: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_15: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_16: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_17: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_18: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_19: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_20: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean 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: - type: string - format: uri-reference - dihe_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 - ligand_param_fname: + 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 - ligand_top_fname: + 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: + default: none + title: Define automatically backbone dihedral angle restraints + description: If turned on, this option will automatically defined backbone + dihedral angle restraints for the selected regions. + $comment: This option allows to utomatically defined backbone dihedral angle + restraints for the selected regions. The restraints will be defined for + the phi and psi backbone dihedral angles of amino acids, with the target + value taken from the measured angle in the input structure, and the error + bound defined by the error_dih parameter. Those restraints can be applied + to the entire structure (all), the alpha/beta secondary structure elements + (alphabeta) or only to the alpha helical regions (alpha). Those are automatically + detected based on the measured dihedral angle combinations. type: string - format: uri-reference - sampling_factor: - default: 1 - type: number - maximum: 9999 - minimum: -9999 - iniseed: - default: 917 + minLength: 0 + maxLength: 100 + enum: + - none + - all + - alpha + - alphabeta + error_dih: + default: 10 + title: Force constant for backbone dihedral angle restraints + description: Force constant for backbone dihedral angle restraints (ssdihed + option) + $comment: Force constant for backbone dihedral angle restraints (ssdihed option) type: number maximum: 9999 minimum: -9999 - keepwater: + 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 - mdsteps_rigid: - default: 500 - type: number - maximum: 9999 - minimum: -9999 - mdsteps_cool1: - default: 500 - type: number - maximum: 9999 - minimum: -9999 - mdsteps_cool2: - default: 1000 - type: number - maximum: 9999 - minimum: -9999 - mdsteps_cool3: - default: 1000 + mrswi_hot: + default: 0.5 type: number maximum: 9999 minimum: -9999 - timestep: - default: 0.002 + mrswi_cool1: + default: 0.5 type: number maximum: 9999 minimum: -9999 - tadfactor: - default: 8 + mrswi_cool2: + default: 0.5 type: number maximum: 9999 minimum: -9999 - sinter_rigid_init: - default: 0.001 + mrswi_cool3: + default: 0.5 type: number maximum: 9999 minimum: -9999 - sinter_rigid_final: - default: 0.001 + rswi_hot: + default: 0.5 type: number maximum: 9999 minimum: -9999 - sinter_cool2_init: - default: 0.001 + rswi_cool1: + default: 0.5 type: number maximum: 9999 minimum: -9999 - sinter_cool2_final: - default: 1.0 + rswi_cool2: + default: 0.5 type: number maximum: 9999 minimum: -9999 - sinter_cool3_init: - default: 0.05 + rswi_cool3: + default: 0.5 type: number maximum: 9999 minimum: -9999 - sinter_cool3_final: - default: 1.0 + masy_hot: + default: -1.0 type: number maximum: 9999 minimum: -9999 - temp_high: - default: 2000 + masy_cool1: + default: -1.0 type: number maximum: 9999 minimum: -9999 - temp_cool1_init: - default: 2000 + masy_cool2: + default: -0.1 type: number maximum: 9999 minimum: -9999 - temp_cool1_final: - default: 500 + masy_cool3: + default: -0.1 type: number maximum: 9999 minimum: -9999 - temp_cool2_init: - default: 1000 + asy_hot: + default: 1.0 type: number maximum: 9999 minimum: -9999 - temp_cool2_final: - default: 50 + asy_cool1: + default: 1.0 type: number maximum: 9999 minimum: -9999 - temp_cool3_init: - default: 1000 + asy_cool2: + default: 0.1 type: number maximum: 9999 minimum: -9999 - temp_cool3_final: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - shape_1: - default: false - type: boolean - shape_2: - default: false - type: boolean - shape_3: - default: false - type: boolean - shape_4: - default: false - type: boolean - shape_5: - default: false - type: boolean - shape_6: - default: false - type: boolean - shape_7: - default: false - type: boolean - shape_8: - default: false - type: boolean - shape_9: - default: false - type: boolean - shape_10: - default: false - type: boolean - shape_11: - default: false - type: boolean - shape_12: - default: false - type: boolean - shape_13: - default: false - type: boolean - shape_14: - default: false - type: boolean - shape_15: - default: false - type: boolean - shape_16: - default: false - type: boolean - shape_17: - default: false - type: boolean - shape_18: - default: false - type: boolean - shape_19: - default: false - type: boolean - shape_20: - default: false - type: boolean - amb_hot: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - amb_cool1: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - amb_cool2: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - amb_cool3: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - unamb_hot: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - unamb_cool1: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - unamb_cool2: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - unamb_cool3: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - hbond_hot: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - hbond_cool1: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - hbond_cool2: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - hbond_cool3: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - hbonds_on: - default: false - type: boolean - noecv: - default: false - type: boolean - ncvpart: - default: 2 - type: number - maximum: 9999 - minimum: -9999 - mrswi_hot: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - mrswi_cool1: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - mrswi_cool2: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - mrswi_cool3: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - rswi_hot: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - rswi_cool1: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - rswi_cool2: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - rswi_cool3: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - masy_hot: - default: -1.0 - type: number - maximum: 9999 - minimum: -9999 - masy_cool1: - default: -1.0 - type: number - maximum: 9999 - minimum: -9999 - masy_cool2: - default: -0.1 - type: number - maximum: 9999 - minimum: -9999 - masy_cool3: - default: -0.1 - type: number - maximum: 9999 - minimum: -9999 - asy_hot: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - asy_cool1: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - asy_cool2: - default: 0.1 - type: number - maximum: 9999 - minimum: -9999 - asy_cool3: - default: 0.1 - type: number - maximum: 9999 - minimum: -9999 - cmrest: - default: false - type: boolean - cmtight: - default: false - type: boolean - ranair: - default: false - type: boolean - kcont: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - ksurf: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - surfrest: - default: false - type: boolean - dihedrals_on: - default: false - type: boolean - dihedrals_hot: - default: 5 - type: number - maximum: 9999 - minimum: -9999 - dihedrals_cool1: - default: 5 - type: number - maximum: 9999 - minimum: -9999 - dihedrals_cool2: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - dihedrals_cool3: - default: 200 - type: number - maximum: 9999 - minimum: -9999 - ssdihed: - default: none - type: string - minLength: 0 - maxLength: 100 - error_dih: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - dnarest_on: - default: false - type: boolean - sym_on: - default: false - type: boolean - ksym: - default: 10.0 - type: number - maximum: 9999 - minimum: -9999 - numc2sym: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - c2sym_sta1_1: - type: number - maximum: 9999 - minimum: -9999 - c2sym_end1_1: - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg1_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c2sym_sta2_1: - type: number - maximum: 9999 - minimum: -9999 - c2sym_end2_1: - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg2_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - numc3sym: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - c3sym_sta1_1: - type: number - maximum: 9999 - minimum: -9999 - c3sym_end1_1: - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg1_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c3sym_sta2_1: - type: number - maximum: 9999 - minimum: -9999 - c3sym_end2_1: - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg2_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c3sym_sta3_1: - type: number - maximum: 9999 - minimum: -9999 - c3sym_end3_1: - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg3_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - numc4sym: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - c4sym_sta1_1: - type: number - maximum: 9999 - minimum: -9999 - c4sym_end1_1: - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg1_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c4sym_sta2_1: - type: number - maximum: 9999 - minimum: -9999 - c4sym_end2_1: - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg2_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c4sym_sta3_1: - type: number - maximum: 9999 - minimum: -9999 - c4sym_end3_1: - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg3_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c4sym_sta4_1: - type: number - maximum: 9999 - minimum: -9999 - c4sym_end4_1: - type: number - maximum: 9999 - minimum: -9999 - c4sym_seg4_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - numc5sym: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - c5sym_sta1_1: - type: number - maximum: 9999 - minimum: -9999 - c5sym_end1_1: - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg1_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c5sym_sta2_1: - type: number - maximum: 9999 - minimum: -9999 - c5sym_end2_1: - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg2_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c5sym_sta3_1: - type: number - maximum: 9999 - minimum: -9999 - c5sym_end3_1: - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg3_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c5sym_sta4_1: - type: number - maximum: 9999 - minimum: -9999 - c5sym_end4_1: - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg4_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c5sym_sta5_1: - type: number - maximum: 9999 - minimum: -9999 - c5sym_end5_1: - type: number - maximum: 9999 - minimum: -9999 - c5sym_seg5_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - numc6sym: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - c6sym_sta1_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_end1_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg1_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c6sym_sta2_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_end2_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg2_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c6sym_sta3_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_end3_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg3_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c6sym_sta4_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_end4_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg4_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c6sym_sta5_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_end5_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg5_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c6sym_sta6_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_end6_1: - type: number - maximum: 9999 - minimum: -9999 - c6sym_seg6_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - nums3sym: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - s3sym_sta1_1: - type: number - maximum: 9999 - minimum: -9999 - s3sym_end1_1: - type: number - maximum: 9999 - minimum: -9999 - s3sym_seg1_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - s3sym_sta2_1: - type: number - maximum: 9999 - minimum: -9999 - s3sym_end2_1: - type: number - 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maximum: 9999 - minimum: -9999 - int_11_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_18_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_18_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_18_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_19_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_19_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_20_20: - default: 1.0 + asy_cool3: + default: 0.1 type: number maximum: 9999 minimum: -9999 + elecflag: + default: true + title: Include electrostatics energy + description: Include electrostatics energy during the calculations. + $comment: Include electrostatics energy during the calculations. If set to + false electrostatics will not be considered. + type: boolean + 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: + mol_shape_1: + ui:group: molecule + mol_shape_2: + ui:group: molecule + mol_shape_3: + ui:group: molecule + mol_shape_4: + ui:group: molecule + mol_shape_5: + ui:group: molecule + mol_shape_6: + ui:group: molecule + mol_shape_7: + ui:group: molecule + mol_shape_8: + ui:group: molecule + mol_shape_9: + ui:group: molecule + mol_shape_10: + ui:group: molecule + mol_shape_11: + ui:group: molecule + mol_shape_12: + ui:group: molecule + mol_shape_13: + ui:group: molecule + mol_shape_14: + ui:group: molecule + mol_shape_15: + ui:group: molecule + mol_shape_16: + ui:group: molecule + mol_shape_17: + ui:group: molecule + mol_shape_18: + ui:group: molecule + mol_shape_19: + ui:group: molecule + mol_shape_20: + ui:group: molecule ambig_fname: ui:widget: file + ui:group: distance restraints unambig_fname: ui:widget: file - dihe_fname: - ui:widget: file + ui:group: distance restraints hbond_fname: ui:widget: file - ligand_param_fname: - ui:widget: file - ligand_top_fname: + 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 - id: mdref category: refinement label: HADDOCK3 module for water refinement. @@ -4633,121 +2460,121 @@ nodes: schema: type: object properties: - shape_1: + mol_shape_1: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_2: + mol_shape_2: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_3: + mol_shape_3: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_4: + mol_shape_4: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_5: + mol_shape_5: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_6: + mol_shape_6: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_7: + mol_shape_7: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_8: + mol_shape_8: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_9: + mol_shape_9: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_10: + mol_shape_10: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_11: + mol_shape_11: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_12: + mol_shape_12: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_13: + mol_shape_13: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_14: + mol_shape_14: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_15: + mol_shape_15: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_16: + mol_shape_16: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_17: + mol_shape_17: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_18: + mol_shape_18: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_19: + mol_shape_19: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_20: + mol_shape_20: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. @@ -4790,16 +2617,6 @@ 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: default: none title: Define automatically backbone dihedral angle restraints @@ -4828,8 +2645,8 @@ 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 @@ -4847,17 +2664,6 @@ nodes: $comment: Include electrostatics energy during the calculations. If set to false electrostatics will not be considered. type: boolean - dihedflag: - default: true - type: boolean - sampling: - default: 200 - title: Number of models to generate - description: Number of MD refined models to generate - $comment: Number of MD refined models to generate - type: number - maximum: 50000 - minimum: 1 solvent: default: water title: Solvent @@ -4875,45 +2681,45 @@ nodes: required: [] additionalProperties: false uiSchema: - shape_1: + mol_shape_1: ui:group: molecule - shape_2: + mol_shape_2: ui:group: molecule - shape_3: + mol_shape_3: ui:group: molecule - shape_4: + mol_shape_4: ui:group: molecule - shape_5: + mol_shape_5: ui:group: molecule - shape_6: + mol_shape_6: ui:group: molecule - shape_7: + mol_shape_7: ui:group: molecule - shape_8: + mol_shape_8: ui:group: molecule - shape_9: + mol_shape_9: ui:group: molecule - shape_10: + mol_shape_10: ui:group: molecule - shape_11: + mol_shape_11: ui:group: molecule - shape_12: + mol_shape_12: ui:group: molecule - shape_13: + mol_shape_13: ui:group: molecule - shape_14: + mol_shape_14: ui:group: molecule - shape_15: + mol_shape_15: ui:group: molecule - shape_16: + mol_shape_16: ui:group: molecule - shape_17: + mol_shape_17: ui:group: molecule - shape_18: + mol_shape_18: ui:group: molecule - shape_19: + mol_shape_19: ui:group: molecule - shape_20: + mol_shape_20: ui:group: molecule ambig_fname: ui:widget: file @@ -4929,8 +2735,6 @@ nodes: ui:group: dihedral restraints dihedrals_on: ui:group: dihedral restraints - dihedrals_scale: - ui:group: dihedral restraints ssdihed: ui:group: dihedral restraints error_dih: @@ -4939,8 +2743,6 @@ nodes: ui:group: other restraints elecflag: ui:group: force field - sampling: - ui:group: sampling - id: emref category: refinement label: HADDOCK3 module for energy minimization refinement. @@ -4948,121 +2750,121 @@ nodes: schema: type: object properties: - shape_1: + mol_shape_1: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_2: + mol_shape_2: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_3: + mol_shape_3: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_4: + mol_shape_4: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_5: + mol_shape_5: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_6: + mol_shape_6: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_7: + mol_shape_7: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_8: + mol_shape_8: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_9: + mol_shape_9: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_10: + mol_shape_10: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_11: + mol_shape_11: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_12: + mol_shape_12: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_13: + mol_shape_13: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_14: + mol_shape_14: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_15: + mol_shape_15: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_16: + mol_shape_16: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_17: + mol_shape_17: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_18: + mol_shape_18: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_19: + mol_shape_19: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_20: + mol_shape_20: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. @@ -5176,45 +2978,45 @@ nodes: required: [] additionalProperties: false uiSchema: - shape_1: + mol_shape_1: ui:group: molecule - shape_2: + mol_shape_2: ui:group: molecule - shape_3: + mol_shape_3: ui:group: molecule - shape_4: + mol_shape_4: ui:group: molecule - shape_5: + mol_shape_5: ui:group: molecule - shape_6: + mol_shape_6: ui:group: molecule - shape_7: + mol_shape_7: ui:group: molecule - shape_8: + mol_shape_8: ui:group: molecule - shape_9: + mol_shape_9: ui:group: molecule - shape_10: + mol_shape_10: ui:group: molecule - shape_11: + mol_shape_11: ui:group: molecule - shape_12: + mol_shape_12: ui:group: molecule - shape_13: + mol_shape_13: ui:group: molecule - shape_14: + mol_shape_14: ui:group: molecule - shape_15: + mol_shape_15: ui:group: molecule - shape_16: + mol_shape_16: ui:group: molecule - shape_17: + mol_shape_17: ui:group: molecule - shape_18: + mol_shape_18: ui:group: molecule - shape_19: + mol_shape_19: ui:group: molecule - shape_20: + mol_shape_20: ui:group: molecule ambig_fname: ui:widget: file diff --git a/public/catalog/haddock3.expert.yaml b/public/catalog/haddock3.expert.yaml index 139baa43..dab2cf74 100644 --- a/public/catalog/haddock3.expert.yaml +++ b/public/catalog/haddock3.expert.yaml @@ -304,241 +304,241 @@ nodes: schema: type: object properties: - fix_origin_1: + mol_fix_origin_1: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_2: + mol_fix_origin_2: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_3: + mol_fix_origin_3: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_4: + mol_fix_origin_4: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_5: + mol_fix_origin_5: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_6: + mol_fix_origin_6: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_7: + mol_fix_origin_7: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_8: + mol_fix_origin_8: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_9: + mol_fix_origin_9: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_10: + mol_fix_origin_10: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_11: + mol_fix_origin_11: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_12: + mol_fix_origin_12: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_13: + mol_fix_origin_13: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_14: + mol_fix_origin_14: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_15: + mol_fix_origin_15: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_16: + mol_fix_origin_16: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_17: + mol_fix_origin_17: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_18: + mol_fix_origin_18: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_19: + mol_fix_origin_19: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_20: + mol_fix_origin_20: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - shape_1: + mol_shape_1: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_2: + mol_shape_2: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_3: + mol_shape_3: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_4: + mol_shape_4: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_5: + mol_shape_5: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_6: + mol_shape_6: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_7: + mol_shape_7: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_8: + mol_shape_8: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_9: + mol_shape_9: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_10: + mol_shape_10: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_11: + mol_shape_11: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_12: + mol_shape_12: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_13: + mol_shape_13: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_14: + mol_shape_14: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_15: + mol_shape_15: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_16: + mol_shape_16: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_17: + mol_shape_17: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_18: + mol_shape_18: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_19: + mol_shape_19: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_20: + mol_shape_20: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. @@ -684,7 +684,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_1_1: + rair_sta_1_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -713,7 +713,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_2_1: + rair_sta_2_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -742,7 +742,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_3_1: + rair_sta_3_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -771,7 +771,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_4_1: + rair_sta_4_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -800,7 +800,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_5_1: + rair_sta_5_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -829,7 +829,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_6_1: + rair_sta_6_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -858,7 +858,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_7_1: + rair_sta_7_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -887,7 +887,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_8_1: + rair_sta_8_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -916,7 +916,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_9_1: + rair_sta_9_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -945,7 +945,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_10_1: + rair_sta_10_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -974,7 +974,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_11_1: + rair_sta_11_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1003,7 +1003,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_12_1: + rair_sta_12_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1032,7 +1032,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_13_1: + rair_sta_13_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1061,7 +1061,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_14_1: + rair_sta_14_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1090,7 +1090,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_15_1: + rair_sta_15_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1119,7 +1119,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_16_1: + rair_sta_16_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1148,7 +1148,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_17_1: + rair_sta_17_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1177,7 +1177,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_18_1: + rair_sta_18_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1206,7 +1206,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_19_1: + rair_sta_19_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1235,7 +1235,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_20_1: + rair_sta_20_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -2119,85 +2119,85 @@ nodes: required: [] additionalProperties: false uiSchema: - fix_origin_1: + mol_fix_origin_1: ui:group: molecule - fix_origin_2: + mol_fix_origin_2: ui:group: molecule - fix_origin_3: + mol_fix_origin_3: ui:group: molecule - fix_origin_4: + mol_fix_origin_4: ui:group: molecule - fix_origin_5: + mol_fix_origin_5: ui:group: molecule - fix_origin_6: + mol_fix_origin_6: ui:group: molecule - fix_origin_7: + mol_fix_origin_7: ui:group: molecule - fix_origin_8: + mol_fix_origin_8: ui:group: molecule - fix_origin_9: + mol_fix_origin_9: ui:group: molecule - fix_origin_10: + mol_fix_origin_10: ui:group: molecule - fix_origin_11: + mol_fix_origin_11: ui:group: molecule - fix_origin_12: + mol_fix_origin_12: ui:group: molecule - fix_origin_13: + mol_fix_origin_13: ui:group: molecule - fix_origin_14: + mol_fix_origin_14: ui:group: molecule - fix_origin_15: + mol_fix_origin_15: ui:group: molecule - fix_origin_16: + mol_fix_origin_16: ui:group: molecule - fix_origin_17: + mol_fix_origin_17: ui:group: molecule - fix_origin_18: + mol_fix_origin_18: ui:group: molecule - fix_origin_19: + mol_fix_origin_19: ui:group: molecule - fix_origin_20: + mol_fix_origin_20: ui:group: molecule - shape_1: + mol_shape_1: ui:group: molecule - shape_2: + mol_shape_2: ui:group: molecule - shape_3: + mol_shape_3: ui:group: molecule - shape_4: + mol_shape_4: ui:group: molecule - shape_5: + mol_shape_5: ui:group: molecule - shape_6: + mol_shape_6: ui:group: molecule - shape_7: + mol_shape_7: ui:group: molecule - shape_8: + mol_shape_8: ui:group: molecule - shape_9: + mol_shape_9: ui:group: molecule - shape_10: + mol_shape_10: ui:group: molecule - shape_11: + mol_shape_11: ui:group: molecule - shape_12: + mol_shape_12: ui:group: molecule - shape_13: + mol_shape_13: ui:group: molecule - shape_14: + mol_shape_14: ui:group: molecule - shape_15: + mol_shape_15: ui:group: molecule - shape_16: + mol_shape_16: ui:group: molecule - shape_17: + mol_shape_17: ui:group: molecule - shape_18: + mol_shape_18: ui:group: molecule - shape_19: + mol_shape_19: ui:group: molecule - shape_20: + mol_shape_20: ui:group: molecule ambig_fname: ui:widget: file @@ -2228,121 +2228,121 @@ nodes: ui:group: ab initio mode nrair_1: ui:group: ab initio mode - rair_start_1_1: + rair_sta_1_1: ui:group: ab initio mode rair_end_1_1: ui:group: ab initio mode nrair_2: ui:group: ab initio mode - rair_start_2_1: + rair_sta_2_1: ui:group: ab initio mode rair_end_2_1: ui:group: ab initio mode nrair_3: ui:group: ab initio mode - rair_start_3_1: + rair_sta_3_1: ui:group: ab initio mode rair_end_3_1: ui:group: ab initio mode nrair_4: ui:group: ab initio mode - rair_start_4_1: + rair_sta_4_1: ui:group: ab initio mode rair_end_4_1: ui:group: ab initio mode nrair_5: ui:group: ab initio mode - rair_start_5_1: + rair_sta_5_1: ui:group: ab initio mode rair_end_5_1: ui:group: ab initio mode nrair_6: ui:group: ab initio mode - rair_start_6_1: + rair_sta_6_1: ui:group: ab initio mode rair_end_6_1: ui:group: ab initio mode nrair_7: ui:group: ab initio mode - rair_start_7_1: + rair_sta_7_1: ui:group: ab initio mode rair_end_7_1: ui:group: ab initio mode nrair_8: ui:group: ab initio mode - rair_start_8_1: + rair_sta_8_1: ui:group: ab initio mode rair_end_8_1: ui:group: ab initio mode nrair_9: ui:group: ab initio mode - rair_start_9_1: + rair_sta_9_1: ui:group: ab initio mode rair_end_9_1: ui:group: ab initio mode nrair_10: ui:group: ab initio mode - rair_start_10_1: + rair_sta_10_1: ui:group: ab initio mode rair_end_10_1: ui:group: ab initio mode nrair_11: ui:group: ab initio mode - rair_start_11_1: + rair_sta_11_1: ui:group: ab initio mode rair_end_11_1: ui:group: ab initio mode nrair_12: ui:group: ab initio mode - rair_start_12_1: + rair_sta_12_1: ui:group: ab initio mode rair_end_12_1: ui:group: ab initio mode nrair_13: ui:group: ab initio mode - rair_start_13_1: + rair_sta_13_1: ui:group: ab initio mode rair_end_13_1: ui:group: ab initio mode nrair_14: ui:group: ab initio mode - rair_start_14_1: + rair_sta_14_1: ui:group: ab initio mode rair_end_14_1: ui:group: ab initio mode nrair_15: ui:group: ab initio mode - rair_start_15_1: + rair_sta_15_1: ui:group: ab initio mode rair_end_15_1: ui:group: ab initio mode nrair_16: ui:group: ab initio mode - rair_start_16_1: + rair_sta_16_1: ui:group: ab initio mode rair_end_16_1: ui:group: ab initio mode nrair_17: ui:group: ab initio mode - rair_start_17_1: + rair_sta_17_1: ui:group: ab initio mode rair_end_17_1: ui:group: ab initio mode nrair_18: ui:group: ab initio mode - rair_start_18_1: + rair_sta_18_1: ui:group: ab initio mode rair_end_18_1: ui:group: ab initio mode nrair_19: ui:group: ab initio mode - rair_start_19_1: + rair_sta_19_1: ui:group: ab initio mode rair_end_19_1: ui:group: ab initio mode nrair_20: ui:group: ab initio mode - rair_start_20_1: + rair_sta_20_1: ui:group: ab initio mode rair_end_20_1: ui:group: ab initio mode @@ -4180,2538 +4180,3184 @@ nodes: schema: type: object properties: - tolerance: - default: 5 - type: number - maximum: 9999 - minimum: -9999 - log_level: - default: verbose - type: string - minLength: 0 - maxLength: 100 - ambig_fname: - type: string - format: uri-reference - unambig_fname: - type: string - format: uri-reference - dihe_fname: - type: string - format: uri-reference - hbond_fname: - type: string - format: uri-reference - ligand_param_fname: - type: string - format: uri-reference - ligand_top_fname: - type: string - format: uri-reference - sampling_factor: - default: 1 - type: number - maximum: 9999 - minimum: -9999 - iniseed: - default: 917 - type: number - maximum: 9999 - minimum: -9999 - keepwater: + mol_fix_origin_1: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - mdsteps_rigid: - default: 500 - type: number - maximum: 9999 - minimum: -9999 - mdsteps_cool1: - default: 500 - type: number - maximum: 9999 - minimum: -9999 - mdsteps_cool2: - default: 1000 - type: number - maximum: 9999 - minimum: -9999 - mdsteps_cool3: - default: 1000 - type: number - maximum: 9999 - minimum: -9999 - timestep: - default: 0.002 - type: number - maximum: 9999 - minimum: -9999 - tadfactor: - default: 8 - type: number - maximum: 9999 - minimum: -9999 - sinter_rigid_init: - default: 0.001 - type: number - maximum: 9999 - minimum: -9999 - sinter_rigid_final: - default: 0.001 - type: number - maximum: 9999 - minimum: -9999 - sinter_cool2_init: - default: 0.001 - type: number - maximum: 9999 - minimum: -9999 - sinter_cool2_final: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - sinter_cool3_init: - default: 0.05 - type: number - maximum: 9999 - minimum: -9999 - sinter_cool3_final: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - temp_high: - default: 2000 - type: number - maximum: 9999 - minimum: -9999 - temp_cool1_init: - default: 2000 - type: number - maximum: 9999 - minimum: -9999 - temp_cool1_final: - default: 500 - type: number - maximum: 9999 - minimum: -9999 - temp_cool2_init: - default: 1000 - type: number - maximum: 9999 - minimum: -9999 - temp_cool2_final: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - temp_cool3_init: - default: 1000 - type: number - maximum: 9999 - minimum: -9999 - temp_cool3_final: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - shape_1: + mol_fix_origin_2: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_2: + mol_fix_origin_3: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_3: + mol_fix_origin_4: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_4: + mol_fix_origin_5: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_5: + mol_fix_origin_6: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_6: + mol_fix_origin_7: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_7: + mol_fix_origin_8: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_8: + mol_fix_origin_9: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_9: + mol_fix_origin_10: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_10: + mol_fix_origin_11: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_11: + mol_fix_origin_12: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_12: + mol_fix_origin_13: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_13: + mol_fix_origin_14: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_14: + mol_fix_origin_15: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_15: + mol_fix_origin_16: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_16: + mol_fix_origin_17: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_17: + mol_fix_origin_18: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_18: + mol_fix_origin_19: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_19: + mol_fix_origin_20: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_20: + mol_shape_1: default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - amb_hot: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - amb_cool1: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - amb_cool2: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - amb_cool3: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - unamb_hot: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - unamb_cool1: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - unamb_cool2: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - unamb_cool3: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - hbond_hot: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - hbond_cool1: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - hbond_cool2: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - hbond_cool3: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - hbonds_on: + mol_shape_2: default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - noecv: + mol_shape_3: default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - ncvpart: - default: 2 - type: number - maximum: 9999 - minimum: -9999 - mrswi_hot: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - mrswi_cool1: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - mrswi_cool2: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - mrswi_cool3: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - rswi_hot: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - rswi_cool1: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - rswi_cool2: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - rswi_cool3: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - masy_hot: - default: -1.0 - type: number - maximum: 9999 - minimum: -9999 - masy_cool1: - default: -1.0 - type: number - maximum: 9999 - minimum: -9999 - masy_cool2: - default: -0.1 - type: number - maximum: 9999 - minimum: -9999 - masy_cool3: - default: -0.1 - type: number - maximum: 9999 - minimum: -9999 - asy_hot: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - asy_cool1: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - asy_cool2: - default: 0.1 - type: number - maximum: 9999 - minimum: -9999 - asy_cool3: - default: 0.1 - type: number - maximum: 9999 - minimum: -9999 - cmrest: + mol_shape_4: default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - cmtight: + mol_shape_5: default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - ranair: + mol_shape_6: default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - kcont: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - ksurf: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - surfrest: + mol_shape_7: default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - dihedrals_on: + mol_shape_8: default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - dihedrals_hot: - default: 5 - type: number - maximum: 9999 - minimum: -9999 - dihedrals_cool1: - default: 5 - type: number - maximum: 9999 - minimum: -9999 - dihedrals_cool2: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - dihedrals_cool3: - default: 200 - type: number - maximum: 9999 - minimum: -9999 - ssdihed: - default: none - type: string - minLength: 0 - maxLength: 100 - error_dih: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - dnarest_on: + mol_shape_9: default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - sym_on: + mol_shape_10: default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - ksym: - default: 10.0 - type: number - maximum: 9999 - minimum: -9999 - numc2sym: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - c2sym_sta1_1: - type: number - maximum: 9999 - minimum: -9999 - c2sym_end1_1: - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg1_1: - default: '' + mol_shape_11: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_12: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_13: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_14: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_15: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_16: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_17: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_18: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_19: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_20: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + 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 - minLength: 0 - maxLength: 100 - c2sym_sta2_1: - type: number - maximum: 9999 - minimum: -9999 - c2sym_end2_1: - type: number - maximum: 9999 - minimum: -9999 - c2sym_seg2_1: - default: '' + 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 - minLength: 0 - maxLength: 100 - numc3sym: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - c3sym_sta1_1: - type: number - maximum: 9999 - minimum: -9999 - c3sym_end1_1: - type: number - maximum: 9999 - minimum: -9999 - c3sym_seg1_1: - default: '' + 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 - minLength: 0 - maxLength: 100 - c3sym_sta2_1: + format: uri-reference + amb_hot: + default: 10 + title: Hot phase SA force constant for ambiguous distance restraints + description: Force constant applied to the distance restraints defined in + ambig_fname during the hot phase of the SA. + $comment: Force constant applied to the distance restraints defined in ambig_fname + during the initial hot phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c3sym_end2_1: + maximum: 1000 + minimum: 0 + amb_cool1: + default: 10 + title: First cooling SA force constant for ambiguous distance restraints + description: Force constant applied to the distance restraints defined in + ambig_fname during the first cooling phase of the SA. + $comment: Force constant applied to the distance restraints defined in ambig_fname + during the first cooling phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c3sym_seg2_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c3sym_sta3_1: + maximum: 1000 + minimum: 0 + amb_cool2: + default: 50 + title: Second cooling SA force constant for ambiguous distance restraints + description: Force constant applied to the distance restraints defined in + ambig_fname during the second cooling phase of the SA. + $comment: Force constant applied to the distance restraints defined in ambig_fname + during the second cooling phase of the simulatd annealing protocol. Side-chains + at the interface are treated as flexible and any region defined in fully + flexible segments as fully flexible (see nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c3sym_end3_1: + maximum: 1000 + minimum: 0 + amb_cool3: + default: 50 + title: Third cooling SA force constant for ambiguous distance restraints + description: Force constant applied to the distance restraints defined in + ambig_fname during the third cooling phase of the SA. + $comment: Force constant applied to the distance restraints defined in ambig_fname + during the third cooling phase of the simulatd annealing protocol. Side-chains + and backbone at the interface are treated as flexible and any region defined + in fully flexible segments as fully flexible (see nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c3sym_seg3_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - numc4sym: - default: 0 + maximum: 1000 + minimum: 0 + unamb_hot: + default: 10 + title: Hot phase SA force constant for unambiguous distance restraints + description: Force constant applied to the distance restraints defined in + unambig_fname during the hot phase of the SA. + $comment: Force constant applied to the distance restraints defined in unambig_fname + during the initial hot phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c4sym_sta1_1: + maximum: 1000 + minimum: 0 + unamb_cool1: + default: 10 + title: Hot phase SA force constant for unambiguous distance restraints + description: Force constant applied to the distance restraints defined in + unambig_fname during the hot phase of the SA. + $comment: Force constant applied to the distance restraints defined in unambig_fname + during the initial hot phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c4sym_end1_1: + maximum: 1000 + minimum: 0 + unamb_cool2: + default: 50 + title: Hot phase SA force constant for unambiguous distance restraints + description: Force constant applied to the distance restraints defined in + ambig_fname during the hot phase of the SA. + $comment: Force constant applied to the distance restraints defined in unambig_fname + during the initial hot phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c4sym_seg1_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c4sym_sta2_1: + maximum: 1000 + minimum: 0 + unamb_cool3: + default: 50 + title: Hot phase SA force constant for unambiguous distance restraints + description: Force constant applied to the distance restraints defined in + unambig_fname during the hot phase of the SA. + $comment: Force constant applied to the distance restraints defined in unambig_fname + during the initial hot phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c4sym_end2_1: + maximum: 1000 + minimum: 0 + hbond_hot: + default: 10 + title: Hot phase SA force constant for hbond distance restraints + description: Force constant applied to the hydrogen bond restraints defined + in hbond_fname during the hot phase of the SA. + $comment: Force constant applied to the hydrogen bond restraints defined in + hbond_fname during the initial hot phase of the simulatd annealing protocol. + Molecules are treated as rigid bodies unless fully flexible segments are + defined (see nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c4sym_seg2_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c4sym_sta3_1: + maximum: 1000 + minimum: 0 + hbond_cool1: + default: 10 + title: Hot phase SA force constant for hydrogen bond restraints + description: Force constant applied to the hydrogen bond restraints defined + in hbond_fname during the hot phase of the SA. + $comment: Force constant applied to the hydrogen bond restraints defined in + hbond_fname during the initial hot phase of the simulatd annealing protocol. + Molecules are treated as rigid bodies unless fully flexible segments are + defined (see nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c4sym_end3_1: + maximum: 1000 + minimum: 0 + hbond_cool2: + default: 50 + title: Hot phase SA force constant for hydrogen bond restraints + description: Force constant applied to the hydrogen bond restraints defined + in hbond_fname during the hot phase of the SA. + $comment: Force constant applied to the hydrogen bond restraints defined in + hbond_fname during the initial hot phase of the simulatd annealing protocol. + Molecules are treated as rigid bodies unless fully flexible segments are + defined (see nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c4sym_seg3_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c4sym_sta4_1: + maximum: 1000 + minimum: 0 + hbond_cool3: + default: 50 + title: Hot phase SA force constant for hydrogen bond restraints + description: Force constant applied to the hydrogen bond restraints defined + in hbond_fname during the hot phase of the SA. + $comment: Force constant applied to the hydrogen bond restraints defined in + hbond_fname during the initial hot phase of the simulatd annealing protocol. + Molecules are treated as rigid bodies unless fully flexible segments are + defined (see nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - c4sym_end4_1: + 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: 9999 - minimum: -9999 - c4sym_seg4_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - numc5sym: - default: 0 + 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: 9999 - minimum: -9999 - c5sym_sta1_1: + 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: 9999 - minimum: -9999 - c5sym_end1_1: + 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_hot: + default: 5 + title: Hot phase SA force constant for dihedral angle restraints + description: Hot phase SA force constant for dihedral angle restraints read + from dihe_fname. + $comment: Force constant applied to the dihedral angle restraints read from + dihe_fname during the initial hot phase of the simulatd annealing protocol. type: number - maximum: 9999 - minimum: -9999 - c5sym_seg1_1: - default: '' + maximum: 1000 + minimum: 0 + dihedrals_cool1: + default: 5 + title: First cooling SA force constant for dihedral angle restraints + description: First cooling SA force constant for dihedral angle restraints + read from dihe_fname. + $comment: Force constant applied to the dihedral angle restraints read from + dihe_fname during the first cooling phase of the simulatd annealing protocol. + type: number + maximum: 1000 + minimum: 0 + dihedrals_cool2: + default: 50 + title: Second cooling SA force constant for dihedral angle restraints + description: Second cooling SA force constant for dihedral angle restraints + read from dihe_fname. + $comment: Force constant applied to the dihedral angle restraints read from + dihe_fname during the second cooling phase of the simulatd annealing protocol. + type: number + maximum: 1000 + minimum: 0 + dihedrals_cool3: + default: 200 + title: Third cooling SA force constant for dihedral angle restraints + description: Third cooling SA force constant for dihedral angle restraints + read from dihe_fname. + $comment: Force constant applied to the dihedral angle restraints read from + dihe_fname during the third cooling phase of the simulatd annealing protocol. + type: number + maximum: 1000 + minimum: 0 + ssdihed: + default: none + title: Define automatically backbone dihedral angle restraints + description: If turned on, this option will automatically defined backbone + dihedral angle restraints for the selected regions. + $comment: This option allows to utomatically defined backbone dihedral angle + restraints for the selected regions. The restraints will be defined for + the phi and psi backbone dihedral angles of amino acids, with the target + value taken from the measured angle in the input structure, and the error + bound defined by the error_dih parameter. Those restraints can be applied + to the entire structure (all), the alpha/beta secondary structure elements + (alphabeta) or only to the alpha helical regions (alpha). Those are automatically + detected based on the measured dihedral angle combinations. type: string minLength: 0 maxLength: 100 - c5sym_sta2_1: + enum: + - none + - all + - alpha + - alphabeta + error_dih: + default: 10 + title: Force constant for backbone dihedral angle restraints + description: Force constant for backbone dihedral angle restraints (ssdihed + option) + $comment: Force constant for backbone dihedral angle restraints (ssdihed option) type: number maximum: 9999 minimum: -9999 - c5sym_end2_1: + 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 + mrswi_hot: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c5sym_seg2_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c5sym_sta3_1: + mrswi_cool1: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c5sym_end3_1: + mrswi_cool2: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c5sym_seg3_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c5sym_sta4_1: + mrswi_cool3: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c5sym_end4_1: + rswi_hot: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c5sym_seg4_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c5sym_sta5_1: + rswi_cool1: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c5sym_end5_1: + rswi_cool2: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c5sym_seg5_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - numc6sym: - default: 0 + rswi_cool3: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c6sym_sta1_1: + masy_hot: + default: -1.0 type: number maximum: 9999 minimum: -9999 - c6sym_end1_1: + masy_cool1: + default: -1.0 type: number maximum: 9999 minimum: -9999 - c6sym_seg1_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c6sym_sta2_1: + masy_cool2: + default: -0.1 type: number maximum: 9999 minimum: -9999 - c6sym_end2_1: + masy_cool3: + default: -0.1 type: number maximum: 9999 minimum: -9999 - c6sym_seg2_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c6sym_sta3_1: + asy_hot: + default: 1.0 type: number maximum: 9999 minimum: -9999 - c6sym_end3_1: + asy_cool1: + default: 1.0 type: number maximum: 9999 minimum: -9999 - c6sym_seg3_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c6sym_sta4_1: + asy_cool2: + default: 0.1 type: number maximum: 9999 minimum: -9999 - c6sym_end4_1: + asy_cool3: + default: 0.1 type: number maximum: 9999 minimum: -9999 - c6sym_seg4_1: - default: '' + sym_on: + default: false + title: Symmetry restraints + description: Enables symmetry restraints + $comment: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 + supported) and the segments to which those apply must be defined. In addition + a custom symmetry restraint file can be supplied (symrest_fname). + type: boolean + ksym: + default: 10.0 + title: Force constant for symmetry restraints + description: Force constant for symmetry restraints + $comment: Force constant for symmetry restraints + type: number + maximum: 1000 + minimum: 0 + symtbl_fname: + title: Custom symmetry restraints filename + description: Filename of the custom symmetry restraints file + $comment: Filename of the custom symmetry restraints file. type: string - minLength: 0 - maxLength: 100 - c6sym_sta5_1: + format: uri-reference + numc2sym: + default: 0 + title: Number of C2 symmetry restraints + description: Defines the number of C2 symmetry restraints. + $comment: Defines the number of C2 symmetry restraints. For each, a pair of + segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + type: number + maximum: 40 + minimum: 0 + c2sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first C2 symmetry segment + $comment: Residue number of first residue in the first C2 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_end5_1: + c2sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first C2 symmetry segment + $comment: Residue number of last residue in the first C2 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_seg5_1: + c2sym_seg1_1: default: '' + title: Segment ID of first C2 segment + description: Segment ID of first C2 segment + $comment: Segment ID of first C2 segment type: string minLength: 0 - maxLength: 100 - c6sym_sta6_1: + maxLength: 4 + c2sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second C2 symmetry segment + $comment: Residue number of first residue in the second C2 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_end6_1: + c2sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second C2 symmetry segment + $comment: Residue number of last residue in the second C2 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_seg6_1: + c2sym_seg2_1: default: '' + title: Segment ID of second C2 segment + description: Segment ID of second C2 segment + $comment: Segment ID of second C2 segment type: string minLength: 0 - maxLength: 100 - nums3sym: + maxLength: 4 + numc3sym: default: 0 + title: Number of C3 symmetry restraints + description: Defines the number of C3 symmetry restraints. + $comment: Defines the number of C3 symmetry restraints. For each, three segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - s3sym_sta1_1: + maximum: 10 + minimum: 0 + c3sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first C3 symmetry segment + $comment: Residue number of first residue in the first C3 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_end1_1: + c3sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first C3 symmetry segment + $comment: Residue number of last residue in the first C3 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_seg1_1: + c3sym_seg1_1: default: '' - type: string - minLength: 0 - maxLength: 100 - s3sym_sta2_1: + title: Segment ID of first C3 segment + description: Segment ID of first C3 segment + $comment: Segment ID of first C3 segment + type: string + minLength: 0 + maxLength: 4 + c3sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second C3 symmetry segment + $comment: Residue number of first residue in the second C3 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_end2_1: + c3sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second C3 symmetry segment + $comment: Residue number of last residue in the second C3 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_seg2_1: + c3sym_seg2_1: default: '' + title: Segment ID of second C3 segment + description: Segment ID of second C3 segment + $comment: Segment ID of second C3 segment type: string minLength: 0 - maxLength: 100 - s3sym_sta3_1: + maxLength: 4 + c3sym_sta3_1: + title: Residue number of first residue + description: Residue number of first residue in the third C3 symmetry segment + $comment: Residue number of first residue in the third C3 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_end3_1: + c3sym_end3_1: + title: Residue number of last residue + description: Residue number of last residue in the third C3 symmetry segment + $comment: Residue number of last residue in the third C3 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_seg3_1: + c3sym_seg3_1: default: '' + title: Segment ID of third C3 segment + description: Segment ID of third C3 segment + $comment: Segment ID of third C3 segment type: string minLength: 0 - maxLength: 100 - ncs_on: - default: false - type: boolean - kncs: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - numncs: + maxLength: 4 + numc4sym: default: 0 + title: Number of C4 symmetry restraints + description: Defines the number of C4 symmetry restraints. + $comment: Defines the number of C4 symmetry restraints. For each, four segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - ncs_sta1_1: + maximum: 10 + minimum: 0 + c4sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first C4 symmetry segment + $comment: Residue number of first residue in the first C4 symmetry segment type: number maximum: 9999 minimum: -9999 - ncs_end1_1: + c4sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first C4 symmetry segment + $comment: Residue number of last residue in the first C4 symmetry segment type: number maximum: 9999 minimum: -9999 - ncs_seg1_1: + c4sym_seg1_1: default: '' + title: Segment ID of first C4 segment + description: Segment ID of first C4 segment + $comment: Segment ID of first C4 segment type: string minLength: 0 - maxLength: 100 - ncs_sta2_1: + maxLength: 4 + c4sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second C4 symmetry segment + $comment: Residue number of first residue in the second C4 symmetry segment type: number maximum: 9999 minimum: -9999 - ncs_end2_1: + c4sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second C4 symmetry segment + $comment: Residue number of last residue in the second C4 symmetry segment type: number maximum: 9999 minimum: -9999 - ncs_seg2_1: + c4sym_seg2_1: default: '' + title: Segment ID of second C4 segment + description: Segment ID of second C4 segment + $comment: Segment ID of second C4 segment type: string minLength: 0 - maxLength: 100 - fix_origin_1: - default: false - type: boolean - fix_origin_2: - default: false - type: boolean - fix_origin_3: - default: false - type: boolean - fix_origin_4: - default: false - type: boolean - fix_origin_5: - default: false - type: boolean - fix_origin_6: - default: false - type: boolean - fix_origin_7: - default: false - type: boolean - fix_origin_8: - default: false - type: boolean - fix_origin_9: - default: false - type: boolean - fix_origin_10: - default: false - type: boolean - fix_origin_11: - default: false - type: boolean - fix_origin_12: - default: false - type: boolean - fix_origin_13: - default: false - type: boolean - fix_origin_14: - default: false - type: boolean - fix_origin_15: - default: false - type: boolean - fix_origin_16: - default: false - type: boolean - fix_origin_17: - default: false - type: boolean - fix_origin_18: - default: false - type: boolean - fix_origin_19: - default: false - type: boolean - fix_origin_20: - default: false - type: boolean - nfle1: - default: 0 + maxLength: 4 + c4sym_sta3_1: + title: Residue number of first residue + description: Residue number of first residue in the third C4 symmetry segment + $comment: Residue number of first residue in the third C4 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta1_1: + c4sym_end3_1: + title: Residue number of last residue + description: Residue number of last residue in the third C4 symmetry segment + $comment: Residue number of last residue in the third C4 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend1_1: + c4sym_seg3_1: + default: '' + title: Segment ID of third C4 segment + description: Segment ID of third C4 segment + $comment: Segment ID of third C4 segment + type: string + minLength: 0 + maxLength: 4 + c4sym_sta4_1: + title: Residue number of first residue + description: Residue number of first residue in the fourth C4 symmetry segment + $comment: Residue number of first residue in the fourth C4 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle2: - default: 0 + c4sym_end4_1: + title: Residue number of last residue + description: Residue number of last residue in the fourth C4 symmetry segment + $comment: Residue number of last residue in the fourth C4 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta2_1: + c4sym_seg4_1: + default: '' + title: Segment ID of fourth C4 segment + description: Segment ID of fourth C4 segment + $comment: Segment ID of fourth C4 segment + type: string + minLength: 0 + maxLength: 4 + numc5sym: + default: 0 + title: Number of C5 symmetry restraints + description: Defines the number of C5 symmetry restraints. + $comment: Defines the number of C5 symmetry restraints. For each, five segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - fleend2_1: + maximum: 10 + minimum: 0 + c5sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first C5 symmetry segment + $comment: Residue number of first residue in the first C5 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle3: - default: 0 + c5sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first C5 symmetry segment + $comment: Residue number of last residue in the first C5 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta3_1: + c5sym_seg1_1: + default: '' + title: Segment ID of first C5 segment + description: Segment ID of first C5 segment + $comment: Segment ID of first C5 segment + type: string + minLength: 0 + maxLength: 4 + c5sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second C5 symmetry segment + $comment: Residue number of first residue in the second C5 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend3_1: + c5sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second C5 symmetry segment + $comment: Residue number of last residue in the second C5 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle4: - default: 0 + c5sym_seg2_1: + default: '' + title: Segment ID of second C5 segment + description: Segment ID of second C5 segment + $comment: Segment ID of second C5 segment + type: string + minLength: 0 + maxLength: 4 + c5sym_sta3_1: + title: Residue number of first residue + description: Residue number of first residue in the third C5 symmetry segment + $comment: Residue number of first residue in the third C5 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta4_1: + c5sym_end3_1: + title: Residue number of last residue + description: Residue number of last residue in the third C5 symmetry segment + $comment: Residue number of last residue in the third C5 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend4_1: + c5sym_seg3_1: + default: '' + title: Segment ID of third C5 segment + description: Segment ID of third C5 segment + $comment: Segment ID of third C5 segment + type: string + minLength: 0 + maxLength: 4 + c5sym_sta4_1: + title: Residue number of first residue + description: Residue number of first residue in the fourth C5 symmetry segment + $comment: Residue number of first residue in the fourth C5 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle5: - default: 0 + c5sym_end4_1: + title: Residue number of last residue + description: Residue number of last residue in the fourth C5 symmetry segment + $comment: Residue number of last residue in the fourth C5 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta5_1: + c5sym_seg4_1: + default: '' + title: Segment ID of fourth C5 segment + description: Segment ID of fourth C5 segment + $comment: Segment ID of fourth C5 segment + type: string + minLength: 0 + maxLength: 4 + c5sym_sta5_1: + title: Residue number of first residue + description: Residue number of first residue in the fifth C5 symmetry segment + $comment: Residue number of first residue in the fifth C5 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend5_1: - type: number - maximum: 9999 - minimum: -9999 - nfle6: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - flesta6_1: - type: number - maximum: 9999 - minimum: -9999 - fleend6_1: + c5sym_end5_1: + title: Residue number of last residue + description: Residue number of last residue in the fifth C5 symmetry segment + $comment: Residue number of last residue in the fifth C5 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle7: + c5sym_seg5_1: + default: '' + title: Segment ID of fifth C5 segment + description: Segment ID of fifth C5 segment + $comment: Segment ID of fifth C5 segment + type: string + minLength: 0 + maxLength: 4 + numc6sym: default: 0 + title: Number of C6 symmetry restraints + description: Defines the number of C6 symmetry restraints. + $comment: Defines the number of C6 symmetry restraints. For each, six segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - flesta7_1: + maximum: 10 + minimum: 0 + c6sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first C6 symmetry segment + $comment: Residue number of first residue in the first C6 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend7_1: + c6sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first C6 symmetry segment + $comment: Residue number of last residue in the first C6 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle8: - default: 0 + c6sym_seg1_1: + default: '' + title: Segment ID of first C6 segment + description: Segment ID of first C6 segment + $comment: Segment ID of first C6 segment + type: string + minLength: 0 + maxLength: 4 + c6sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second C6 symmetry segment + $comment: Residue number of first residue in the second C6 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta8_1: + c6sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second C6 symmetry segment + $comment: Residue number of last residue in the second C6 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend8_1: + c6sym_seg2_1: + default: '' + title: Segment ID of second C6 segment + description: Segment ID of second C6 segment + $comment: Segment ID of second C6 segment + type: string + minLength: 0 + maxLength: 4 + c6sym_sta3_1: + title: Residue number of first residue + description: Residue number of first residue in the third C6 symmetry segment + $comment: Residue number of first residue in the third C6 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle9: - default: 0 + c6sym_end3_1: + title: Residue number of last residue + description: Residue number of last residue in the third C6 symmetry segment + $comment: Residue number of last residue in the third C6 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta9_1: + c6sym_seg3_1: + default: '' + title: Segment ID of third C6 segment + description: Segment ID of third C6 segment + $comment: Segment ID of third C6 segment + type: string + minLength: 0 + maxLength: 4 + c6sym_sta4_1: + title: Residue number of first residue + description: Residue number of first residue in the fourth C6 symmetry segment + $comment: Residue number of first residue in the fourth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend9_1: + c6sym_end4_1: + title: Residue number of last residue + description: Residue number of last residue in the fourth C6 symmetry segment + $comment: Residue number of last residue in the fourth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle10: - default: 0 + c6sym_seg4_1: + default: '' + title: Segment ID of fourth C6 segment + description: Segment ID of fourth C6 segment + $comment: Segment ID of fourth C6 segment + type: string + minLength: 0 + maxLength: 4 + c6sym_sta5_1: + title: Residue number of first residue + description: Residue number of first residue in the fifth C6 symmetry segment + $comment: Residue number of first residue in the fifth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta10_1: + c6sym_end5_1: + title: Residue number of last residue + description: Residue number of last residue in the fifth C6 symmetry segment + $comment: Residue number of last residue in the fifth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend10_1: + c6sym_seg5_1: + default: '' + title: Segment ID of fifth C6 segment + description: Segment ID of fifth C6 segment + $comment: Segment ID of fifth C6 segment + type: string + minLength: 0 + maxLength: 4 + c6sym_sta6_1: + title: Residue number of first residue + description: Residue number of first residue in the sixth C6 symmetry segment + $comment: Residue number of first residue in the sixth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle11: - default: 0 + c6sym_end6_1: + title: Residue number of last residue + description: Residue number of last residue in the sixth C6 symmetry segment + $comment: Residue number of last residue in the sixth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta11_1: + c6sym_seg6_1: + default: '' + title: Segment ID of sixth C6 segment + description: Segment ID of sixth C6 segment + $comment: Segment ID of sixth C6 segment + type: string + minLength: 0 + maxLength: 4 + nums3sym: + default: 0 + title: Number of S3 symmetry restraints + description: Defines the number of S3 symmetry restraints. + $comment: Defines the number of S3 symmetry restraints. For each, three segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - fleend11_1: + maximum: 10 + minimum: 0 + s3sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first S3 symmetry segment + $comment: Residue number of first residue in the first S3 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle12: - default: 0 + s3sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first S3 symmetry segment + $comment: Residue number of last residue in the first S3 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta12_1: + s3sym_seg1_1: + default: '' + title: Segment ID of first S3 segment + description: Segment ID of first S3 segment + $comment: Segment ID of first S3 segment + type: string + minLength: 0 + maxLength: 4 + s3sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second S3 symmetry segment + $comment: Residue number of first residue in the second S3 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend12_1: + s3sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second S3 symmetry segment + $comment: Residue number of last residue in the second S3 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle13: - default: 0 + s3sym_seg2_1: + default: '' + title: Segment ID of second S3 segment + description: Segment ID of second S3 segment + $comment: Segment ID of second S3 segment + type: string + minLength: 0 + maxLength: 4 + s3sym_sta3_1: + title: Residue number of first residue + description: Residue number of first residue in the third S3 symmetry segment + $comment: Residue number of first residue in the third S3 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta13_1: + s3sym_end3_1: + title: Residue number of last residue + description: Residue number of last residue in the third S3 symmetry segment + $comment: Residue number of last residue in the third S3 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend13_1: + s3sym_seg3_1: + default: '' + title: Segment ID of third S3 segment + description: Segment ID of third S3 segment + $comment: Segment ID of third S3 segment + type: string + minLength: 0 + maxLength: 4 + ncs_on: + default: false + title: Non-crystallographic symmetry restraints + description: Non-crystallographic symmetry restraints to ensure two molecules + will have the same conformation. + $comment: Non-crystallographic symmetry restraints to ensure two molecules + will have the same conformation. This does not apply any symmetry between + the two molecules but rather defines restraints such as the RMSD between + those is 0. + type: boolean + kncs: + default: 1.0 + title: Force constant for non-crystallographic restraints + description: Force constant for non-crystallographic restraints + $comment: Force constant for non-crystallographic restraints type: number - maximum: 9999 - minimum: -9999 - nfle14: + maximum: 1000 + minimum: 0 + numncs: default: 0 + title: Number of non-crystallographic symmetry restraints + description: Number of non-crystallographic symmetry restraints (NCS). + $comment: Number of non-crystallographic symmetry restraints. For each pairs + of segments will have to be defined. Note that those must contain exactly + the same residues/atom combinations. type: number - maximum: 9999 - minimum: -9999 - flesta14_1: + maximum: 100 + minimum: 0 + ncs_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first NCS segment + $comment: Residue number of first residue in the first NCS segment type: number maximum: 9999 minimum: -9999 - fleend14_1: + ncs_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first NCS segment + $comment: Residue number of last residue in the first NCS segment type: number maximum: 9999 minimum: -9999 - nfle15: - default: 0 + ncs_seg1_1: + default: '' + title: Segment ID of first NCS segment + description: Segment ID of first NCS segment + $comment: Segment ID of first NCS segment + type: string + minLength: 0 + maxLength: 100 + ncs_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second NCS segment + $comment: Residue number of first residue in the second NCS segment type: number maximum: 9999 minimum: -9999 - flesta15_1: + ncs_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second NCS segment + $comment: Residue number of last residue in the second NCS segment type: number maximum: 9999 minimum: -9999 - fleend15_1: + ncs_seg2_1: + default: '' + title: Segment ID of second NCS segment + description: Segment ID of second NCS segment + $comment: Segment ID of second NCS segment + type: string + minLength: 0 + maxLength: 100 + w_air: + default: 0.1 + title: Weight of the distance restraint energy + description: Weight of the distance restraints energy in the scoring function + $comment: Weight of the distance restraints energy in the scoring function. + Note that this is different from the force constants used during the calculations. type: number maximum: 9999 - minimum: -9999 - nfle16: - default: 0 + minimum: 0 + w_bsa: + default: -0.01 + title: Weight of the buried surface area term + description: Weight of the buried surface area term in the scoring function + $comment: Weight of the buried surface area (BSA) term in the scoring function. + Note that the BSA is only used for scoring. type: number maximum: 9999 minimum: -9999 - flesta16_1: + w_cdih: + default: 0.0 + title: Weight of the dihedral angle restraint energy + description: Weight of the dihedral angle restraints energy in the scoring + function + $comment: Weight of the dihedral angle restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. type: number maximum: 9999 - minimum: -9999 - fleend16_1: + 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 - nfle17: - default: 0 + w_elec: + default: 1.0 + title: Weight of the intermolecular electrostatic energy + description: Weight of the intermolecular electrostatic energy in the scoring + function + $comment: Weight of the intermolecular electrostatic energy in the scoring + function. Note that this does not affect the electostatic energy during + the MD refinement. type: number maximum: 9999 minimum: -9999 - flesta17_1: + w_sym: + default: 0.1 + title: Weight of the symmetry restraint energy + description: Weight of the symmetry restraints energy in the scoring function + $comment: Weight of the symmetry restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. type: number maximum: 9999 - minimum: -9999 - fleend17_1: + minimum: 0 + 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 MD refinement. type: number maximum: 9999 minimum: -9999 - nfle18: - default: 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 + format: uri-reference + ligand_top_fname: + title: Custom ligand topology file + description: Ligand topology file in CNS format + $comment: Ligand topology file in CNS format containing the ligand topologies + (atoms, masses, charges, bond definitions...) for any ligand not supported + by default by HADDOCK + type: string + format: uri-reference + elecflag: + default: true + title: Include electrostatics energy + description: Include electrostatics energy during the calculations. + $comment: Include electrostatics energy during the calculations. If set to + false electrostatics will not be considered. + type: boolean + dielec: + default: rdie + title: Constant (cdie) or distance-dependent dielectric (rdie) constant. + description: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. + $comment: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. A distance dependent dielectric + constant will effectively scale down the electrostatic energy by having + a 1/r**2 dependency instead of 1/r + type: string + minLength: 0 + maxLength: 4 + enum: + - cdie + - rdie + epsilon: + default: 1.0 + title: Dielectric constant + description: Dielectric constant for the electrostatic Coulomb energy term. + $comment: Dielectric constant for the electrostatic Coulomb energy term. type: number - maximum: 9999 - minimum: -9999 - flesta18_1: + maximum: 78 + minimum: 1 + 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. type: number - maximum: 9999 - minimum: -9999 - fleend18_1: + maximum: 1 + minimum: 1 + 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 - nfle19: - default: 0 + maximum: 10000 + minimum: 1 + mdsteps_rigid: + default: 500 + title: Hot phase SA MD steps + description: Number of MD steps for the hot phase of the SA. + $comment: Number of MD steps for the hot phase rigid body dynamics of the + simulated annealing protocol. type: number - maximum: 9999 - minimum: -9999 - flesta19_1: + maximum: 10000 + minimum: 0 + mdsteps_cool1: + default: 500 + title: First cooling phase SA MD steps + description: Number of MD steps for the first cooling phase of the SA. + $comment: Number of MD steps for the first cooling phase of rigid body dynamics + of the simulated annealing protocol. type: number - maximum: 9999 - minimum: -9999 - fleend19_1: + maximum: 10000 + minimum: 0 + mdsteps_cool2: + default: 1000 + title: Second cooling phase SA MD steps + description: Number of MD steps for the second cooling phase of the SA. + $comment: Number of MD steps for the second cooling phase of torsion angle + dynamics of the simulated annealing protocol with flexible side-chains at + the interface. Full flexibility is applied to the segments defined as fully + flexible (see nfle_X and related parameters). type: number - maximum: 9999 - minimum: -9999 - nfle20: - default: 0 + maximum: 10000 + minimum: 0 + mdsteps_cool3: + default: 1000 + title: Third cooling phase SA MD steps + description: Number of MD steps for the third cooling phase of the SA. + $comment: Number of MD steps for the third cooling phase of torsion angle + dynamics of the simulated annealing protocol with flexible side-chains and + backbone at the interface. Full flexibility is applied to the segments defined + as fully flexible (see nfle_X and related parameters). type: number - maximum: 9999 - minimum: -9999 - flesta20_1: + maximum: 10000 + minimum: 0 + 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: 9999 - minimum: -9999 - fleend20_1: + maximum: 1 + minimum: 1.0e-05 + tolerance: + default: 0 + title: Failure tolerance percentage + description: Percentage of allowed failures for a module to successfully complete + $comment: Percentage of allowed failures for a module to successfully complete type: number - maximum: 9999 - minimum: -9999 + maximum: 99 + minimum: 0 nseg1: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta1_1: + maximum: 1000 + minimum: -1 + seg_sta_1_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend1_1: + seg_end_1_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg2: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta2_1: + maximum: 1000 + minimum: -1 + seg_sta_2_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend2_1: + seg_end_2_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg3: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta3_1: + maximum: 1000 + minimum: -1 + seg_sta_3_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend3_1: + seg_end_3_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg4: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta4_1: + maximum: 1000 + minimum: -1 + seg_sta_4_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend4_1: + seg_end_4_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg5: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta5_1: + maximum: 1000 + minimum: -1 + seg_sta_5_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend5_1: + seg_end_5_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg6: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta6_1: + maximum: 1000 + minimum: -1 + seg_sta_6_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend6_1: + seg_end_6_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg7: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta7_1: + maximum: 1000 + minimum: -1 + seg_sta_7_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend7_1: + seg_end_7_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg8: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta8_1: + maximum: 1000 + minimum: -1 + seg_sta_8_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend8_1: + seg_end_8_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg9: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta9_1: + maximum: 1000 + minimum: -1 + seg_sta_9_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend9_1: + seg_end_9_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg10: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta10_1: + maximum: 1000 + minimum: -1 + seg_sta_10_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend10_1: + seg_end_10_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg11: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta11_1: + maximum: 1000 + minimum: -1 + seg_sta_11_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend11_1: + seg_end_11_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg12: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta12_1: + maximum: 1000 + minimum: -1 + seg_sta_12_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend12_1: + seg_end_12_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg13: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta13_1: + maximum: 1000 + minimum: -1 + seg_sta_13_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend13_1: + seg_end_13_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg14: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta14_1: + maximum: 1000 + minimum: -1 + seg_sta_14_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend14_1: + seg_end_14_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg15: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta15_1: + maximum: 1000 + minimum: -1 + seg_sta_15_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend15_1: + seg_end_15_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg16: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta16_1: + maximum: 1000 + minimum: -1 + seg_sta_16_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend16_1: + seg_end_16_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg17: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. + type: number + maximum: 1000 + minimum: -1 + seg_sta_17_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segsta17_1: - type: number - maximum: 9999 - minimum: -9999 - segend17_1: + seg_end_17_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg18: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta18_1: + maximum: 1000 + minimum: -1 + seg_sta_18_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend18_1: + seg_end_18_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg19: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta19_1: + maximum: 1000 + minimum: -1 + seg_sta_19_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend19_1: + seg_end_19_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg20: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta20_1: - type: number - maximum: 9999 - minimum: -9999 - segend20_1: + maximum: 1000 + minimum: -1 + seg_sta_20_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - w_air: - default: 0.1 + seg_end_20_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - w_bsa: - default: -0.01 + nfle1: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - w_cdih: - default: 0.0 + maximum: 1000 + minimum: 0 + fle_sta_1_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_dani: - default: 0.1 + fle_end_1_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_deint: - default: 0.0 + nfle2: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - w_desolv: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_2_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_dist: - default: 0.1 + fle_end_2_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_elec: - default: 1.0 + nfle3: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - w_lcc: - default: -10000.0 + maximum: 1000 + minimum: 0 + fle_sta_3_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_rg: - default: 1.0 + fle_end_3_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_sani: - default: 0.1 + nfle4: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - w_sym: - default: 0.1 + maximum: 1000 + minimum: 0 + fle_sta_4_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_vdw: - default: 1.0 + fle_end_4_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_vean: - default: 0.1 + nfle5: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - w_xpcs: - default: 0.1 + maximum: 1000 + minimum: 0 + fle_sta_5_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_xrdc: - default: 0.1 + fle_end_5_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_zres: - default: 0.1 + nfle6: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - elecflag: - default: true - type: boolean - dielec: - default: rdie - type: string - minLength: 0 - maxLength: 100 - epsilon: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_6_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - dihedflag: - default: true - type: boolean - par_nonbonded: - default: OPLSX - type: string - minLength: 0 - maxLength: 100 - int_1_1: - default: 1.0 + fle_end_6_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_2: - default: 1.0 + nfle7: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_1_3: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_7_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_4: - default: 1.0 + fle_end_7_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_5: - default: 1.0 + nfle8: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_1_6: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_8_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_7: - default: 1.0 + fle_end_8_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_8: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_15: - default: 1.0 + nfle9: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_1_16: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_9_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_17: - default: 1.0 + fle_end_9_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_18: - default: 1.0 + nfle10: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_1_19: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_10_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_20: - default: 1.0 + fle_end_10_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_2: - default: 1.0 + nfle11: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_3: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_11_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_4: - default: 1.0 + fle_end_11_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_5: - default: 1.0 + nfle12: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_6: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_12_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_7: - default: 1.0 + fle_end_12_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_8: - default: 1.0 + nfle13: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_9: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_13_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_10: - default: 1.0 + fle_end_13_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_11: - default: 1.0 + nfle14: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_12: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_14_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_13: - default: 1.0 + fle_end_14_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_14: - default: 1.0 + nfle15: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_15: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_15_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_16: - default: 1.0 + fle_end_15_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_17: - default: 1.0 + nfle16: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_18: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_16_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_19: - default: 1.0 + fle_end_16_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_20: - default: 1.0 + nfle17: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_3_3: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_17_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_4: - default: 1.0 + fle_end_17_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_5: - default: 1.0 + nfle18: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_3_6: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_18_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_7: - default: 1.0 + fle_end_18_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_8: - default: 1.0 + nfle19: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_3_9: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_19_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_10: - default: 1.0 + fle_end_19_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_11: - default: 1.0 + nfle20: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_3_12: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_20_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_3_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_3_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_3_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_3_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_3_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_3_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_3_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_4: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_5: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_6: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_7: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_8: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_5: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_6: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_7: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_8: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_6: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_7: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_8: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_7: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_8: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_8: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_18_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_18_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_18_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_19_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_19_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_20_20: - default: 1.0 + fle_end_20_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 required: [] additionalProperties: false uiSchema: + mol_fix_origin_1: + ui:group: molecule + mol_fix_origin_2: + ui:group: molecule + mol_fix_origin_3: + ui:group: molecule + mol_fix_origin_4: + ui:group: molecule + mol_fix_origin_5: + ui:group: molecule + mol_fix_origin_6: + ui:group: molecule + mol_fix_origin_7: + ui:group: molecule + mol_fix_origin_8: + ui:group: molecule + mol_fix_origin_9: + ui:group: molecule + mol_fix_origin_10: + ui:group: molecule + mol_fix_origin_11: + ui:group: molecule + mol_fix_origin_12: + ui:group: molecule + mol_fix_origin_13: + ui:group: molecule + mol_fix_origin_14: + ui:group: molecule + mol_fix_origin_15: + ui:group: molecule + mol_fix_origin_16: + ui:group: molecule + mol_fix_origin_17: + ui:group: molecule + mol_fix_origin_18: + ui:group: molecule + mol_fix_origin_19: + ui:group: molecule + mol_fix_origin_20: + ui:group: molecule + mol_shape_1: + ui:group: molecule + mol_shape_2: + ui:group: molecule + mol_shape_3: + ui:group: molecule + mol_shape_4: + ui:group: molecule + mol_shape_5: + ui:group: molecule + mol_shape_6: + ui:group: molecule + mol_shape_7: + ui:group: molecule + mol_shape_8: + ui:group: molecule + mol_shape_9: + ui:group: molecule + mol_shape_10: + ui:group: molecule + mol_shape_11: + ui:group: molecule + mol_shape_12: + ui:group: molecule + mol_shape_13: + ui:group: molecule + mol_shape_14: + ui:group: molecule + mol_shape_15: + ui:group: molecule + mol_shape_16: + ui:group: molecule + mol_shape_17: + ui:group: molecule + mol_shape_18: + ui:group: molecule + mol_shape_19: + ui:group: molecule + mol_shape_20: + ui:group: molecule ambig_fname: ui:widget: file + ui:group: distance restraints unambig_fname: ui:widget: file + ui:group: distance restraints + hbond_fname: + ui:widget: file + ui:group: distance restraints + amb_hot: + ui:group: distance restraints + amb_cool1: + ui:group: distance restraints + amb_cool2: + ui:group: distance restraints + amb_cool3: + ui:group: distance restraints + unamb_hot: + ui:group: distance restraints + unamb_cool1: + ui:group: distance restraints + unamb_cool2: + ui:group: distance restraints + unamb_cool3: + ui:group: distance restraints + hbond_hot: + ui:group: distance restraints + hbond_cool1: + ui:group: distance restraints + hbond_cool2: + ui:group: distance restraints + hbond_cool3: + ui:group: distance restraints + randremoval: + ui:group: distance restraints + npart: + ui:group: distance restraints + contactairs: + 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 - hbond_fname: + ui:group: dihedral restraints + dihedrals_on: + ui:group: dihedral restraints + dihedrals_hot: + ui:group: dihedral restraints + dihedrals_cool1: + ui:group: dihedral restraints + dihedrals_cool2: + ui:group: dihedral restraints + dihedrals_cool3: + ui:group: dihedral restraints + ssdihed: + ui:group: dihedral restraints + error_dih: + ui:group: dihedral restraints + dnarest_on: + ui:group: other restraints + sym_on: + ui:group: symmetry + ksym: + ui:group: symmetry + symtbl_fname: ui:widget: file + ui:group: symmetry + numc2sym: + ui:group: symmetry + c2sym_sta1_1: + ui:group: symmetry + c2sym_end1_1: + ui:group: symmetry + c2sym_seg1_1: + ui:group: symmetry + c2sym_sta2_1: + ui:group: symmetry + c2sym_end2_1: + ui:group: symmetry + c2sym_seg2_1: + ui:group: symmetry + numc3sym: + ui:group: symmetry + c3sym_sta1_1: + ui:group: symmetry + c3sym_end1_1: + ui:group: symmetry + c3sym_seg1_1: + ui:group: symmetry + c3sym_sta2_1: + ui:group: symmetry + c3sym_end2_1: + ui:group: symmetry + c3sym_seg2_1: + ui:group: symmetry + c3sym_sta3_1: + ui:group: symmetry + c3sym_end3_1: + ui:group: symmetry + c3sym_seg3_1: + ui:group: symmetry + numc4sym: + ui:group: symmetry + c4sym_sta1_1: + ui:group: symmetry + c4sym_end1_1: + ui:group: symmetry + c4sym_seg1_1: + ui:group: symmetry + c4sym_sta2_1: + ui:group: symmetry + c4sym_end2_1: + ui:group: symmetry + c4sym_seg2_1: + ui:group: symmetry + c4sym_sta3_1: + ui:group: symmetry + c4sym_end3_1: + ui:group: symmetry + c4sym_seg3_1: + ui:group: symmetry + c4sym_sta4_1: + ui:group: symmetry + c4sym_end4_1: + ui:group: symmetry + c4sym_seg4_1: + ui:group: symmetry + numc5sym: + ui:group: symmetry + c5sym_sta1_1: + ui:group: symmetry + c5sym_end1_1: + ui:group: symmetry + c5sym_seg1_1: + ui:group: symmetry + c5sym_sta2_1: + ui:group: symmetry + c5sym_end2_1: + ui:group: symmetry + c5sym_seg2_1: + ui:group: symmetry + c5sym_sta3_1: + ui:group: symmetry + c5sym_end3_1: + ui:group: symmetry + c5sym_seg3_1: + ui:group: symmetry + c5sym_sta4_1: + ui:group: symmetry + c5sym_end4_1: + ui:group: symmetry + c5sym_seg4_1: + ui:group: symmetry + c5sym_sta5_1: + ui:group: symmetry + c5sym_end5_1: + ui:group: symmetry + c5sym_seg5_1: + ui:group: symmetry + numc6sym: + ui:group: symmetry + c6sym_sta1_1: + ui:group: symmetry + c6sym_end1_1: + ui:group: symmetry + c6sym_seg1_1: + ui:group: symmetry + c6sym_sta2_1: + ui:group: symmetry + c6sym_end2_1: + ui:group: symmetry + c6sym_seg2_1: + ui:group: symmetry + c6sym_sta3_1: + ui:group: symmetry + c6sym_end3_1: + ui:group: symmetry + c6sym_seg3_1: + ui:group: symmetry + c6sym_sta4_1: + ui:group: symmetry + c6sym_end4_1: + ui:group: symmetry + c6sym_seg4_1: + ui:group: symmetry + c6sym_sta5_1: + ui:group: symmetry + c6sym_end5_1: + ui:group: symmetry + c6sym_seg5_1: + ui:group: symmetry + c6sym_sta6_1: + ui:group: symmetry + c6sym_end6_1: + ui:group: symmetry + c6sym_seg6_1: + ui:group: symmetry + nums3sym: + ui:group: symmetry + s3sym_sta1_1: + ui:group: symmetry + s3sym_end1_1: + ui:group: symmetry + s3sym_seg1_1: + ui:group: symmetry + s3sym_sta2_1: + ui:group: symmetry + s3sym_end2_1: + ui:group: symmetry + s3sym_seg2_1: + ui:group: symmetry + s3sym_sta3_1: + ui:group: symmetry + s3sym_end3_1: + ui:group: symmetry + s3sym_seg3_1: + ui:group: symmetry + ncs_on: + ui:group: symmetry + kncs: + ui:group: symmetry + numncs: + ui:group: symmetry + ncs_sta1_1: + ui:group: symmetry + ncs_end1_1: + ui:group: symmetry + ncs_seg1_1: + ui:group: symmetry + ncs_sta2_1: + ui:group: symmetry + ncs_end2_1: + ui:group: symmetry + ncs_seg2_1: + ui:group: symmetry + w_air: + ui:group: scoring + w_bsa: + ui:group: scoring + w_cdih: + ui:group: scoring + w_desolv: + ui:group: scoring + w_elec: + ui:group: scoring + w_sym: + 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 + sampling_factor: + ui:group: sampling + nemsteps: + ui:group: sampling + mdsteps_rigid: + ui:group: sampling + mdsteps_cool1: + ui:group: sampling + mdsteps_cool2: + ui:group: sampling + mdsteps_cool3: + ui:group: sampling + tolerance: + ui:group: module + nseg1: + ui:group: flexibility + seg_sta_1_1: + ui:group: flexibility + seg_end_1_1: + ui:group: flexibility + nseg2: + ui:group: flexibility + seg_sta_2_1: + ui:group: flexibility + seg_end_2_1: + ui:group: flexibility + nseg3: + ui:group: flexibility + seg_sta_3_1: + ui:group: flexibility + seg_end_3_1: + ui:group: flexibility + nseg4: + ui:group: flexibility + seg_sta_4_1: + ui:group: flexibility + seg_end_4_1: + ui:group: flexibility + nseg5: + ui:group: flexibility + seg_sta_5_1: + ui:group: flexibility + seg_end_5_1: + ui:group: flexibility + nseg6: + ui:group: flexibility + seg_sta_6_1: + ui:group: flexibility + seg_end_6_1: + ui:group: flexibility + nseg7: + ui:group: flexibility + seg_sta_7_1: + ui:group: flexibility + seg_end_7_1: + ui:group: flexibility + nseg8: + ui:group: flexibility + seg_sta_8_1: + ui:group: flexibility + seg_end_8_1: + ui:group: flexibility + nseg9: + ui:group: flexibility + seg_sta_9_1: + ui:group: flexibility + seg_end_9_1: + ui:group: flexibility + nseg10: + ui:group: flexibility + seg_sta_10_1: + ui:group: flexibility + seg_end_10_1: + ui:group: flexibility + nseg11: + ui:group: flexibility + seg_sta_11_1: + ui:group: flexibility + seg_end_11_1: + ui:group: flexibility + nseg12: + ui:group: flexibility + seg_sta_12_1: + ui:group: flexibility + seg_end_12_1: + ui:group: flexibility + nseg13: + ui:group: flexibility + seg_sta_13_1: + ui:group: flexibility + seg_end_13_1: + ui:group: flexibility + nseg14: + ui:group: flexibility + seg_sta_14_1: + ui:group: flexibility + seg_end_14_1: + ui:group: flexibility + nseg15: + ui:group: flexibility + seg_sta_15_1: + ui:group: flexibility + seg_end_15_1: + ui:group: flexibility + nseg16: + ui:group: flexibility + seg_sta_16_1: + ui:group: flexibility + seg_end_16_1: + ui:group: flexibility + nseg17: + ui:group: flexibility + seg_sta_17_1: + ui:group: flexibility + seg_end_17_1: + ui:group: flexibility + nseg18: + ui:group: flexibility + seg_sta_18_1: + ui:group: flexibility + seg_end_18_1: + ui:group: flexibility + nseg19: + ui:group: flexibility + seg_sta_19_1: + ui:group: flexibility + seg_end_19_1: + ui:group: flexibility + nseg20: + ui:group: flexibility + seg_sta_20_1: + ui:group: flexibility + seg_end_20_1: + ui:group: flexibility + nfle1: + ui:group: flexibility + fle_sta_1_1: + ui:group: flexibility + fle_end_1_1: + ui:group: flexibility + nfle2: + ui:group: flexibility + fle_sta_2_1: + ui:group: flexibility + fle_end_2_1: + ui:group: flexibility + nfle3: + ui:group: flexibility + fle_sta_3_1: + ui:group: flexibility + fle_end_3_1: + ui:group: flexibility + nfle4: + ui:group: flexibility + fle_sta_4_1: + ui:group: flexibility + fle_end_4_1: + ui:group: flexibility + nfle5: + ui:group: flexibility + fle_sta_5_1: + ui:group: flexibility + fle_end_5_1: + ui:group: flexibility + nfle6: + ui:group: flexibility + fle_sta_6_1: + ui:group: flexibility + fle_end_6_1: + ui:group: flexibility + nfle7: + ui:group: flexibility + fle_sta_7_1: + ui:group: flexibility + fle_end_7_1: + ui:group: flexibility + nfle8: + ui:group: flexibility + fle_sta_8_1: + ui:group: flexibility + fle_end_8_1: + ui:group: flexibility + nfle9: + ui:group: flexibility + fle_sta_9_1: + ui:group: flexibility + fle_end_9_1: + ui:group: flexibility + nfle10: + ui:group: flexibility + fle_sta_10_1: + ui:group: flexibility + fle_end_10_1: + ui:group: flexibility + nfle11: + ui:group: flexibility + fle_sta_11_1: + ui:group: flexibility + fle_end_11_1: + ui:group: flexibility + nfle12: + ui:group: flexibility + fle_sta_12_1: + ui:group: flexibility + fle_end_12_1: + ui:group: flexibility + nfle13: + ui:group: flexibility + fle_sta_13_1: + ui:group: flexibility + fle_end_13_1: + ui:group: flexibility + nfle14: + ui:group: flexibility + fle_sta_14_1: + ui:group: flexibility + fle_end_14_1: + ui:group: flexibility + nfle15: + ui:group: flexibility + fle_sta_15_1: + ui:group: flexibility + fle_end_15_1: + ui:group: flexibility + nfle16: + ui:group: flexibility + fle_sta_16_1: + ui:group: flexibility + fle_end_16_1: + ui:group: flexibility + nfle17: + ui:group: flexibility + fle_sta_17_1: + ui:group: flexibility + fle_end_17_1: + ui:group: flexibility + nfle18: + ui:group: flexibility + fle_sta_18_1: + ui:group: flexibility + fle_end_18_1: + ui:group: flexibility + nfle19: + ui:group: flexibility + fle_sta_19_1: + ui:group: flexibility + fle_end_19_1: + ui:group: flexibility + nfle20: + ui:group: flexibility + fle_sta_20_1: + ui:group: flexibility + fle_end_20_1: + ui:group: flexibility - id: mdref category: refinement label: HADDOCK3 module for water refinement. @@ -6719,241 +7365,241 @@ nodes: schema: type: object properties: - fix_origin_1: + mol_fix_origin_1: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_2: + mol_fix_origin_2: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_3: + mol_fix_origin_3: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_4: + mol_fix_origin_4: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_5: + mol_fix_origin_5: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_6: + mol_fix_origin_6: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_7: + mol_fix_origin_7: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_8: + mol_fix_origin_8: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_9: + mol_fix_origin_9: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_10: + mol_fix_origin_10: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_11: + mol_fix_origin_11: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_12: + mol_fix_origin_12: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_13: + mol_fix_origin_13: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_14: + mol_fix_origin_14: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_15: + mol_fix_origin_15: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_16: + mol_fix_origin_16: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_17: + mol_fix_origin_17: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_18: + mol_fix_origin_18: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_19: + mol_fix_origin_19: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_20: + mol_fix_origin_20: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - shape_1: + mol_shape_1: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_2: + mol_shape_2: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_3: + mol_shape_3: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_4: + mol_shape_4: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_5: + mol_shape_5: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_6: + mol_shape_6: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_7: + mol_shape_7: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_8: + mol_shape_8: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_9: + mol_shape_9: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_10: + mol_shape_10: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_11: + mol_shape_11: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_12: + mol_shape_12: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_13: + mol_shape_13: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_14: + mol_shape_14: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_15: + mol_shape_15: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_16: + mol_shape_16: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_17: + mol_shape_17: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_18: + mol_shape_18: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_19: + mol_shape_19: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_20: + mol_shape_20: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. @@ -7114,8 +7760,8 @@ 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: default: none title: Define automatically backbone dihedral angle restraints @@ -7144,8 +7790,8 @@ 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 @@ -7930,17 +8576,6 @@ nodes: type: number maximum: 78 minimum: 1 - dihedflag: - default: true - type: boolean - sampling: - default: 200 - title: Number of models to generate - description: Number of MD refined models to generate - $comment: Number of MD refined models to generate - type: number - maximum: 50000 - minimum: 1 sampling_factor: default: 1 title: Sampling factor for each starting model @@ -8025,14 +8660,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta1_1: + seg_sta_1_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend1_1: + seg_end_1_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8054,14 +8689,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta2_1: + seg_sta_2_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend2_1: + seg_end_2_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8083,14 +8718,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta3_1: + seg_sta_3_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend3_1: + seg_end_3_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8112,14 +8747,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta4_1: + seg_sta_4_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend4_1: + seg_end_4_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8141,14 +8776,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta5_1: + seg_sta_5_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend5_1: + seg_end_5_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8170,14 +8805,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta6_1: + seg_sta_6_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend6_1: + seg_end_6_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8199,14 +8834,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta7_1: + seg_sta_7_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend7_1: + seg_end_7_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8228,14 +8863,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta8_1: + seg_sta_8_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend8_1: + seg_end_8_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8257,14 +8892,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta9_1: + seg_sta_9_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend9_1: + seg_end_9_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8286,14 +8921,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta10_1: + seg_sta_10_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend10_1: + seg_end_10_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8315,14 +8950,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta11_1: + seg_sta_11_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend11_1: + seg_end_11_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8344,14 +8979,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta12_1: + seg_sta_12_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend12_1: + seg_end_12_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8373,14 +9008,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta13_1: + seg_sta_13_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend13_1: + seg_end_13_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8402,14 +9037,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta14_1: + seg_sta_14_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend14_1: + seg_end_14_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8431,14 +9066,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta15_1: + seg_sta_15_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend15_1: + seg_end_15_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8460,14 +9095,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta16_1: + seg_sta_16_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend16_1: + seg_end_16_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8489,14 +9124,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta17_1: + seg_sta_17_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend17_1: + seg_end_17_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8518,14 +9153,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta18_1: + seg_sta_18_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend18_1: + seg_end_18_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8547,14 +9182,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta19_1: + seg_sta_19_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend19_1: + seg_end_19_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8576,14 +9211,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta20_1: + seg_sta_20_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend20_1: + seg_end_20_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8596,18 +9231,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta1_1: + fle_sta_1_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend1_1: + fle_end_1_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8620,18 +9255,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta2_1: + fle_sta_2_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend2_1: + fle_end_2_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8644,18 +9279,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta3_1: + fle_sta_3_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend3_1: + fle_end_3_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8668,18 +9303,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta4_1: + fle_sta_4_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend4_1: + fle_end_4_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8692,18 +9327,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta5_1: + fle_sta_5_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend5_1: + fle_end_5_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8716,18 +9351,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta6_1: + fle_sta_6_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend6_1: + fle_end_6_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8740,18 +9375,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta7_1: + fle_sta_7_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend7_1: + fle_end_7_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8764,18 +9399,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta8_1: + fle_sta_8_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend8_1: + fle_end_8_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8788,18 +9423,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta9_1: + fle_sta_9_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend9_1: + fle_end_9_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8812,18 +9447,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta10_1: + fle_sta_10_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend10_1: + fle_end_10_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8836,18 +9471,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta11_1: + fle_sta_11_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend11_1: + fle_end_11_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8860,18 +9495,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta12_1: + fle_sta_12_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend12_1: + fle_end_12_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8884,18 +9519,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta13_1: + fle_sta_13_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend13_1: + fle_end_13_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8908,18 +9543,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta14_1: + fle_sta_14_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend14_1: + fle_end_14_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8932,18 +9567,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta15_1: + fle_sta_15_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend15_1: + fle_end_15_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8956,18 +9591,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta16_1: + fle_sta_16_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend16_1: + fle_end_16_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8980,18 +9615,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta17_1: + fle_sta_17_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend17_1: + fle_end_17_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9004,18 +9639,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta18_1: + fle_sta_18_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend18_1: + fle_end_18_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9028,18 +9663,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta19_1: + fle_sta_19_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend19_1: + fle_end_19_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9052,18 +9687,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta20_1: + fle_sta_20_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend20_1: + fle_end_20_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9073,85 +9708,85 @@ nodes: required: [] additionalProperties: false uiSchema: - fix_origin_1: + mol_fix_origin_1: ui:group: molecule - fix_origin_2: + mol_fix_origin_2: ui:group: molecule - fix_origin_3: + mol_fix_origin_3: ui:group: molecule - fix_origin_4: + mol_fix_origin_4: ui:group: molecule - fix_origin_5: + mol_fix_origin_5: ui:group: molecule - fix_origin_6: + mol_fix_origin_6: ui:group: molecule - fix_origin_7: + mol_fix_origin_7: ui:group: molecule - fix_origin_8: + mol_fix_origin_8: ui:group: molecule - fix_origin_9: + mol_fix_origin_9: ui:group: molecule - fix_origin_10: + mol_fix_origin_10: ui:group: molecule - fix_origin_11: + mol_fix_origin_11: ui:group: molecule - fix_origin_12: + mol_fix_origin_12: ui:group: molecule - fix_origin_13: + mol_fix_origin_13: ui:group: molecule - fix_origin_14: + mol_fix_origin_14: ui:group: molecule - fix_origin_15: + mol_fix_origin_15: ui:group: molecule - fix_origin_16: + mol_fix_origin_16: ui:group: molecule - fix_origin_17: + mol_fix_origin_17: ui:group: molecule - fix_origin_18: + mol_fix_origin_18: ui:group: molecule - fix_origin_19: + mol_fix_origin_19: ui:group: molecule - fix_origin_20: + mol_fix_origin_20: ui:group: molecule - shape_1: + mol_shape_1: ui:group: molecule - shape_2: + mol_shape_2: ui:group: molecule - shape_3: + mol_shape_3: ui:group: molecule - shape_4: + mol_shape_4: ui:group: molecule - shape_5: + mol_shape_5: ui:group: molecule - shape_6: + mol_shape_6: ui:group: molecule - shape_7: + mol_shape_7: ui:group: molecule - shape_8: + mol_shape_8: ui:group: molecule - shape_9: + mol_shape_9: ui:group: molecule - shape_10: + mol_shape_10: ui:group: molecule - shape_11: + mol_shape_11: ui:group: molecule - shape_12: + mol_shape_12: ui:group: molecule - shape_13: + mol_shape_13: ui:group: molecule - shape_14: + mol_shape_14: ui:group: molecule - shape_15: + mol_shape_15: ui:group: molecule - shape_16: + mol_shape_16: ui:group: molecule - shape_17: + mol_shape_17: ui:group: molecule - shape_18: + mol_shape_18: ui:group: molecule - shape_19: + mol_shape_19: ui:group: molecule - shape_20: + mol_shape_20: ui:group: molecule ambig_fname: ui:widget: file @@ -9396,8 +10031,6 @@ nodes: ui:group: force field epsilon: ui:group: force field - sampling: - ui:group: sampling sampling_factor: ui:group: sampling nemsteps: @@ -9412,243 +10045,243 @@ nodes: ui:group: module nseg1: ui:group: flexibility - segsta1_1: + seg_sta_1_1: ui:group: flexibility - segend1_1: + seg_end_1_1: ui:group: flexibility nseg2: ui:group: flexibility - segsta2_1: + seg_sta_2_1: ui:group: flexibility - segend2_1: + seg_end_2_1: ui:group: flexibility nseg3: ui:group: flexibility - segsta3_1: + seg_sta_3_1: ui:group: flexibility - segend3_1: + seg_end_3_1: ui:group: flexibility nseg4: ui:group: flexibility - segsta4_1: + seg_sta_4_1: ui:group: flexibility - segend4_1: + seg_end_4_1: ui:group: flexibility nseg5: ui:group: flexibility - segsta5_1: + seg_sta_5_1: ui:group: flexibility - segend5_1: + seg_end_5_1: ui:group: flexibility nseg6: ui:group: flexibility - segsta6_1: + seg_sta_6_1: ui:group: flexibility - segend6_1: + seg_end_6_1: ui:group: flexibility nseg7: ui:group: flexibility - segsta7_1: + seg_sta_7_1: ui:group: flexibility - segend7_1: + seg_end_7_1: ui:group: flexibility nseg8: ui:group: flexibility - segsta8_1: + seg_sta_8_1: ui:group: flexibility - segend8_1: + seg_end_8_1: ui:group: flexibility nseg9: ui:group: flexibility - segsta9_1: + seg_sta_9_1: ui:group: flexibility - segend9_1: + seg_end_9_1: ui:group: flexibility nseg10: ui:group: flexibility - segsta10_1: + seg_sta_10_1: ui:group: flexibility - segend10_1: + seg_end_10_1: ui:group: flexibility nseg11: ui:group: flexibility - segsta11_1: + seg_sta_11_1: ui:group: flexibility - segend11_1: + seg_end_11_1: ui:group: flexibility nseg12: ui:group: flexibility - segsta12_1: + seg_sta_12_1: ui:group: flexibility - segend12_1: + seg_end_12_1: ui:group: flexibility nseg13: ui:group: flexibility - segsta13_1: + seg_sta_13_1: ui:group: flexibility - segend13_1: + seg_end_13_1: ui:group: flexibility nseg14: ui:group: flexibility - segsta14_1: + seg_sta_14_1: ui:group: flexibility - segend14_1: + seg_end_14_1: ui:group: flexibility nseg15: ui:group: flexibility - segsta15_1: + seg_sta_15_1: ui:group: flexibility - segend15_1: + seg_end_15_1: ui:group: flexibility nseg16: ui:group: flexibility - segsta16_1: + seg_sta_16_1: ui:group: flexibility - segend16_1: + seg_end_16_1: ui:group: flexibility nseg17: ui:group: flexibility - segsta17_1: + seg_sta_17_1: ui:group: flexibility - segend17_1: + seg_end_17_1: ui:group: flexibility nseg18: ui:group: flexibility - segsta18_1: + seg_sta_18_1: ui:group: flexibility - segend18_1: + seg_end_18_1: ui:group: flexibility nseg19: ui:group: flexibility - segsta19_1: + seg_sta_19_1: ui:group: flexibility - segend19_1: + seg_end_19_1: ui:group: flexibility nseg20: ui:group: flexibility - segsta20_1: + seg_sta_20_1: ui:group: flexibility - segend20_1: + seg_end_20_1: ui:group: flexibility nfle1: ui:group: flexibility - flesta1_1: + fle_sta_1_1: ui:group: flexibility - fleend1_1: + fle_end_1_1: ui:group: flexibility nfle2: ui:group: flexibility - flesta2_1: + fle_sta_2_1: ui:group: flexibility - fleend2_1: + fle_end_2_1: ui:group: flexibility nfle3: ui:group: flexibility - flesta3_1: + fle_sta_3_1: ui:group: flexibility - fleend3_1: + fle_end_3_1: ui:group: flexibility nfle4: ui:group: flexibility - flesta4_1: + fle_sta_4_1: ui:group: flexibility - fleend4_1: + fle_end_4_1: ui:group: flexibility nfle5: ui:group: flexibility - flesta5_1: + fle_sta_5_1: ui:group: flexibility - fleend5_1: + fle_end_5_1: ui:group: flexibility nfle6: ui:group: flexibility - flesta6_1: + fle_sta_6_1: ui:group: flexibility - fleend6_1: + fle_end_6_1: ui:group: flexibility nfle7: ui:group: flexibility - flesta7_1: + fle_sta_7_1: ui:group: flexibility - fleend7_1: + fle_end_7_1: ui:group: flexibility nfle8: ui:group: flexibility - flesta8_1: + fle_sta_8_1: ui:group: flexibility - fleend8_1: + fle_end_8_1: ui:group: flexibility nfle9: ui:group: flexibility - flesta9_1: + fle_sta_9_1: ui:group: flexibility - fleend9_1: + fle_end_9_1: ui:group: flexibility nfle10: ui:group: flexibility - flesta10_1: + fle_sta_10_1: ui:group: flexibility - fleend10_1: + fle_end_10_1: ui:group: flexibility nfle11: ui:group: flexibility - flesta11_1: + fle_sta_11_1: ui:group: flexibility - fleend11_1: + fle_end_11_1: ui:group: flexibility nfle12: ui:group: flexibility - flesta12_1: + fle_sta_12_1: ui:group: flexibility - fleend12_1: + fle_end_12_1: ui:group: flexibility nfle13: ui:group: flexibility - flesta13_1: + fle_sta_13_1: ui:group: flexibility - fleend13_1: + fle_end_13_1: ui:group: flexibility nfle14: ui:group: flexibility - flesta14_1: + fle_sta_14_1: ui:group: flexibility - fleend14_1: + fle_end_14_1: ui:group: flexibility nfle15: ui:group: flexibility - flesta15_1: + fle_sta_15_1: ui:group: flexibility - fleend15_1: + fle_end_15_1: ui:group: flexibility nfle16: ui:group: flexibility - flesta16_1: + fle_sta_16_1: ui:group: flexibility - fleend16_1: + fle_end_16_1: ui:group: flexibility nfle17: ui:group: flexibility - flesta17_1: + fle_sta_17_1: ui:group: flexibility - fleend17_1: + fle_end_17_1: ui:group: flexibility nfle18: ui:group: flexibility - flesta18_1: + fle_sta_18_1: ui:group: flexibility - fleend18_1: + fle_end_18_1: ui:group: flexibility nfle19: ui:group: flexibility - flesta19_1: + fle_sta_19_1: ui:group: flexibility - fleend19_1: + fle_end_19_1: ui:group: flexibility nfle20: ui:group: flexibility - flesta20_1: + fle_sta_20_1: ui:group: flexibility - fleend20_1: + fle_end_20_1: ui:group: flexibility - id: emref category: refinement @@ -9657,241 +10290,241 @@ nodes: schema: type: object properties: - fix_origin_1: + mol_fix_origin_1: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_2: + mol_fix_origin_2: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_3: + mol_fix_origin_3: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_4: + mol_fix_origin_4: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_5: + mol_fix_origin_5: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_6: + mol_fix_origin_6: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_7: + mol_fix_origin_7: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_8: + mol_fix_origin_8: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_9: + mol_fix_origin_9: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_10: + mol_fix_origin_10: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_11: + mol_fix_origin_11: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_12: + mol_fix_origin_12: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_13: + mol_fix_origin_13: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_14: + mol_fix_origin_14: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_15: + mol_fix_origin_15: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_16: + mol_fix_origin_16: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_17: + mol_fix_origin_17: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_18: + mol_fix_origin_18: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_19: + mol_fix_origin_19: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_20: + mol_fix_origin_20: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - shape_1: + mol_shape_1: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_2: + mol_shape_2: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_3: + mol_shape_3: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_4: + mol_shape_4: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_5: + mol_shape_5: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_6: + mol_shape_6: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_7: + mol_shape_7: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_8: + mol_shape_8: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_9: + mol_shape_9: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_10: + mol_shape_10: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_11: + mol_shape_11: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_12: + mol_shape_12: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_13: + mol_shape_13: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_14: + mol_shape_14: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_15: + mol_shape_15: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_16: + mol_shape_16: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_17: + mol_shape_17: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_18: + mol_shape_18: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_19: + mol_shape_19: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_20: + mol_shape_20: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. @@ -10881,14 +11514,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta1_1: + seg_sta_1_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend1_1: + seg_end_1_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -10910,14 +11543,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta2_1: + seg_sta_2_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend2_1: + seg_end_2_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -10939,14 +11572,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta3_1: + seg_sta_3_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend3_1: + seg_end_3_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -10968,14 +11601,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta4_1: + seg_sta_4_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend4_1: + seg_end_4_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -10997,14 +11630,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta5_1: + seg_sta_5_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend5_1: + seg_end_5_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11026,14 +11659,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta6_1: + seg_sta_6_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend6_1: + seg_end_6_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11055,14 +11688,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta7_1: + seg_sta_7_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend7_1: + seg_end_7_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11084,14 +11717,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta8_1: + seg_sta_8_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend8_1: + seg_end_8_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11113,14 +11746,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta9_1: + seg_sta_9_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend9_1: + seg_end_9_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11142,14 +11775,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta10_1: + seg_sta_10_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend10_1: + seg_end_10_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11171,14 +11804,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta11_1: + seg_sta_11_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend11_1: + seg_end_11_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11200,14 +11833,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta12_1: + seg_sta_12_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend12_1: + seg_end_12_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11229,14 +11862,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta13_1: + seg_sta_13_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend13_1: + seg_end_13_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11258,14 +11891,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta14_1: + seg_sta_14_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend14_1: + seg_end_14_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11287,14 +11920,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta15_1: + seg_sta_15_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend15_1: + seg_end_15_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11316,14 +11949,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta16_1: + seg_sta_16_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend16_1: + seg_end_16_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11345,14 +11978,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta17_1: + seg_sta_17_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend17_1: + seg_end_17_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11374,14 +12007,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta18_1: + seg_sta_18_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend18_1: + seg_end_18_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11403,14 +12036,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta19_1: + seg_sta_19_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend19_1: + seg_end_19_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11432,14 +12065,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta20_1: + seg_sta_20_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend20_1: + seg_end_20_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11452,18 +12085,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta1_1: + fle_sta_1_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend1_1: + fle_end_1_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11476,18 +12109,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta2_1: + fle_sta_2_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend2_1: + fle_end_2_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11500,18 +12133,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta3_1: + fle_sta_3_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend3_1: + fle_end_3_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11524,18 +12157,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta4_1: + fle_sta_4_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend4_1: + fle_end_4_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11548,18 +12181,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta5_1: + fle_sta_5_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend5_1: + fle_end_5_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11572,18 +12205,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta6_1: + fle_sta_6_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend6_1: + fle_end_6_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11596,18 +12229,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta7_1: + fle_sta_7_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend7_1: + fle_end_7_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11620,18 +12253,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta8_1: + fle_sta_8_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend8_1: + fle_end_8_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11644,18 +12277,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta9_1: + fle_sta_9_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend9_1: + fle_end_9_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11668,18 +12301,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta10_1: + fle_sta_10_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend10_1: + fle_end_10_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11692,18 +12325,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta11_1: + fle_sta_11_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend11_1: + fle_end_11_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11716,18 +12349,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta12_1: + fle_sta_12_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend12_1: + fle_end_12_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11740,18 +12373,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta13_1: + fle_sta_13_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend13_1: + fle_end_13_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11764,18 +12397,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta14_1: + fle_sta_14_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend14_1: + fle_end_14_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11788,18 +12421,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta15_1: + fle_sta_15_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend15_1: + fle_end_15_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11812,18 +12445,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta16_1: + fle_sta_16_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend16_1: + fle_end_16_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11836,18 +12469,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta17_1: + fle_sta_17_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend17_1: + fle_end_17_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11860,18 +12493,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta18_1: + fle_sta_18_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend18_1: + fle_end_18_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11884,18 +12517,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta19_1: + fle_sta_19_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend19_1: + fle_end_19_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11908,18 +12541,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta20_1: + fle_sta_20_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend20_1: + fle_end_20_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11929,85 +12562,85 @@ nodes: required: [] additionalProperties: false uiSchema: - fix_origin_1: + mol_fix_origin_1: ui:group: molecule - fix_origin_2: + mol_fix_origin_2: ui:group: molecule - fix_origin_3: + mol_fix_origin_3: ui:group: molecule - fix_origin_4: + mol_fix_origin_4: ui:group: molecule - fix_origin_5: + mol_fix_origin_5: ui:group: molecule - fix_origin_6: + mol_fix_origin_6: ui:group: molecule - fix_origin_7: + mol_fix_origin_7: ui:group: molecule - fix_origin_8: + mol_fix_origin_8: ui:group: molecule - fix_origin_9: + mol_fix_origin_9: ui:group: molecule - fix_origin_10: + mol_fix_origin_10: ui:group: molecule - fix_origin_11: + mol_fix_origin_11: ui:group: molecule - fix_origin_12: + mol_fix_origin_12: ui:group: molecule - fix_origin_13: + mol_fix_origin_13: ui:group: molecule - fix_origin_14: + mol_fix_origin_14: ui:group: molecule - fix_origin_15: + mol_fix_origin_15: ui:group: molecule - fix_origin_16: + mol_fix_origin_16: ui:group: molecule - fix_origin_17: + mol_fix_origin_17: ui:group: molecule - fix_origin_18: + mol_fix_origin_18: ui:group: molecule - fix_origin_19: + mol_fix_origin_19: ui:group: molecule - fix_origin_20: + mol_fix_origin_20: ui:group: molecule - shape_1: + mol_shape_1: ui:group: molecule - shape_2: + mol_shape_2: ui:group: molecule - shape_3: + mol_shape_3: ui:group: molecule - shape_4: + mol_shape_4: ui:group: molecule - shape_5: + mol_shape_5: ui:group: molecule - shape_6: + mol_shape_6: ui:group: molecule - shape_7: + mol_shape_7: ui:group: molecule - shape_8: + mol_shape_8: ui:group: molecule - shape_9: + mol_shape_9: ui:group: molecule - shape_10: + mol_shape_10: ui:group: molecule - shape_11: + mol_shape_11: ui:group: molecule - shape_12: + mol_shape_12: ui:group: molecule - shape_13: + mol_shape_13: ui:group: molecule - shape_14: + mol_shape_14: ui:group: molecule - shape_15: + mol_shape_15: ui:group: molecule - shape_16: + mol_shape_16: ui:group: molecule - shape_17: + mol_shape_17: ui:group: molecule - shape_18: + mol_shape_18: ui:group: molecule - shape_19: + mol_shape_19: ui:group: molecule - shape_20: + mol_shape_20: ui:group: molecule ambig_fname: ui:widget: file @@ -12256,243 +12889,243 @@ nodes: ui:group: module nseg1: ui:group: flexibility - segsta1_1: + seg_sta_1_1: ui:group: flexibility - segend1_1: + seg_end_1_1: ui:group: flexibility nseg2: ui:group: flexibility - segsta2_1: + seg_sta_2_1: ui:group: flexibility - segend2_1: + seg_end_2_1: ui:group: flexibility nseg3: ui:group: flexibility - segsta3_1: + seg_sta_3_1: ui:group: flexibility - segend3_1: + seg_end_3_1: ui:group: flexibility nseg4: ui:group: flexibility - segsta4_1: + seg_sta_4_1: ui:group: flexibility - segend4_1: + seg_end_4_1: ui:group: flexibility nseg5: ui:group: flexibility - segsta5_1: + seg_sta_5_1: ui:group: flexibility - segend5_1: + seg_end_5_1: ui:group: flexibility nseg6: ui:group: flexibility - segsta6_1: + seg_sta_6_1: ui:group: flexibility - segend6_1: + seg_end_6_1: ui:group: flexibility nseg7: ui:group: flexibility - segsta7_1: + seg_sta_7_1: ui:group: flexibility - segend7_1: + seg_end_7_1: ui:group: flexibility nseg8: ui:group: flexibility - segsta8_1: + seg_sta_8_1: ui:group: flexibility - segend8_1: + seg_end_8_1: ui:group: flexibility nseg9: ui:group: flexibility - segsta9_1: + seg_sta_9_1: ui:group: flexibility - segend9_1: + seg_end_9_1: ui:group: flexibility nseg10: ui:group: flexibility - segsta10_1: + seg_sta_10_1: ui:group: flexibility - segend10_1: + seg_end_10_1: ui:group: flexibility nseg11: ui:group: flexibility - segsta11_1: + seg_sta_11_1: ui:group: flexibility - segend11_1: + seg_end_11_1: ui:group: flexibility nseg12: ui:group: flexibility - segsta12_1: + seg_sta_12_1: ui:group: flexibility - segend12_1: + seg_end_12_1: ui:group: flexibility nseg13: ui:group: flexibility - segsta13_1: + seg_sta_13_1: ui:group: flexibility - segend13_1: + seg_end_13_1: ui:group: flexibility nseg14: ui:group: flexibility - segsta14_1: + seg_sta_14_1: ui:group: flexibility - segend14_1: + seg_end_14_1: ui:group: flexibility nseg15: ui:group: flexibility - segsta15_1: + seg_sta_15_1: ui:group: flexibility - segend15_1: + seg_end_15_1: ui:group: flexibility nseg16: ui:group: flexibility - segsta16_1: + seg_sta_16_1: ui:group: flexibility - segend16_1: + seg_end_16_1: ui:group: flexibility nseg17: ui:group: flexibility - segsta17_1: + seg_sta_17_1: ui:group: flexibility - segend17_1: + seg_end_17_1: ui:group: flexibility nseg18: ui:group: flexibility - segsta18_1: + seg_sta_18_1: ui:group: flexibility - segend18_1: + seg_end_18_1: ui:group: flexibility nseg19: ui:group: flexibility - segsta19_1: + seg_sta_19_1: ui:group: flexibility - segend19_1: + seg_end_19_1: ui:group: flexibility nseg20: ui:group: flexibility - segsta20_1: + seg_sta_20_1: ui:group: flexibility - segend20_1: + seg_end_20_1: ui:group: flexibility nfle1: ui:group: flexibility - flesta1_1: + fle_sta_1_1: ui:group: flexibility - fleend1_1: + fle_end_1_1: ui:group: flexibility nfle2: ui:group: flexibility - flesta2_1: + fle_sta_2_1: ui:group: flexibility - fleend2_1: + fle_end_2_1: ui:group: flexibility nfle3: ui:group: flexibility - flesta3_1: + fle_sta_3_1: ui:group: flexibility - fleend3_1: + fle_end_3_1: ui:group: flexibility nfle4: ui:group: flexibility - flesta4_1: + fle_sta_4_1: ui:group: flexibility - fleend4_1: + fle_end_4_1: ui:group: flexibility nfle5: ui:group: flexibility - flesta5_1: + fle_sta_5_1: ui:group: flexibility - fleend5_1: + fle_end_5_1: ui:group: flexibility nfle6: ui:group: flexibility - flesta6_1: + fle_sta_6_1: ui:group: flexibility - fleend6_1: + fle_end_6_1: ui:group: flexibility nfle7: ui:group: flexibility - flesta7_1: + fle_sta_7_1: ui:group: flexibility - fleend7_1: + fle_end_7_1: ui:group: flexibility nfle8: ui:group: flexibility - flesta8_1: + fle_sta_8_1: ui:group: flexibility - fleend8_1: + fle_end_8_1: ui:group: flexibility nfle9: ui:group: flexibility - flesta9_1: + fle_sta_9_1: ui:group: flexibility - fleend9_1: + fle_end_9_1: ui:group: flexibility nfle10: ui:group: flexibility - flesta10_1: + fle_sta_10_1: ui:group: flexibility - fleend10_1: + fle_end_10_1: ui:group: flexibility nfle11: ui:group: flexibility - flesta11_1: + fle_sta_11_1: ui:group: flexibility - fleend11_1: + fle_end_11_1: ui:group: flexibility nfle12: ui:group: flexibility - flesta12_1: + fle_sta_12_1: ui:group: flexibility - fleend12_1: + fle_end_12_1: ui:group: flexibility nfle13: ui:group: flexibility - flesta13_1: + fle_sta_13_1: ui:group: flexibility - fleend13_1: + fle_end_13_1: ui:group: flexibility nfle14: ui:group: flexibility - flesta14_1: + fle_sta_14_1: ui:group: flexibility - fleend14_1: + fle_end_14_1: ui:group: flexibility nfle15: ui:group: flexibility - flesta15_1: + fle_sta_15_1: ui:group: flexibility - fleend15_1: + fle_end_15_1: ui:group: flexibility nfle16: ui:group: flexibility - flesta16_1: + fle_sta_16_1: ui:group: flexibility - fleend16_1: + fle_end_16_1: ui:group: flexibility nfle17: ui:group: flexibility - flesta17_1: + fle_sta_17_1: ui:group: flexibility - fleend17_1: + fle_end_17_1: ui:group: flexibility nfle18: ui:group: flexibility - flesta18_1: + fle_sta_18_1: ui:group: flexibility - fleend18_1: + fle_end_18_1: ui:group: flexibility nfle19: ui:group: flexibility - flesta19_1: + fle_sta_19_1: ui:group: flexibility - fleend19_1: + fle_end_19_1: ui:group: flexibility nfle20: ui:group: flexibility - flesta20_1: + fle_sta_20_1: ui:group: flexibility - fleend20_1: + fle_end_20_1: ui:group: flexibility examples: docking-protein-ligand: /examples/docking-protein-ligand.zip diff --git a/public/catalog/haddock3.guru.yaml b/public/catalog/haddock3.guru.yaml index 0516cc3f..6a548215 100644 --- a/public/catalog/haddock3.guru.yaml +++ b/public/catalog/haddock3.guru.yaml @@ -316,241 +316,241 @@ nodes: schema: type: object properties: - fix_origin_1: + mol_fix_origin_1: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_2: + mol_fix_origin_2: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_3: + mol_fix_origin_3: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_4: + mol_fix_origin_4: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_5: + mol_fix_origin_5: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_6: + mol_fix_origin_6: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_7: + mol_fix_origin_7: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_8: + mol_fix_origin_8: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_9: + mol_fix_origin_9: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_10: + mol_fix_origin_10: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_11: + mol_fix_origin_11: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_12: + mol_fix_origin_12: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_13: + mol_fix_origin_13: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_14: + mol_fix_origin_14: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_15: + mol_fix_origin_15: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_16: + mol_fix_origin_16: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_17: + mol_fix_origin_17: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_18: + mol_fix_origin_18: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_19: + mol_fix_origin_19: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_20: + mol_fix_origin_20: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - shape_1: + mol_shape_1: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_2: + mol_shape_2: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_3: + mol_shape_3: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_4: + mol_shape_4: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_5: + mol_shape_5: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_6: + mol_shape_6: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_7: + mol_shape_7: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_8: + mol_shape_8: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_9: + mol_shape_9: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_10: + mol_shape_10: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_11: + mol_shape_11: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_12: + mol_shape_12: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_13: + mol_shape_13: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_14: + mol_shape_14: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_15: + mol_shape_15: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_16: + mol_shape_16: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_17: + mol_shape_17: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_18: + mol_shape_18: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_19: + mol_shape_19: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_20: + mol_shape_20: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. @@ -696,7 +696,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_1_1: + rair_sta_1_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -725,7 +725,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_2_1: + rair_sta_2_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -754,7 +754,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_3_1: + rair_sta_3_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -783,7 +783,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_4_1: + rair_sta_4_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -812,7 +812,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_5_1: + rair_sta_5_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -841,7 +841,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_6_1: + rair_sta_6_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -870,7 +870,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_7_1: + rair_sta_7_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -899,7 +899,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_8_1: + rair_sta_8_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -928,7 +928,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_9_1: + rair_sta_9_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -957,7 +957,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_10_1: + rair_sta_10_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -986,7 +986,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_11_1: + rair_sta_11_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1015,7 +1015,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_12_1: + rair_sta_12_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1044,7 +1044,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_13_1: + rair_sta_13_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1073,7 +1073,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_14_1: + rair_sta_14_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1102,7 +1102,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_15_1: + rair_sta_15_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1131,7 +1131,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_16_1: + rair_sta_16_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1160,7 +1160,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_17_1: + rair_sta_17_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1189,7 +1189,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_18_1: + rair_sta_18_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1218,7 +1218,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_19_1: + rair_sta_19_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -1247,7 +1247,7 @@ nodes: type: number maximum: 100 minimum: 0 - rair_start_20_1: + rair_sta_20_1: title: Starting residue number description: Starting residue number for segment from which to define random interaction restraints @@ -2162,85 +2162,85 @@ nodes: required: [] additionalProperties: false uiSchema: - fix_origin_1: + mol_fix_origin_1: ui:group: molecule - fix_origin_2: + mol_fix_origin_2: ui:group: molecule - fix_origin_3: + mol_fix_origin_3: ui:group: molecule - fix_origin_4: + mol_fix_origin_4: ui:group: molecule - fix_origin_5: + mol_fix_origin_5: ui:group: molecule - fix_origin_6: + mol_fix_origin_6: ui:group: molecule - fix_origin_7: + mol_fix_origin_7: ui:group: molecule - fix_origin_8: + mol_fix_origin_8: ui:group: molecule - fix_origin_9: + mol_fix_origin_9: ui:group: molecule - fix_origin_10: + mol_fix_origin_10: ui:group: molecule - fix_origin_11: + mol_fix_origin_11: ui:group: molecule - fix_origin_12: + mol_fix_origin_12: ui:group: molecule - fix_origin_13: + mol_fix_origin_13: ui:group: molecule - fix_origin_14: + mol_fix_origin_14: ui:group: molecule - fix_origin_15: + mol_fix_origin_15: ui:group: molecule - fix_origin_16: + mol_fix_origin_16: ui:group: molecule - fix_origin_17: + mol_fix_origin_17: ui:group: molecule - fix_origin_18: + mol_fix_origin_18: ui:group: molecule - fix_origin_19: + mol_fix_origin_19: ui:group: molecule - fix_origin_20: + mol_fix_origin_20: ui:group: molecule - shape_1: + mol_shape_1: ui:group: molecule - shape_2: + mol_shape_2: ui:group: molecule - shape_3: + mol_shape_3: ui:group: molecule - shape_4: + mol_shape_4: ui:group: molecule - shape_5: + mol_shape_5: ui:group: molecule - shape_6: + mol_shape_6: ui:group: molecule - shape_7: + mol_shape_7: ui:group: molecule - shape_8: + mol_shape_8: ui:group: molecule - shape_9: + mol_shape_9: ui:group: molecule - shape_10: + mol_shape_10: ui:group: molecule - shape_11: + mol_shape_11: ui:group: molecule - shape_12: + mol_shape_12: ui:group: molecule - shape_13: + mol_shape_13: ui:group: molecule - shape_14: + mol_shape_14: ui:group: molecule - shape_15: + mol_shape_15: ui:group: molecule - shape_16: + mol_shape_16: ui:group: molecule - shape_17: + mol_shape_17: ui:group: molecule - shape_18: + mol_shape_18: ui:group: molecule - shape_19: + mol_shape_19: ui:group: molecule - shape_20: + mol_shape_20: ui:group: molecule ambig_fname: ui:widget: file @@ -2271,121 +2271,121 @@ nodes: ui:group: ab initio mode nrair_1: ui:group: ab initio mode - rair_start_1_1: + rair_sta_1_1: ui:group: ab initio mode rair_end_1_1: ui:group: ab initio mode nrair_2: ui:group: ab initio mode - rair_start_2_1: + rair_sta_2_1: ui:group: ab initio mode rair_end_2_1: ui:group: ab initio mode nrair_3: ui:group: ab initio mode - rair_start_3_1: + rair_sta_3_1: ui:group: ab initio mode rair_end_3_1: ui:group: ab initio mode nrair_4: ui:group: ab initio mode - rair_start_4_1: + rair_sta_4_1: ui:group: ab initio mode rair_end_4_1: ui:group: ab initio mode nrair_5: ui:group: ab initio mode - rair_start_5_1: + rair_sta_5_1: ui:group: ab initio mode rair_end_5_1: ui:group: ab initio mode nrair_6: ui:group: ab initio mode - rair_start_6_1: + rair_sta_6_1: ui:group: ab initio mode rair_end_6_1: ui:group: ab initio mode nrair_7: ui:group: ab initio mode - rair_start_7_1: + rair_sta_7_1: ui:group: ab initio mode rair_end_7_1: ui:group: ab initio mode nrair_8: ui:group: ab initio mode - rair_start_8_1: + rair_sta_8_1: ui:group: ab initio mode rair_end_8_1: ui:group: ab initio mode nrair_9: ui:group: ab initio mode - rair_start_9_1: + rair_sta_9_1: ui:group: ab initio mode rair_end_9_1: ui:group: ab initio mode nrair_10: ui:group: ab initio mode - rair_start_10_1: + rair_sta_10_1: ui:group: ab initio mode rair_end_10_1: ui:group: ab initio mode nrair_11: ui:group: ab initio mode - rair_start_11_1: + rair_sta_11_1: ui:group: ab initio mode rair_end_11_1: ui:group: ab initio mode nrair_12: ui:group: ab initio mode - rair_start_12_1: + rair_sta_12_1: ui:group: ab initio mode rair_end_12_1: ui:group: ab initio mode nrair_13: ui:group: ab initio mode - rair_start_13_1: + rair_sta_13_1: ui:group: ab initio mode rair_end_13_1: ui:group: ab initio mode nrair_14: ui:group: ab initio mode - rair_start_14_1: + rair_sta_14_1: ui:group: ab initio mode rair_end_14_1: ui:group: ab initio mode nrair_15: ui:group: ab initio mode - rair_start_15_1: + rair_sta_15_1: ui:group: ab initio mode rair_end_15_1: ui:group: ab initio mode nrair_16: ui:group: ab initio mode - rair_start_16_1: + rair_sta_16_1: ui:group: ab initio mode rair_end_16_1: ui:group: ab initio mode nrair_17: ui:group: ab initio mode - rair_start_17_1: + rair_sta_17_1: ui:group: ab initio mode rair_end_17_1: ui:group: ab initio mode nrair_18: ui:group: ab initio mode - rair_start_18_1: + rair_sta_18_1: ui:group: ab initio mode rair_end_18_1: ui:group: ab initio mode nrair_19: ui:group: ab initio mode - rair_start_19_1: + rair_sta_19_1: ui:group: ab initio mode rair_end_19_1: ui:group: ab initio mode nrair_20: ui:group: ab initio mode - rair_start_20_1: + rair_sta_20_1: ui:group: ab initio mode rair_end_20_1: ui:group: ab initio mode @@ -4253,2538 +4253,3400 @@ nodes: schema: type: object properties: - tolerance: - default: 5 - type: number - maximum: 9999 - minimum: -9999 - log_level: - default: verbose - type: string - minLength: 0 - maxLength: 100 - ambig_fname: - type: string - format: uri-reference - unambig_fname: - type: string - format: uri-reference - dihe_fname: - type: string - format: uri-reference - hbond_fname: - type: string - format: uri-reference - ligand_param_fname: - type: string - format: uri-reference - ligand_top_fname: - type: string - format: uri-reference - sampling_factor: - default: 1 - type: number - maximum: 9999 - minimum: -9999 - iniseed: - default: 917 - type: number - maximum: 9999 - minimum: -9999 - keepwater: + mol_fix_origin_1: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - mdsteps_rigid: - default: 500 - type: number - maximum: 9999 - minimum: -9999 - mdsteps_cool1: - default: 500 - type: number - maximum: 9999 - minimum: -9999 - mdsteps_cool2: - default: 1000 - type: number - maximum: 9999 - minimum: -9999 - mdsteps_cool3: - default: 1000 - type: number - maximum: 9999 - minimum: -9999 - timestep: - default: 0.002 - type: number - maximum: 9999 - minimum: -9999 - tadfactor: - default: 8 - type: number - maximum: 9999 - minimum: -9999 - sinter_rigid_init: - default: 0.001 - type: number - maximum: 9999 - minimum: -9999 - sinter_rigid_final: - default: 0.001 - type: number - maximum: 9999 - minimum: -9999 - sinter_cool2_init: - default: 0.001 - type: number - maximum: 9999 - minimum: -9999 - sinter_cool2_final: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - sinter_cool3_init: - default: 0.05 - type: number - maximum: 9999 - minimum: -9999 - sinter_cool3_final: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - temp_high: - default: 2000 - type: number - maximum: 9999 - minimum: -9999 - temp_cool1_init: - default: 2000 - type: number - maximum: 9999 - minimum: -9999 - temp_cool1_final: - default: 500 - type: number - maximum: 9999 - minimum: -9999 - temp_cool2_init: - default: 1000 - type: number - maximum: 9999 - minimum: -9999 - temp_cool2_final: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - temp_cool3_init: - default: 1000 - type: number - maximum: 9999 - minimum: -9999 - temp_cool3_final: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - shape_1: + mol_fix_origin_2: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_2: + mol_fix_origin_3: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_3: + mol_fix_origin_4: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_4: + mol_fix_origin_5: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_5: + mol_fix_origin_6: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_6: + mol_fix_origin_7: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_7: + mol_fix_origin_8: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_8: + mol_fix_origin_9: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_9: + mol_fix_origin_10: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_10: + mol_fix_origin_11: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_11: + mol_fix_origin_12: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_12: + mol_fix_origin_13: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_13: + mol_fix_origin_14: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_14: + mol_fix_origin_15: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_15: + mol_fix_origin_16: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_16: + mol_fix_origin_17: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_17: + mol_fix_origin_18: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_18: + mol_fix_origin_19: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_19: + mol_fix_origin_20: default: false + title: Fix molecule + description: Fixes the molecule in its original position. + $comment: Fixes the molecule in its original position. type: boolean - shape_20: + mol_shape_1: default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - amb_hot: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - amb_cool1: - default: 10 - type: number - maximum: 9999 - minimum: -9999 - amb_cool2: - default: 50 - type: number - maximum: 9999 - minimum: -9999 - amb_cool3: - default: 50 - type: number - maximum: 9999 - minimum: -9999 + mol_shape_2: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_3: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_4: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_5: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_6: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_7: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_8: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_9: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_10: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_11: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_12: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_13: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_14: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_15: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_16: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_17: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_18: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_19: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + mol_shape_20: + default: false + title: Is the molecule a shape? + description: Defines a molecule as a shape. + $comment: Defines a molecule as a shape, which is a collection of beads. + type: boolean + 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 + amb_hot: + default: 10 + title: Hot phase SA force constant for ambiguous distance restraints + description: Force constant applied to the distance restraints defined in + ambig_fname during the hot phase of the SA. + $comment: Force constant applied to the distance restraints defined in ambig_fname + during the initial hot phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). + type: number + maximum: 1000 + minimum: 0 + amb_cool1: + default: 10 + title: First cooling SA force constant for ambiguous distance restraints + description: Force constant applied to the distance restraints defined in + ambig_fname during the first cooling phase of the SA. + $comment: Force constant applied to the distance restraints defined in ambig_fname + during the first cooling phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). + type: number + maximum: 1000 + minimum: 0 + amb_cool2: + default: 50 + title: Second cooling SA force constant for ambiguous distance restraints + description: Force constant applied to the distance restraints defined in + ambig_fname during the second cooling phase of the SA. + $comment: Force constant applied to the distance restraints defined in ambig_fname + during the second cooling phase of the simulatd annealing protocol. Side-chains + at the interface are treated as flexible and any region defined in fully + flexible segments as fully flexible (see nfle_X parameter). + type: number + maximum: 1000 + minimum: 0 + amb_cool3: + default: 50 + title: Third cooling SA force constant for ambiguous distance restraints + description: Force constant applied to the distance restraints defined in + ambig_fname during the third cooling phase of the SA. + $comment: Force constant applied to the distance restraints defined in ambig_fname + during the third cooling phase of the simulatd annealing protocol. Side-chains + and backbone at the interface are treated as flexible and any region defined + in fully flexible segments as fully flexible (see nfle_X parameter). + type: number + maximum: 1000 + minimum: 0 unamb_hot: default: 10 + title: Hot phase SA force constant for unambiguous distance restraints + description: Force constant applied to the distance restraints defined in + unambig_fname during the hot phase of the SA. + $comment: Force constant applied to the distance restraints defined in unambig_fname + during the initial hot phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 unamb_cool1: default: 10 + title: Hot phase SA force constant for unambiguous distance restraints + description: Force constant applied to the distance restraints defined in + unambig_fname during the hot phase of the SA. + $comment: Force constant applied to the distance restraints defined in unambig_fname + during the initial hot phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 unamb_cool2: default: 50 + title: Hot phase SA force constant for unambiguous distance restraints + description: Force constant applied to the distance restraints defined in + ambig_fname during the hot phase of the SA. + $comment: Force constant applied to the distance restraints defined in unambig_fname + during the initial hot phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 unamb_cool3: default: 50 + title: Hot phase SA force constant for unambiguous distance restraints + description: Force constant applied to the distance restraints defined in + unambig_fname during the hot phase of the SA. + $comment: Force constant applied to the distance restraints defined in unambig_fname + during the initial hot phase of the simulatd annealing protocol. Molecules + are treated as rigid bodies unless fully flexible segments are defined (see + nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 hbond_hot: default: 10 + title: Hot phase SA force constant for hbond distance restraints + description: Force constant applied to the hydrogen bond restraints defined + in hbond_fname during the hot phase of the SA. + $comment: Force constant applied to the hydrogen bond restraints defined in + hbond_fname during the initial hot phase of the simulatd annealing protocol. + Molecules are treated as rigid bodies unless fully flexible segments are + defined (see nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 hbond_cool1: default: 10 + title: Hot phase SA force constant for hydrogen bond restraints + description: Force constant applied to the hydrogen bond restraints defined + in hbond_fname during the hot phase of the SA. + $comment: Force constant applied to the hydrogen bond restraints defined in + hbond_fname during the initial hot phase of the simulatd annealing protocol. + Molecules are treated as rigid bodies unless fully flexible segments are + defined (see nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 hbond_cool2: default: 50 + title: Hot phase SA force constant for hydrogen bond restraints + description: Force constant applied to the hydrogen bond restraints defined + in hbond_fname during the hot phase of the SA. + $comment: Force constant applied to the hydrogen bond restraints defined in + hbond_fname during the initial hot phase of the simulatd annealing protocol. + Molecules are treated as rigid bodies unless fully flexible segments are + defined (see nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 hbond_cool3: default: 50 + title: Hot phase SA force constant for hydrogen bond restraints + description: Force constant applied to the hydrogen bond restraints defined + in hbond_fname during the hot phase of the SA. + $comment: Force constant applied to the hydrogen bond restraints defined in + hbond_fname during the initial hot phase of the simulatd annealing protocol. + Molecules are treated as rigid bodies unless fully flexible segments are + defined (see nfle_X parameter). type: number - maximum: 9999 - minimum: -9999 - hbonds_on: - default: false - type: boolean - noecv: - default: false + 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 - ncvpart: + 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: 9999 - minimum: -9999 - mrswi_hot: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - mrswi_cool1: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - mrswi_cool2: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - mrswi_cool3: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - rswi_hot: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - rswi_cool1: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - rswi_cool2: - default: 0.5 + 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: 9999 - minimum: -9999 - rswi_cool3: - default: 0.5 - type: number - maximum: 9999 - minimum: -9999 - masy_hot: - default: -1.0 - type: number - maximum: 9999 - minimum: -9999 - masy_cool1: - default: -1.0 - type: number - maximum: 9999 - minimum: -9999 - masy_cool2: - default: -0.1 - type: number - maximum: 9999 - minimum: -9999 - masy_cool3: - default: -0.1 - type: number - maximum: 9999 - minimum: -9999 - asy_hot: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - asy_cool1: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - asy_cool2: - default: 0.1 - type: number - maximum: 9999 - minimum: -9999 - asy_cool3: - default: 0.1 - type: number - maximum: 9999 - minimum: -9999 + 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: false - type: boolean - ranair: - default: false + 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 - kcont: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - ksurf: + 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: 9999 - minimum: -9999 - surfrest: - default: false - type: boolean + 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_hot: default: 5 + title: Hot phase SA force constant for dihedral angle restraints + description: Hot phase SA force constant for dihedral angle restraints read + from dihe_fname. + $comment: Force constant applied to the dihedral angle restraints read from + dihe_fname during the initial hot phase of the simulatd annealing protocol. type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 dihedrals_cool1: default: 5 + title: First cooling SA force constant for dihedral angle restraints + description: First cooling SA force constant for dihedral angle restraints + read from dihe_fname. + $comment: Force constant applied to the dihedral angle restraints read from + dihe_fname during the first cooling phase of the simulatd annealing protocol. type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 dihedrals_cool2: default: 50 + title: Second cooling SA force constant for dihedral angle restraints + description: Second cooling SA force constant for dihedral angle restraints + read from dihe_fname. + $comment: Force constant applied to the dihedral angle restraints read from + dihe_fname during the second cooling phase of the simulatd annealing protocol. type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 dihedrals_cool3: default: 200 + title: Third cooling SA force constant for dihedral angle restraints + description: Third cooling SA force constant for dihedral angle restraints + read from dihe_fname. + $comment: Force constant applied to the dihedral angle restraints read from + dihe_fname during the third cooling phase of the simulatd annealing protocol. type: number - maximum: 9999 - minimum: -9999 + maximum: 1000 + minimum: 0 ssdihed: default: none + title: Define automatically backbone dihedral angle restraints + description: If turned on, this option will automatically defined backbone + dihedral angle restraints for the selected regions. + $comment: This option allows to utomatically defined backbone dihedral angle + restraints for the selected regions. The restraints will be defined for + the phi and psi backbone dihedral angles of amino acids, with the target + value taken from the measured angle in the input structure, and the error + bound defined by the error_dih parameter. Those restraints can be applied + to the entire structure (all), the alpha/beta secondary structure elements + (alphabeta) or only to the alpha helical regions (alpha). Those are automatically + detected based on the measured dihedral angle combinations. type: string minLength: 0 maxLength: 100 + enum: + - none + - all + - alpha + - alphabeta error_dih: default: 10 + title: Force constant for backbone dihedral angle restraints + description: Force constant for backbone dihedral angle restraints (ssdihed + option) + $comment: Force constant for backbone dihedral angle restraints (ssdihed option) type: number maximum: 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 - sym_on: - default: false - type: boolean - ksym: - default: 10.0 - type: number - maximum: 9999 - minimum: -9999 - numc2sym: - default: 0 + mrswi_hot: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c2sym_sta1_1: + mrswi_cool1: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c2sym_end1_1: + mrswi_cool2: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c2sym_seg1_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c2sym_sta2_1: + mrswi_cool3: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c2sym_end2_1: + rswi_hot: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c2sym_seg2_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - numc3sym: - default: 0 + rswi_cool1: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c3sym_sta1_1: + rswi_cool2: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c3sym_end1_1: + rswi_cool3: + default: 0.5 type: number maximum: 9999 minimum: -9999 - c3sym_seg1_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c3sym_sta2_1: + masy_hot: + default: -1.0 type: number maximum: 9999 minimum: -9999 - c3sym_end2_1: + masy_cool1: + default: -1.0 type: number maximum: 9999 minimum: -9999 - c3sym_seg2_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c3sym_sta3_1: + masy_cool2: + default: -0.1 type: number maximum: 9999 minimum: -9999 - c3sym_end3_1: + masy_cool3: + default: -0.1 type: number maximum: 9999 minimum: -9999 - c3sym_seg3_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - numc4sym: - default: 0 + asy_hot: + default: 1.0 type: number maximum: 9999 minimum: -9999 - c4sym_sta1_1: + asy_cool1: + default: 1.0 type: number maximum: 9999 minimum: -9999 - c4sym_end1_1: + asy_cool2: + default: 0.1 type: number maximum: 9999 minimum: -9999 - c4sym_seg1_1: - default: '' - type: string - minLength: 0 - maxLength: 100 - c4sym_sta2_1: + asy_cool3: + default: 0.1 type: number maximum: 9999 minimum: -9999 - c4sym_end2_1: + sym_on: + default: false + title: Symmetry restraints + description: Enables symmetry restraints + $comment: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 + supported) and the segments to which those apply must be defined. In addition + a custom symmetry restraint file can be supplied (symrest_fname). + type: boolean + ksym: + default: 10.0 + title: Force constant for symmetry restraints + description: Force constant for symmetry restraints + $comment: Force constant for symmetry restraints type: number - maximum: 9999 - minimum: -9999 - c4sym_seg2_1: - default: '' + maximum: 1000 + minimum: 0 + symtbl_fname: + title: Custom symmetry restraints filename + description: Filename of the custom symmetry restraints file + $comment: Filename of the custom symmetry restraints file. type: string - minLength: 0 - maxLength: 100 - c4sym_sta3_1: + format: uri-reference + numc2sym: + default: 0 + title: Number of C2 symmetry restraints + description: Defines the number of C2 symmetry restraints. + $comment: Defines the number of C2 symmetry restraints. For each, a pair of + segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + type: number + maximum: 40 + minimum: 0 + c2sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first C2 symmetry segment + $comment: Residue number of first residue in the first C2 symmetry segment type: number maximum: 9999 minimum: -9999 - c4sym_end3_1: + c2sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first C2 symmetry segment + $comment: Residue number of last residue in the first C2 symmetry segment type: number maximum: 9999 minimum: -9999 - c4sym_seg3_1: + c2sym_seg1_1: default: '' + title: Segment ID of first C2 segment + description: Segment ID of first C2 segment + $comment: Segment ID of first C2 segment type: string minLength: 0 - maxLength: 100 - c4sym_sta4_1: + maxLength: 4 + c2sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second C2 symmetry segment + $comment: Residue number of first residue in the second C2 symmetry segment type: number maximum: 9999 minimum: -9999 - c4sym_end4_1: + c2sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second C2 symmetry segment + $comment: Residue number of last residue in the second C2 symmetry segment type: number maximum: 9999 minimum: -9999 - c4sym_seg4_1: + c2sym_seg2_1: default: '' + title: Segment ID of second C2 segment + description: Segment ID of second C2 segment + $comment: Segment ID of second C2 segment type: string minLength: 0 - maxLength: 100 - numc5sym: + maxLength: 4 + numc3sym: default: 0 + title: Number of C3 symmetry restraints + description: Defines the number of C3 symmetry restraints. + $comment: Defines the number of C3 symmetry restraints. For each, three segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. type: number - maximum: 9999 - minimum: -9999 - c5sym_sta1_1: + maximum: 10 + minimum: 0 + c3sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first C3 symmetry segment + $comment: Residue number of first residue in the first C3 symmetry segment type: number maximum: 9999 minimum: -9999 - c5sym_end1_1: + c3sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first C3 symmetry segment + $comment: Residue number of last residue in the first C3 symmetry segment type: number maximum: 9999 minimum: -9999 - c5sym_seg1_1: + c3sym_seg1_1: default: '' + title: Segment ID of first C3 segment + description: Segment ID of first C3 segment + $comment: Segment ID of first C3 segment type: string minLength: 0 - maxLength: 100 - c5sym_sta2_1: + maxLength: 4 + c3sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second C3 symmetry segment + $comment: Residue number of first residue in the second C3 symmetry segment type: number maximum: 9999 minimum: -9999 - c5sym_end2_1: + c3sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second C3 symmetry segment + $comment: Residue number of last residue in the second C3 symmetry segment type: number maximum: 9999 minimum: -9999 - c5sym_seg2_1: + c3sym_seg2_1: default: '' + title: Segment ID of second C3 segment + description: Segment ID of second C3 segment + $comment: Segment ID of second C3 segment type: string minLength: 0 - maxLength: 100 - c5sym_sta3_1: + maxLength: 4 + c3sym_sta3_1: + title: Residue number of first residue + description: Residue number of first residue in the third C3 symmetry segment + $comment: Residue number of first residue in the third C3 symmetry segment type: number maximum: 9999 minimum: -9999 - c5sym_end3_1: + c3sym_end3_1: + title: Residue number of last residue + description: Residue number of last residue in the third C3 symmetry segment + $comment: Residue number of last residue in the third C3 symmetry segment type: number maximum: 9999 minimum: -9999 - c5sym_seg3_1: + c3sym_seg3_1: default: '' + title: Segment ID of third C3 segment + description: Segment ID of third C3 segment + $comment: Segment ID of third C3 segment type: string minLength: 0 - maxLength: 100 - c5sym_sta4_1: + maxLength: 4 + numc4sym: + default: 0 + title: Number of C4 symmetry restraints + description: Defines the number of C4 symmetry restraints. + $comment: Defines the number of C4 symmetry restraints. For each, four segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. + type: number + maximum: 10 + minimum: 0 + c4sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first C4 symmetry segment + $comment: Residue number of first residue in the first C4 symmetry segment type: number maximum: 9999 minimum: -9999 - c5sym_end4_1: + c4sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first C4 symmetry segment + $comment: Residue number of last residue in the first C4 symmetry segment type: number maximum: 9999 minimum: -9999 - c5sym_seg4_1: + c4sym_seg1_1: default: '' + title: Segment ID of first C4 segment + description: Segment ID of first C4 segment + $comment: Segment ID of first C4 segment type: string minLength: 0 - maxLength: 100 - c5sym_sta5_1: + maxLength: 4 + c4sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second C4 symmetry segment + $comment: Residue number of first residue in the second C4 symmetry segment type: number maximum: 9999 minimum: -9999 - c5sym_end5_1: + c4sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second C4 symmetry segment + $comment: Residue number of last residue in the second C4 symmetry segment type: number maximum: 9999 minimum: -9999 - c5sym_seg5_1: + c4sym_seg2_1: default: '' + title: Segment ID of second C4 segment + description: Segment ID of second C4 segment + $comment: Segment ID of second C4 segment type: string minLength: 0 - maxLength: 100 - numc6sym: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - c6sym_sta1_1: + maxLength: 4 + c4sym_sta3_1: + title: Residue number of first residue + description: Residue number of first residue in the third C4 symmetry segment + $comment: Residue number of first residue in the third C4 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_end1_1: + c4sym_end3_1: + title: Residue number of last residue + description: Residue number of last residue in the third C4 symmetry segment + $comment: Residue number of last residue in the third C4 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_seg1_1: + c4sym_seg3_1: default: '' + title: Segment ID of third C4 segment + description: Segment ID of third C4 segment + $comment: Segment ID of third C4 segment type: string minLength: 0 - maxLength: 100 - c6sym_sta2_1: + maxLength: 4 + c4sym_sta4_1: + title: Residue number of first residue + description: Residue number of first residue in the fourth C4 symmetry segment + $comment: Residue number of first residue in the fourth C4 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_end2_1: + c4sym_end4_1: + title: Residue number of last residue + description: Residue number of last residue in the fourth C4 symmetry segment + $comment: Residue number of last residue in the fourth C4 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_seg2_1: + c4sym_seg4_1: default: '' + title: Segment ID of fourth C4 segment + description: Segment ID of fourth C4 segment + $comment: Segment ID of fourth C4 segment type: string minLength: 0 - maxLength: 100 - c6sym_sta3_1: + maxLength: 4 + numc5sym: + default: 0 + title: Number of C5 symmetry restraints + description: Defines the number of C5 symmetry restraints. + $comment: Defines the number of C5 symmetry restraints. For each, five segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. + type: number + maximum: 10 + minimum: 0 + c5sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first C5 symmetry segment + $comment: Residue number of first residue in the first C5 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_end3_1: + c5sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first C5 symmetry segment + $comment: Residue number of last residue in the first C5 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_seg3_1: + c5sym_seg1_1: default: '' + title: Segment ID of first C5 segment + description: Segment ID of first C5 segment + $comment: Segment ID of first C5 segment type: string minLength: 0 - maxLength: 100 - c6sym_sta4_1: + maxLength: 4 + c5sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second C5 symmetry segment + $comment: Residue number of first residue in the second C5 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_end4_1: + c5sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second C5 symmetry segment + $comment: Residue number of last residue in the second C5 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_seg4_1: + c5sym_seg2_1: default: '' + title: Segment ID of second C5 segment + description: Segment ID of second C5 segment + $comment: Segment ID of second C5 segment type: string minLength: 0 - maxLength: 100 - c6sym_sta5_1: + maxLength: 4 + c5sym_sta3_1: + title: Residue number of first residue + description: Residue number of first residue in the third C5 symmetry segment + $comment: Residue number of first residue in the third C5 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_end5_1: + c5sym_end3_1: + title: Residue number of last residue + description: Residue number of last residue in the third C5 symmetry segment + $comment: Residue number of last residue in the third C5 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_seg5_1: + c5sym_seg3_1: default: '' + title: Segment ID of third C5 segment + description: Segment ID of third C5 segment + $comment: Segment ID of third C5 segment type: string minLength: 0 - maxLength: 100 - c6sym_sta6_1: + maxLength: 4 + c5sym_sta4_1: + title: Residue number of first residue + description: Residue number of first residue in the fourth C5 symmetry segment + $comment: Residue number of first residue in the fourth C5 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_end6_1: + c5sym_end4_1: + title: Residue number of last residue + description: Residue number of last residue in the fourth C5 symmetry segment + $comment: Residue number of last residue in the fourth C5 symmetry segment type: number maximum: 9999 minimum: -9999 - c6sym_seg6_1: + c5sym_seg4_1: default: '' + title: Segment ID of fourth C5 segment + description: Segment ID of fourth C5 segment + $comment: Segment ID of fourth C5 segment type: string minLength: 0 - maxLength: 100 - nums3sym: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - s3sym_sta1_1: + maxLength: 4 + c5sym_sta5_1: + title: Residue number of first residue + description: Residue number of first residue in the fifth C5 symmetry segment + $comment: Residue number of first residue in the fifth C5 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_end1_1: + c5sym_end5_1: + title: Residue number of last residue + description: Residue number of last residue in the fifth C5 symmetry segment + $comment: Residue number of last residue in the fifth C5 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_seg1_1: + c5sym_seg5_1: default: '' + title: Segment ID of fifth C5 segment + description: Segment ID of fifth C5 segment + $comment: Segment ID of fifth C5 segment type: string minLength: 0 - maxLength: 100 - s3sym_sta2_1: + maxLength: 4 + numc6sym: + default: 0 + title: Number of C6 symmetry restraints + description: Defines the number of C6 symmetry restraints. + $comment: Defines the number of C6 symmetry restraints. For each, six segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. + type: number + maximum: 10 + minimum: 0 + c6sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first C6 symmetry segment + $comment: Residue number of first residue in the first C6 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_end2_1: + c6sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first C6 symmetry segment + $comment: Residue number of last residue in the first C6 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_seg2_1: + c6sym_seg1_1: default: '' + title: Segment ID of first C6 segment + description: Segment ID of first C6 segment + $comment: Segment ID of first C6 segment type: string minLength: 0 - maxLength: 100 - s3sym_sta3_1: + maxLength: 4 + c6sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second C6 symmetry segment + $comment: Residue number of first residue in the second C6 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_end3_1: + c6sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second C6 symmetry segment + $comment: Residue number of last residue in the second C6 symmetry segment type: number maximum: 9999 minimum: -9999 - s3sym_seg3_1: + c6sym_seg2_1: default: '' + title: Segment ID of second C6 segment + description: Segment ID of second C6 segment + $comment: Segment ID of second C6 segment type: string minLength: 0 - maxLength: 100 - ncs_on: - default: false - type: boolean - kncs: - default: 1.0 + maxLength: 4 + c6sym_sta3_1: + title: Residue number of first residue + description: Residue number of first residue in the third C6 symmetry segment + $comment: Residue number of first residue in the third C6 symmetry segment type: number maximum: 9999 minimum: -9999 - numncs: - default: 0 + c6sym_end3_1: + title: Residue number of last residue + description: Residue number of last residue in the third C6 symmetry segment + $comment: Residue number of last residue in the third C6 symmetry segment type: number maximum: 9999 minimum: -9999 - ncs_sta1_1: + c6sym_seg3_1: + default: '' + title: Segment ID of third C6 segment + description: Segment ID of third C6 segment + $comment: Segment ID of third C6 segment + type: string + minLength: 0 + maxLength: 4 + c6sym_sta4_1: + title: Residue number of first residue + description: Residue number of first residue in the fourth C6 symmetry segment + $comment: Residue number of first residue in the fourth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - ncs_end1_1: + c6sym_end4_1: + title: Residue number of last residue + description: Residue number of last residue in the fourth C6 symmetry segment + $comment: Residue number of last residue in the fourth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - ncs_seg1_1: + c6sym_seg4_1: default: '' + title: Segment ID of fourth C6 segment + description: Segment ID of fourth C6 segment + $comment: Segment ID of fourth C6 segment type: string minLength: 0 - maxLength: 100 - ncs_sta2_1: + maxLength: 4 + c6sym_sta5_1: + title: Residue number of first residue + description: Residue number of first residue in the fifth C6 symmetry segment + $comment: Residue number of first residue in the fifth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - ncs_end2_1: + c6sym_end5_1: + title: Residue number of last residue + description: Residue number of last residue in the fifth C6 symmetry segment + $comment: Residue number of last residue in the fifth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - ncs_seg2_1: + c6sym_seg5_1: default: '' + title: Segment ID of fifth C6 segment + description: Segment ID of fifth C6 segment + $comment: Segment ID of fifth C6 segment type: string minLength: 0 - maxLength: 100 - fix_origin_1: - default: false - type: boolean - fix_origin_2: - default: false - type: boolean - fix_origin_3: - default: false - type: boolean - fix_origin_4: - default: false - type: boolean - fix_origin_5: - default: false - type: boolean - fix_origin_6: - default: false - type: boolean - fix_origin_7: - default: false - type: boolean - fix_origin_8: - default: false - type: boolean - fix_origin_9: - default: false - type: boolean - fix_origin_10: - default: false - type: boolean - fix_origin_11: - default: false - type: boolean - fix_origin_12: - default: false - type: boolean - fix_origin_13: - default: false - type: boolean - fix_origin_14: - default: false - type: boolean - fix_origin_15: - default: false - type: boolean - fix_origin_16: - default: false - type: boolean - fix_origin_17: - default: false - type: boolean - fix_origin_18: - default: false - type: boolean - fix_origin_19: - default: false - type: boolean - fix_origin_20: - default: false - type: boolean - nfle1: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - flesta1_1: + maxLength: 4 + c6sym_sta6_1: + title: Residue number of first residue + description: Residue number of first residue in the sixth C6 symmetry segment + $comment: Residue number of first residue in the sixth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend1_1: + c6sym_end6_1: + title: Residue number of last residue + description: Residue number of last residue in the sixth C6 symmetry segment + $comment: Residue number of last residue in the sixth C6 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle2: + c6sym_seg6_1: + default: '' + title: Segment ID of sixth C6 segment + description: Segment ID of sixth C6 segment + $comment: Segment ID of sixth C6 segment + type: string + minLength: 0 + maxLength: 4 + nums3sym: default: 0 + title: Number of S3 symmetry restraints + description: Defines the number of S3 symmetry restraints. + $comment: Defines the number of S3 symmetry restraints. For each, three segments + on which the symmetry restraint is applied will have to be defined. Those + must all have the same length. + type: number + maximum: 10 + minimum: 0 + s3sym_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first S3 symmetry segment + $comment: Residue number of first residue in the first S3 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta2_1: + s3sym_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first S3 symmetry segment + $comment: Residue number of last residue in the first S3 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend2_1: + s3sym_seg1_1: + default: '' + title: Segment ID of first S3 segment + description: Segment ID of first S3 segment + $comment: Segment ID of first S3 segment + type: string + minLength: 0 + maxLength: 4 + s3sym_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second S3 symmetry segment + $comment: Residue number of first residue in the second S3 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle3: - default: 0 + s3sym_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second S3 symmetry segment + $comment: Residue number of last residue in the second S3 symmetry segment type: number maximum: 9999 minimum: -9999 - flesta3_1: + s3sym_seg2_1: + default: '' + title: Segment ID of second S3 segment + description: Segment ID of second S3 segment + $comment: Segment ID of second S3 segment + type: string + minLength: 0 + maxLength: 4 + s3sym_sta3_1: + title: Residue number of first residue + description: Residue number of first residue in the third S3 symmetry segment + $comment: Residue number of first residue in the third S3 symmetry segment type: number maximum: 9999 minimum: -9999 - fleend3_1: + s3sym_end3_1: + title: Residue number of last residue + description: Residue number of last residue in the third S3 symmetry segment + $comment: Residue number of last residue in the third S3 symmetry segment type: number maximum: 9999 minimum: -9999 - nfle4: + s3sym_seg3_1: + default: '' + title: Segment ID of third S3 segment + description: Segment ID of third S3 segment + $comment: Segment ID of third S3 segment + type: string + minLength: 0 + maxLength: 4 + ncs_on: + default: false + title: Non-crystallographic symmetry restraints + description: Non-crystallographic symmetry restraints to ensure two molecules + will have the same conformation. + $comment: Non-crystallographic symmetry restraints to ensure two molecules + will have the same conformation. This does not apply any symmetry between + the two molecules but rather defines restraints such as the RMSD between + those is 0. + type: boolean + kncs: + default: 1.0 + title: Force constant for non-crystallographic restraints + description: Force constant for non-crystallographic restraints + $comment: Force constant for non-crystallographic restraints + type: number + maximum: 1000 + minimum: 0 + numncs: default: 0 + title: Number of non-crystallographic symmetry restraints + description: Number of non-crystallographic symmetry restraints (NCS). + $comment: Number of non-crystallographic symmetry restraints. For each pairs + of segments will have to be defined. Note that those must contain exactly + the same residues/atom combinations. type: number - maximum: 9999 - minimum: -9999 - flesta4_1: + maximum: 100 + minimum: 0 + ncs_sta1_1: + title: Residue number of first residue + description: Residue number of first residue in the first NCS segment + $comment: Residue number of first residue in the first NCS segment type: number maximum: 9999 minimum: -9999 - fleend4_1: + ncs_end1_1: + title: Residue number of last residue + description: Residue number of last residue in the first NCS segment + $comment: Residue number of last residue in the first NCS segment type: number maximum: 9999 minimum: -9999 - nfle5: - default: 0 + ncs_seg1_1: + default: '' + title: Segment ID of first NCS segment + description: Segment ID of first NCS segment + $comment: Segment ID of first NCS segment + type: string + minLength: 0 + maxLength: 100 + ncs_sta2_1: + title: Residue number of first residue + description: Residue number of first residue in the second NCS segment + $comment: Residue number of first residue in the second NCS segment type: number maximum: 9999 minimum: -9999 - flesta5_1: + ncs_end2_1: + title: Residue number of last residue + description: Residue number of last residue in the second NCS segment + $comment: Residue number of last residue in the second NCS segment type: number maximum: 9999 minimum: -9999 - fleend5_1: + ncs_seg2_1: + default: '' + title: Segment ID of second NCS segment + description: Segment ID of second NCS segment + $comment: Segment ID of second NCS segment + type: string + minLength: 0 + maxLength: 100 + w_air: + default: 0.1 + title: Weight of the distance restraint energy + description: Weight of the distance restraints energy in the scoring function + $comment: Weight of the distance restraints energy in the scoring function. + Note that this is different from the force constants used during the calculations. type: number maximum: 9999 - minimum: -9999 - nfle6: - default: 0 + minimum: 0 + w_bsa: + default: -0.01 + title: Weight of the buried surface area term + description: Weight of the buried surface area term in the scoring function + $comment: Weight of the buried surface area (BSA) term in the scoring function. + Note that the BSA is only used for scoring. type: number maximum: 9999 minimum: -9999 - flesta6_1: + w_cdih: + default: 0.0 + title: Weight of the dihedral angle restraint energy + description: Weight of the dihedral angle restraints energy in the scoring + function + $comment: Weight of the dihedral angle restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. type: number maximum: 9999 - minimum: -9999 - fleend6_1: + 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 - nfle7: - default: 0 + w_elec: + default: 1.0 + title: Weight of the intermolecular electrostatic energy + description: Weight of the intermolecular electrostatic energy in the scoring + function + $comment: Weight of the intermolecular electrostatic energy in the scoring + function. Note that this does not affect the electostatic energy during + the MD refinement. type: number maximum: 9999 minimum: -9999 - flesta7_1: + w_sym: + default: 0.1 + title: Weight of the symmetry restraint energy + description: Weight of the symmetry restraints energy in the scoring function + $comment: Weight of the symmetry restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. type: number maximum: 9999 - minimum: -9999 - fleend7_1: + minimum: 0 + 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 MD refinement. type: number maximum: 9999 minimum: -9999 - nfle8: - default: 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 + format: uri-reference + ligand_top_fname: + title: Custom ligand topology file + description: Ligand topology file in CNS format + $comment: Ligand topology file in CNS format containing the ligand topologies + (atoms, masses, charges, bond definitions...) for any ligand not supported + by default by HADDOCK + type: string + format: uri-reference + elecflag: + default: true + title: Include electrostatics energy + description: Include electrostatics energy during the calculations. + $comment: Include electrostatics energy during the calculations. If set to + false electrostatics will not be considered. + type: boolean + dielec: + default: rdie + title: Constant (cdie) or distance-dependent dielectric (rdie) constant. + description: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. + $comment: Use a constant (cdie option) or a distance-dependent dielectric + (rdie) constant in the Coulomb potential. A distance dependent dielectric + constant will effectively scale down the electrostatic energy by having + a 1/r**2 dependency instead of 1/r + type: string + minLength: 0 + maxLength: 4 + enum: + - cdie + - rdie + epsilon: + default: 1.0 + title: Dielectric constant + description: Dielectric constant for the electrostatic Coulomb energy term. + $comment: Dielectric constant for the electrostatic Coulomb energy term. type: number - maximum: 9999 - minimum: -9999 - flesta8_1: + maximum: 78 + minimum: 1 + dihedflag: + default: true + title: Use torsion angle dihedral energy term + description: Turns on the torsion angle dihedral energy terms of the force + field. + $comment: Turns on the torsion angle dihedral energy terms of the force field. + type: boolean + sampling_factor: + default: 1 + title: Sampling factor for each starting model + description: This paramater control how many times a model will be refined. + $comment: This paramater control how many times a model will be refined. type: number - maximum: 9999 - minimum: -9999 - fleend8_1: + maximum: 1 + minimum: 1 + 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 - nfle9: - default: 0 + maximum: 10000 + minimum: 1 + mdsteps_rigid: + default: 500 + title: Hot phase SA MD steps + description: Number of MD steps for the hot phase of the SA. + $comment: Number of MD steps for the hot phase rigid body dynamics of the + simulated annealing protocol. type: number - maximum: 9999 - minimum: -9999 - flesta9_1: + maximum: 10000 + minimum: 0 + mdsteps_cool1: + default: 500 + title: First cooling phase SA MD steps + description: Number of MD steps for the first cooling phase of the SA. + $comment: Number of MD steps for the first cooling phase of rigid body dynamics + of the simulated annealing protocol. type: number - maximum: 9999 - minimum: -9999 - fleend9_1: + maximum: 10000 + minimum: 0 + mdsteps_cool2: + default: 1000 + title: Second cooling phase SA MD steps + description: Number of MD steps for the second cooling phase of the SA. + $comment: Number of MD steps for the second cooling phase of torsion angle + dynamics of the simulated annealing protocol with flexible side-chains at + the interface. Full flexibility is applied to the segments defined as fully + flexible (see nfle_X and related parameters). type: number - maximum: 9999 - minimum: -9999 - nfle10: - default: 0 + maximum: 10000 + minimum: 0 + mdsteps_cool3: + default: 1000 + title: Third cooling phase SA MD steps + description: Number of MD steps for the third cooling phase of the SA. + $comment: Number of MD steps for the third cooling phase of torsion angle + dynamics of the simulated annealing protocol with flexible side-chains and + backbone at the interface. Full flexibility is applied to the segments defined + as fully flexible (see nfle_X and related parameters). type: number - maximum: 9999 - minimum: -9999 - flesta10_1: + maximum: 10000 + minimum: 0 + timestep: + default: 0.002 + title: MD integrating time step + description: Integration time step for the torsion angle molecular dynamics. + $comment: Integration time step for the torsion angle molecular dynamics. type: number - maximum: 9999 - minimum: -9999 - fleend10_1: + maximum: 0.004 + minimum: 0.0005 + tadfactor: + default: 8 + title: Scaling factor for the integration time step. + description: Initial scaling factor for the integration time step of the hot + phase SA. + $comment: Scaling factor applied at the start of the simulated annealing protocol + to the timestep using during torsion angle molecular dynamics. This factor + is automatically reduced during the SA protocol. type: number - maximum: 9999 - minimum: -9999 - nfle11: - default: 0 + maximum: 10 + minimum: 1 + temp_high: + default: 2000 + title: Initial rigid-body MD temperature + description: Temperature for the initial rigid-body MD phase in Kelvin. + $comment: Temperature in Kelvin for the initial rigid-body molecular dynamic + phase of the simulated annealing protocol. type: number - maximum: 9999 - minimum: -9999 - flesta11_1: + maximum: 5000 + minimum: 1 + temp_cool1_init: + default: 2000 + title: Start temperature for the 1st cooling phase + description: Starting temperature for the first rigid-body MD cooling phase + in Kelvin. + $comment: Starting temperature in Kelvin for the first rigid-body molecular + dynamic cooling phase of the simulated annealing protocol. type: number - maximum: 9999 - minimum: -9999 - fleend11_1: - type: number - maximum: 9999 - minimum: -9999 - nfle12: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - flesta12_1: - type: number - maximum: 9999 - minimum: -9999 - fleend12_1: - type: number - maximum: 9999 - minimum: -9999 - nfle13: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - flesta13_1: - type: number - maximum: 9999 - minimum: -9999 - fleend13_1: - type: number - maximum: 9999 - minimum: -9999 - nfle14: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - flesta14_1: - type: number - maximum: 9999 - minimum: -9999 - fleend14_1: - type: number - maximum: 9999 - minimum: -9999 - nfle15: - default: 0 - type: number - maximum: 9999 - minimum: -9999 - flesta15_1: - type: number - maximum: 9999 - minimum: -9999 - fleend15_1: - type: number - maximum: 9999 - minimum: -9999 - nfle16: - default: 0 + maximum: 5000 + minimum: 1 + temp_cool1_final: + default: 500 + title: End temperature for the 1st cooling phase + description: End temperature for the first rigid-body MD cooling phase in + Kelvin. + $comment: End temperature in Kelvin for the first rigid-body molecular dynamic + cooling phase of the simulated annealing protocol. type: number - maximum: 9999 - minimum: -9999 - flesta16_1: + maximum: 1000 + minimum: 1 + temp_cool2_init: + default: 1000 + title: Start temperature for the 2nd cooling phase + description: Starting temperature for the second MD cooling phase in Kelvin. + $comment: Starting temperature in Kelvin for the second torsion angle molecular + dynamic cooling phase of the simulated annealing protocol in which side-chains + at the interface are treated as flexible. type: number - maximum: 9999 - minimum: -9999 - fleend16_1: + maximum: 2000 + minimum: 1 + temp_cool2_final: + default: 50 + title: End temperature for the 2nd cooling phase + description: End temperature for the second MD cooling phase in Kelvin. + $comment: End temperature in Kelvin for the second torsion angle molecular + dynamic cooling phase of the simulated annealing protocol in which side-chains + at the interface are treated as flexible. type: number - maximum: 9999 - minimum: -9999 - nfle17: - default: 0 + maximum: 1000 + minimum: 1 + temp_cool3_init: + default: 1000 + title: Start temperature for the 3rd cooling phase + description: Starting temperature for the third MD cooling phase in Kelvin. + $comment: Starting temperature in Kelvin for the third and final torsion angle + molecular dynamic cooling phase of the simulated annealing protocol in which + side-chains and backbone at the interface are treated as flexible. type: number - maximum: 9999 - minimum: -9999 - flesta17_1: + maximum: 1000 + minimum: 1 + temp_cool3_final: + default: 50 + title: End temperature for the 3rd cooling phase + description: End temperature for the third MD cooling phase in Kelvin. + $comment: End temperature in Kelvin for the third and final torsion angle + molecular dynamic cooling phase of the simulated annealing protocol in which + side-chains and backbone at the interface are treated as flexible. type: number - maximum: 9999 - minimum: -9999 - fleend17_1: + maximum: 1000 + minimum: 1 + sinter_rigid_init: + default: 0.001 + title: Initial rigid-body MD intermolecular interactions scaling factor. + description: Initial scaling factor for intermolecular interactions in the + first two SA stages + $comment: Initial scaling factor applied to intermolecular interactions during + the first rigid-body molecular dynamics stage and at the start of the first + cooling stage of the of the simulated annealing protocol. type: number - maximum: 9999 - minimum: -9999 - nfle18: - default: 0 + maximum: 1 + minimum: 1.0e-05 + 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: 9999 - minimum: -9999 - flesta18_1: + maximum: 1 + minimum: 1.0e-05 + sinter_cool2_init: + default: 0.001 + title: Initial intermolecular interactions scaling factor for the 2nd cooling + phase. + description: Initial scaling factor for intermolecular interactions in the + second MD cooling SA stage. + $comment: Initial scaling factor applied to intermolecular interactions during + the second torsion angle molecular dynamics cooling stage of the simulated + annealing protocol during which side-chains at the interface are treated + as flexible. type: number - maximum: 9999 - minimum: -9999 - fleend18_1: + maximum: 1 + minimum: 1.0e-05 + sinter_cool2_final: + default: 1.0 + title: End intermolecular interactions scaling factor for the 2nd cooling + phase. + description: End scaling factor for intermolecular interactions in the second + MD cooling SA stage. + $comment: End scaling factor applied to intermolecular interactions during + the second torsion angle molecular dynamics cooling stage of the simulated + annealing protocol during which side-chains at the interface are treated + as flexible. type: number - maximum: 9999 - minimum: -9999 - nfle19: - default: 0 + maximum: 1 + minimum: 1.0e-05 + sinter_cool3_init: + default: 0.05 + title: Initial intermolecular interactions scaling factor for the 3rd cooling + phase. + description: Initial scaling factor for intermolecular interactions in the + third MD cooling SA stage. + $comment: Initial scaling factor applied to intermolecular interactions during + the third and final torsion angle molecular dynamics cooling stage of the + simulated annealing protocol during which both side-chains and backbone + at the interface are treated as flexible. type: number - maximum: 9999 - minimum: -9999 - flesta19_1: + maximum: 1 + minimum: 1.0e-05 + sinter_cool3_final: + default: 1.0 + title: End intermolecular interactions scaling factor for the 3rd cooling + phase. + description: End scaling factor for intermolecular interactions in the third + MD cooling SA stage. + $comment: End scaling factor applied to intermolecular interactions during + the third and final torsion angle molecular dynamics cooling stage of the + simulated annealing protocol during which both side-chains and backbone + at the interface are treated as flexible. type: number - maximum: 9999 - minimum: -9999 - fleend19_1: + maximum: 1 + minimum: 1.0e-05 + 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 - nfle20: + maximum: 9999999999999999 + minimum: 0 + keepwater: + default: false + title: Write water molecules to output file + description: Write water molecules if present to the output file. + $comment: Write water molecules if present to the output file. + type: boolean + tolerance: default: 0 + title: Failure tolerance percentage + description: Percentage of allowed failures for a module to successfully complete + $comment: Percentage of allowed failures for a module to successfully complete type: number - maximum: 9999 - minimum: -9999 - flesta20_1: - type: number - maximum: 9999 - minimum: -9999 - fleend20_1: - type: number - maximum: 9999 - minimum: -9999 + maximum: 99 + minimum: 0 + log_level: + default: verbose + title: Log level verbosity for CNS + description: Set the log level verbosity for CNS (minimal or verbose) + $comment: CNS, the computational engine used by HADDOCK can generate a lot + of output messages. This parameter controls the verbosity of CNS (minimal + or verbose) + type: string + minLength: 0 + maxLength: 100 nseg1: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta1_1: + maximum: 1000 + minimum: -1 + seg_sta_1_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend1_1: + seg_end_1_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg2: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta2_1: + maximum: 1000 + minimum: -1 + seg_sta_2_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend2_1: + seg_end_2_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg3: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta3_1: + maximum: 1000 + minimum: -1 + seg_sta_3_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend3_1: + seg_end_3_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg4: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta4_1: + maximum: 1000 + minimum: -1 + seg_sta_4_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend4_1: + seg_end_4_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg5: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta5_1: + maximum: 1000 + minimum: -1 + seg_sta_5_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend5_1: + seg_end_5_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg6: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta6_1: + maximum: 1000 + minimum: -1 + seg_sta_6_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend6_1: + seg_end_6_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg7: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta7_1: + maximum: 1000 + minimum: -1 + seg_sta_7_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend7_1: + seg_end_7_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg8: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta8_1: + maximum: 1000 + minimum: -1 + seg_sta_8_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend8_1: + seg_end_8_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg9: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta9_1: + maximum: 1000 + minimum: -1 + seg_sta_9_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend9_1: + seg_end_9_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg10: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta10_1: + maximum: 1000 + minimum: -1 + seg_sta_10_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend10_1: + seg_end_10_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg11: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta11_1: + maximum: 1000 + minimum: -1 + seg_sta_11_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend11_1: + seg_end_11_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg12: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta12_1: + maximum: 1000 + minimum: -1 + seg_sta_12_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend12_1: + seg_end_12_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg13: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta13_1: + maximum: 1000 + minimum: -1 + seg_sta_13_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend13_1: + seg_end_13_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg14: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta14_1: + maximum: 1000 + minimum: -1 + seg_sta_14_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend14_1: + seg_end_14_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg15: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta15_1: + maximum: 1000 + minimum: -1 + seg_sta_15_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend15_1: + seg_end_15_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg16: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta16_1: + maximum: 1000 + minimum: -1 + seg_sta_16_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend16_1: + seg_end_16_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg17: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta17_1: + maximum: 1000 + minimum: -1 + seg_sta_17_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend17_1: + seg_end_17_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg18: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. + type: number + maximum: 1000 + minimum: -1 + seg_sta_18_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segsta18_1: - type: number - maximum: 9999 - minimum: -9999 - segend18_1: + seg_end_18_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg19: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta19_1: + maximum: 1000 + minimum: -1 + seg_sta_19_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend19_1: + seg_end_19_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 nseg20: default: -1 + title: Number of semi-flexible segments + description: This defines the number of semi-flexible segments (-1 automatic, + 0 ridig, >1 manual definition). + $comment: This parameter defines the number of semi-flexible segments for + the specified molecule. If set to -1 then those are automatically defined + based on contacts. Those can also be manually defined by defining the number + of segment (nseg>=1). In that case the starting and ending residues of each + segment must be defined. The position of atoms in regions outside the semi-flexible + regions will have weak harmonic positional restraints during the energy + minimisation. If nseg is set to 0, then the molecule will be kept ridig. type: number - maximum: 9999 - minimum: -9999 - segsta20_1: - type: number - maximum: 9999 - minimum: -9999 - segend20_1: + maximum: 1000 + minimum: -1 + seg_sta_20_1: + title: Starting residue number + description: Residue number defining the start of the semi-flexible segment. + $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - w_air: - default: 0.1 + seg_end_20_1: + title: Ending residue number + description: Residue number defining the end of the semi-flexible segment. + $comment: Residue number defining the end of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - w_bsa: - default: -0.01 + nfle1: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - w_cdih: - default: 0.0 + maximum: 1000 + minimum: 0 + fle_sta_1_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_dani: - default: 0.1 + fle_end_1_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_deint: - default: 0.0 + nfle2: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - w_desolv: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_2_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_dist: - default: 0.1 + fle_end_2_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_elec: - default: 1.0 + nfle3: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - w_lcc: - default: -10000.0 + maximum: 1000 + minimum: 0 + fle_sta_3_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_rg: - default: 1.0 + fle_end_3_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_sani: - default: 0.1 + nfle4: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - w_sym: - default: 0.1 + maximum: 1000 + minimum: 0 + fle_sta_4_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_vdw: - default: 1.0 + fle_end_4_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_vean: - default: 0.1 + nfle5: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - w_xpcs: - default: 0.1 + maximum: 1000 + minimum: 0 + fle_sta_5_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_xrdc: - default: 0.1 + fle_end_5_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - w_zres: - default: 0.1 + nfle6: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - elecflag: - default: true - type: boolean - dielec: - default: rdie - type: string - minLength: 0 - maxLength: 100 - epsilon: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_6_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - dihedflag: - default: true - type: boolean - par_nonbonded: - default: OPLSX - type: string - minLength: 0 - maxLength: 100 - int_1_1: - default: 1.0 + fle_end_6_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_2: - default: 1.0 + nfle7: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_1_3: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_7_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_4: - default: 1.0 + fle_end_7_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_5: - default: 1.0 + nfle8: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_1_6: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_8_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_7: - default: 1.0 + fle_end_8_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_8: - default: 1.0 + nfle9: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_1_9: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_9_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_10: - default: 1.0 + fle_end_9_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_1_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_1_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_2_2: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_2_3: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_2_4: - default: 1.0 + nfle10: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_5: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_10_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_6: - default: 1.0 + fle_end_10_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_7: - default: 1.0 + nfle11: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_8: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_11_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_9: - default: 1.0 + fle_end_11_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_10: - default: 1.0 + nfle12: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_11: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_12_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_12: - default: 1.0 + fle_end_12_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_13: - default: 1.0 + nfle13: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_14: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_13_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_15: - default: 1.0 + fle_end_13_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_16: - default: 1.0 + nfle14: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_17: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_14_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_18: - default: 1.0 + fle_end_14_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_2_19: - default: 1.0 + nfle15: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_2_20: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_15_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_3: - default: 1.0 + fle_end_15_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_4: - default: 1.0 + nfle16: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_3_5: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_16_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_6: - default: 1.0 + fle_end_16_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_7: - default: 1.0 + nfle17: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_3_8: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_17_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_9: - default: 1.0 + fle_end_17_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_10: - default: 1.0 + nfle18: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_3_11: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_18_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_12: - default: 1.0 + fle_end_18_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_13: - default: 1.0 + nfle19: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_3_14: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_19_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_15: - default: 1.0 + fle_end_19_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_16: - default: 1.0 + nfle20: + default: 0 + title: Number of fully flexible segments + description: This defines the number of fully flexible segments. + $comment: This parameter defines the number of fully flexible segments for + the specified molecule. If >=1 then those must be defined manually with + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number - maximum: 9999 - minimum: -9999 - int_3_17: - default: 1.0 + maximum: 1000 + minimum: 0 + fle_sta_20_1: + title: Starting residue number + description: Residue number defining the start of the fully flexible segment. + $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - int_3_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_3_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_3_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_4: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_5: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_6: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_7: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_8: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_4_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_5: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_6: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_7: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_8: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_5_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_6: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_7: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_8: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_6_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_7: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_8: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_8: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_7_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_8_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_9: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_9_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_10: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_10_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_11: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_11_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_12: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_12_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_13: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_13_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_14: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_14_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_15: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_15_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_16: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_16_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_17: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_17_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_18_18: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_18_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_18_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_19_19: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_19_20: - default: 1.0 - type: number - maximum: 9999 - minimum: -9999 - int_20_20: - default: 1.0 + fle_end_20_1: + title: End residue number + description: Residue number defining the end of the fully flexible segment. + $comment: Residue number defining the end of the fully flexible segment. type: number maximum: 9999 minimum: -9999 required: [] additionalProperties: false uiSchema: + mol_fix_origin_1: + ui:group: molecule + mol_fix_origin_2: + ui:group: molecule + mol_fix_origin_3: + ui:group: molecule + mol_fix_origin_4: + ui:group: molecule + mol_fix_origin_5: + ui:group: molecule + mol_fix_origin_6: + ui:group: molecule + mol_fix_origin_7: + ui:group: molecule + mol_fix_origin_8: + ui:group: molecule + mol_fix_origin_9: + ui:group: molecule + mol_fix_origin_10: + ui:group: molecule + mol_fix_origin_11: + ui:group: molecule + mol_fix_origin_12: + ui:group: molecule + mol_fix_origin_13: + ui:group: molecule + mol_fix_origin_14: + ui:group: molecule + mol_fix_origin_15: + ui:group: molecule + mol_fix_origin_16: + ui:group: molecule + mol_fix_origin_17: + ui:group: molecule + mol_fix_origin_18: + ui:group: molecule + mol_fix_origin_19: + ui:group: molecule + mol_fix_origin_20: + ui:group: molecule + mol_shape_1: + ui:group: molecule + mol_shape_2: + ui:group: molecule + mol_shape_3: + ui:group: molecule + mol_shape_4: + ui:group: molecule + mol_shape_5: + ui:group: molecule + mol_shape_6: + ui:group: molecule + mol_shape_7: + ui:group: molecule + mol_shape_8: + ui:group: molecule + mol_shape_9: + ui:group: molecule + mol_shape_10: + ui:group: molecule + mol_shape_11: + ui:group: molecule + mol_shape_12: + ui:group: molecule + mol_shape_13: + ui:group: molecule + mol_shape_14: + ui:group: molecule + mol_shape_15: + ui:group: molecule + mol_shape_16: + ui:group: molecule + mol_shape_17: + ui:group: molecule + mol_shape_18: + ui:group: molecule + mol_shape_19: + ui:group: molecule + mol_shape_20: + ui:group: molecule ambig_fname: ui:widget: file + ui:group: distance restraints unambig_fname: ui:widget: file + ui:group: distance restraints + hbond_fname: + ui:widget: file + ui:group: distance restraints + amb_hot: + ui:group: distance restraints + amb_cool1: + ui:group: distance restraints + amb_cool2: + ui:group: distance restraints + amb_cool3: + ui:group: distance restraints + unamb_hot: + ui:group: distance restraints + unamb_cool1: + ui:group: distance restraints + unamb_cool2: + ui:group: distance restraints + unamb_cool3: + ui:group: distance restraints + hbond_hot: + ui:group: distance restraints + hbond_cool1: + ui:group: distance restraints + hbond_cool2: + ui:group: distance restraints + hbond_cool3: + ui:group: distance restraints + randremoval: + ui:group: distance restraints + npart: + ui:group: distance restraints + contactairs: + 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 - hbond_fname: + ui:group: dihedral restraints + dihedrals_on: + ui:group: dihedral restraints + dihedrals_hot: + ui:group: dihedral restraints + dihedrals_cool1: + ui:group: dihedral restraints + dihedrals_cool2: + ui:group: dihedral restraints + dihedrals_cool3: + ui:group: dihedral restraints + ssdihed: + ui:group: dihedral restraints + error_dih: + ui:group: dihedral restraints + dnarest_on: + ui:group: other restraints + sym_on: + ui:group: symmetry + ksym: + ui:group: symmetry + symtbl_fname: ui:widget: file + ui:group: symmetry + numc2sym: + ui:group: symmetry + c2sym_sta1_1: + ui:group: symmetry + c2sym_end1_1: + ui:group: symmetry + c2sym_seg1_1: + ui:group: symmetry + c2sym_sta2_1: + ui:group: symmetry + c2sym_end2_1: + ui:group: symmetry + c2sym_seg2_1: + ui:group: symmetry + numc3sym: + ui:group: symmetry + c3sym_sta1_1: + ui:group: symmetry + c3sym_end1_1: + ui:group: symmetry + c3sym_seg1_1: + ui:group: symmetry + c3sym_sta2_1: + ui:group: symmetry + c3sym_end2_1: + ui:group: symmetry + c3sym_seg2_1: + ui:group: symmetry + c3sym_sta3_1: + ui:group: symmetry + c3sym_end3_1: + ui:group: symmetry + c3sym_seg3_1: + ui:group: symmetry + numc4sym: + ui:group: symmetry + c4sym_sta1_1: + ui:group: symmetry + c4sym_end1_1: + ui:group: symmetry + c4sym_seg1_1: + ui:group: symmetry + c4sym_sta2_1: + ui:group: symmetry + c4sym_end2_1: + ui:group: symmetry + c4sym_seg2_1: + ui:group: symmetry + c4sym_sta3_1: + ui:group: symmetry + c4sym_end3_1: + ui:group: symmetry + c4sym_seg3_1: + ui:group: symmetry + c4sym_sta4_1: + ui:group: symmetry + c4sym_end4_1: + ui:group: symmetry + c4sym_seg4_1: + ui:group: symmetry + numc5sym: + ui:group: symmetry + c5sym_sta1_1: + ui:group: symmetry + c5sym_end1_1: + ui:group: symmetry + c5sym_seg1_1: + ui:group: symmetry + c5sym_sta2_1: + ui:group: symmetry + c5sym_end2_1: + ui:group: symmetry + c5sym_seg2_1: + ui:group: symmetry + c5sym_sta3_1: + ui:group: symmetry + c5sym_end3_1: + ui:group: symmetry + c5sym_seg3_1: + ui:group: symmetry + c5sym_sta4_1: + ui:group: symmetry + c5sym_end4_1: + ui:group: symmetry + c5sym_seg4_1: + ui:group: symmetry + c5sym_sta5_1: + ui:group: symmetry + c5sym_end5_1: + ui:group: symmetry + c5sym_seg5_1: + ui:group: symmetry + numc6sym: + ui:group: symmetry + c6sym_sta1_1: + ui:group: symmetry + c6sym_end1_1: + ui:group: symmetry + c6sym_seg1_1: + ui:group: symmetry + c6sym_sta2_1: + ui:group: symmetry + c6sym_end2_1: + ui:group: symmetry + c6sym_seg2_1: + ui:group: symmetry + c6sym_sta3_1: + ui:group: symmetry + c6sym_end3_1: + ui:group: symmetry + c6sym_seg3_1: + ui:group: symmetry + c6sym_sta4_1: + ui:group: symmetry + c6sym_end4_1: + ui:group: symmetry + c6sym_seg4_1: + ui:group: symmetry + c6sym_sta5_1: + ui:group: symmetry + c6sym_end5_1: + ui:group: symmetry + c6sym_seg5_1: + ui:group: symmetry + c6sym_sta6_1: + ui:group: symmetry + c6sym_end6_1: + ui:group: symmetry + c6sym_seg6_1: + ui:group: symmetry + nums3sym: + ui:group: symmetry + s3sym_sta1_1: + ui:group: symmetry + s3sym_end1_1: + ui:group: symmetry + s3sym_seg1_1: + ui:group: symmetry + s3sym_sta2_1: + ui:group: symmetry + s3sym_end2_1: + ui:group: symmetry + s3sym_seg2_1: + ui:group: symmetry + s3sym_sta3_1: + ui:group: symmetry + s3sym_end3_1: + ui:group: symmetry + s3sym_seg3_1: + ui:group: symmetry + ncs_on: + ui:group: symmetry + kncs: + ui:group: symmetry + numncs: + ui:group: symmetry + ncs_sta1_1: + ui:group: symmetry + ncs_end1_1: + ui:group: symmetry + ncs_seg1_1: + ui:group: symmetry + ncs_sta2_1: + ui:group: symmetry + ncs_end2_1: + ui:group: symmetry + ncs_seg2_1: + ui:group: symmetry + w_air: + ui:group: scoring + w_bsa: + ui:group: scoring + w_cdih: + ui:group: scoring + w_desolv: + ui:group: scoring + w_elec: + ui:group: scoring + w_sym: + 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 + sampling_factor: + ui:group: sampling + nemsteps: + ui:group: sampling + mdsteps_rigid: + ui:group: sampling + mdsteps_cool1: + ui:group: sampling + mdsteps_cool2: + ui:group: sampling + mdsteps_cool3: + ui:group: sampling + timestep: + ui:group: sampling + tadfactor: + ui:group: sampling + temp_high: + ui:group: sampling + temp_cool1_init: + ui:group: sampling + temp_cool1_final: + ui:group: sampling + temp_cool2_init: + ui:group: sampling + temp_cool2_final: + ui:group: sampling + temp_cool3_init: + ui:group: sampling + temp_cool3_final: + ui:group: sampling + sinter_rigid_init: + ui:group: sampling + sinter_cool2_init: + ui:group: sampling + sinter_cool2_final: + ui:group: sampling + sinter_cool3_init: + ui:group: sampling + sinter_cool3_final: + ui:group: sampling + iniseed: + ui:group: sampling + keepwater: + ui:group: sampling + tolerance: + ui:group: module + log_level: + ui:group: module + nseg1: + ui:group: flexibility + seg_sta_1_1: + ui:group: flexibility + seg_end_1_1: + ui:group: flexibility + nseg2: + ui:group: flexibility + seg_sta_2_1: + ui:group: flexibility + seg_end_2_1: + ui:group: flexibility + nseg3: + ui:group: flexibility + seg_sta_3_1: + ui:group: flexibility + seg_end_3_1: + ui:group: flexibility + nseg4: + ui:group: flexibility + seg_sta_4_1: + ui:group: flexibility + seg_end_4_1: + ui:group: flexibility + nseg5: + ui:group: flexibility + seg_sta_5_1: + ui:group: flexibility + seg_end_5_1: + ui:group: flexibility + nseg6: + ui:group: flexibility + seg_sta_6_1: + ui:group: flexibility + seg_end_6_1: + ui:group: flexibility + nseg7: + ui:group: flexibility + seg_sta_7_1: + ui:group: flexibility + seg_end_7_1: + ui:group: flexibility + nseg8: + ui:group: flexibility + seg_sta_8_1: + ui:group: flexibility + seg_end_8_1: + ui:group: flexibility + nseg9: + ui:group: flexibility + seg_sta_9_1: + ui:group: flexibility + seg_end_9_1: + ui:group: flexibility + nseg10: + ui:group: flexibility + seg_sta_10_1: + ui:group: flexibility + seg_end_10_1: + ui:group: flexibility + nseg11: + ui:group: flexibility + seg_sta_11_1: + ui:group: flexibility + seg_end_11_1: + ui:group: flexibility + nseg12: + ui:group: flexibility + seg_sta_12_1: + ui:group: flexibility + seg_end_12_1: + ui:group: flexibility + nseg13: + ui:group: flexibility + seg_sta_13_1: + ui:group: flexibility + seg_end_13_1: + ui:group: flexibility + nseg14: + ui:group: flexibility + seg_sta_14_1: + ui:group: flexibility + seg_end_14_1: + ui:group: flexibility + nseg15: + ui:group: flexibility + seg_sta_15_1: + ui:group: flexibility + seg_end_15_1: + ui:group: flexibility + nseg16: + ui:group: flexibility + seg_sta_16_1: + ui:group: flexibility + seg_end_16_1: + ui:group: flexibility + nseg17: + ui:group: flexibility + seg_sta_17_1: + ui:group: flexibility + seg_end_17_1: + ui:group: flexibility + nseg18: + ui:group: flexibility + seg_sta_18_1: + ui:group: flexibility + seg_end_18_1: + ui:group: flexibility + nseg19: + ui:group: flexibility + seg_sta_19_1: + ui:group: flexibility + seg_end_19_1: + ui:group: flexibility + nseg20: + ui:group: flexibility + seg_sta_20_1: + ui:group: flexibility + seg_end_20_1: + ui:group: flexibility + nfle1: + ui:group: flexibility + fle_sta_1_1: + ui:group: flexibility + fle_end_1_1: + ui:group: flexibility + nfle2: + ui:group: flexibility + fle_sta_2_1: + ui:group: flexibility + fle_end_2_1: + ui:group: flexibility + nfle3: + ui:group: flexibility + fle_sta_3_1: + ui:group: flexibility + fle_end_3_1: + ui:group: flexibility + nfle4: + ui:group: flexibility + fle_sta_4_1: + ui:group: flexibility + fle_end_4_1: + ui:group: flexibility + nfle5: + ui:group: flexibility + fle_sta_5_1: + ui:group: flexibility + fle_end_5_1: + ui:group: flexibility + nfle6: + ui:group: flexibility + fle_sta_6_1: + ui:group: flexibility + fle_end_6_1: + ui:group: flexibility + nfle7: + ui:group: flexibility + fle_sta_7_1: + ui:group: flexibility + fle_end_7_1: + ui:group: flexibility + nfle8: + ui:group: flexibility + fle_sta_8_1: + ui:group: flexibility + fle_end_8_1: + ui:group: flexibility + nfle9: + ui:group: flexibility + fle_sta_9_1: + ui:group: flexibility + fle_end_9_1: + ui:group: flexibility + nfle10: + ui:group: flexibility + fle_sta_10_1: + ui:group: flexibility + fle_end_10_1: + ui:group: flexibility + nfle11: + ui:group: flexibility + fle_sta_11_1: + ui:group: flexibility + fle_end_11_1: + ui:group: flexibility + nfle12: + ui:group: flexibility + fle_sta_12_1: + ui:group: flexibility + fle_end_12_1: + ui:group: flexibility + nfle13: + ui:group: flexibility + fle_sta_13_1: + ui:group: flexibility + fle_end_13_1: + ui:group: flexibility + nfle14: + ui:group: flexibility + fle_sta_14_1: + ui:group: flexibility + fle_end_14_1: + ui:group: flexibility + nfle15: + ui:group: flexibility + fle_sta_15_1: + ui:group: flexibility + fle_end_15_1: + ui:group: flexibility + nfle16: + ui:group: flexibility + fle_sta_16_1: + ui:group: flexibility + fle_end_16_1: + ui:group: flexibility + nfle17: + ui:group: flexibility + fle_sta_17_1: + ui:group: flexibility + fle_end_17_1: + ui:group: flexibility + nfle18: + ui:group: flexibility + fle_sta_18_1: + ui:group: flexibility + fle_end_18_1: + ui:group: flexibility + nfle19: + ui:group: flexibility + fle_sta_19_1: + ui:group: flexibility + fle_end_19_1: + ui:group: flexibility + nfle20: + ui:group: flexibility + fle_sta_20_1: + ui:group: flexibility + fle_end_20_1: + ui:group: flexibility - id: mdref category: refinement label: HADDOCK3 module for water refinement. @@ -6792,241 +7654,241 @@ nodes: schema: type: object properties: - fix_origin_1: + mol_fix_origin_1: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_2: + mol_fix_origin_2: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_3: + mol_fix_origin_3: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_4: + mol_fix_origin_4: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_5: + mol_fix_origin_5: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_6: + mol_fix_origin_6: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_7: + mol_fix_origin_7: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_8: + mol_fix_origin_8: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_9: + mol_fix_origin_9: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_10: + mol_fix_origin_10: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_11: + mol_fix_origin_11: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_12: + mol_fix_origin_12: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_13: + mol_fix_origin_13: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_14: + mol_fix_origin_14: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_15: + mol_fix_origin_15: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_16: + mol_fix_origin_16: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_17: + mol_fix_origin_17: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_18: + mol_fix_origin_18: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_19: + mol_fix_origin_19: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_20: + mol_fix_origin_20: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - shape_1: + mol_shape_1: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_2: + mol_shape_2: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_3: + mol_shape_3: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_4: + mol_shape_4: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_5: + mol_shape_5: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_6: + mol_shape_6: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_7: + mol_shape_7: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_8: + mol_shape_8: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_9: + mol_shape_9: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_10: + mol_shape_10: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_11: + mol_shape_11: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_12: + mol_shape_12: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_13: + mol_shape_13: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_14: + mol_shape_14: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_15: + mol_shape_15: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_16: + mol_shape_16: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_17: + mol_shape_17: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_18: + mol_shape_18: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_19: + mol_shape_19: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_20: + mol_shape_20: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. @@ -7187,8 +8049,8 @@ 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: default: none title: Define automatically backbone dihedral angle restraints @@ -7217,8 +8079,8 @@ 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 @@ -8005,15 +8867,11 @@ 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: - default: 200 - title: Number of models to generate - description: Number of MD refined models to generate - $comment: Number of MD refined models to generate - type: number - maximum: 50000 - minimum: 1 sampling_factor: default: 1 title: Sampling factor for each starting model @@ -8130,14 +8988,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta1_1: + seg_sta_1_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend1_1: + seg_end_1_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8159,14 +9017,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta2_1: + seg_sta_2_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend2_1: + seg_end_2_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8188,14 +9046,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta3_1: + seg_sta_3_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend3_1: + seg_end_3_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8217,14 +9075,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta4_1: + seg_sta_4_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend4_1: + seg_end_4_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8246,14 +9104,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta5_1: + seg_sta_5_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend5_1: + seg_end_5_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8275,14 +9133,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta6_1: + seg_sta_6_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend6_1: + seg_end_6_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8304,14 +9162,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta7_1: + seg_sta_7_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend7_1: + seg_end_7_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8333,14 +9191,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta8_1: + seg_sta_8_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend8_1: + seg_end_8_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8362,14 +9220,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta9_1: + seg_sta_9_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend9_1: + seg_end_9_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8391,14 +9249,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta10_1: + seg_sta_10_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend10_1: + seg_end_10_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8420,14 +9278,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta11_1: + seg_sta_11_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend11_1: + seg_end_11_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8449,14 +9307,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta12_1: + seg_sta_12_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend12_1: + seg_end_12_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8478,14 +9336,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta13_1: + seg_sta_13_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend13_1: + seg_end_13_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8507,14 +9365,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta14_1: + seg_sta_14_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend14_1: + seg_end_14_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8536,14 +9394,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta15_1: + seg_sta_15_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend15_1: + seg_end_15_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8565,14 +9423,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta16_1: + seg_sta_16_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend16_1: + seg_end_16_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8594,14 +9452,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta17_1: + seg_sta_17_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend17_1: + seg_end_17_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8623,14 +9481,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta18_1: + seg_sta_18_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend18_1: + seg_end_18_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8652,14 +9510,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta19_1: + seg_sta_19_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend19_1: + seg_end_19_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8681,14 +9539,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta20_1: + seg_sta_20_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend20_1: + seg_end_20_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -8701,18 +9559,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta1_1: + fle_sta_1_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend1_1: + fle_end_1_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8725,18 +9583,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta2_1: + fle_sta_2_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend2_1: + fle_end_2_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8749,18 +9607,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta3_1: + fle_sta_3_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend3_1: + fle_end_3_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8773,18 +9631,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta4_1: + fle_sta_4_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend4_1: + fle_end_4_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8797,18 +9655,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta5_1: + fle_sta_5_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend5_1: + fle_end_5_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8821,18 +9679,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta6_1: + fle_sta_6_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend6_1: + fle_end_6_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8845,18 +9703,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta7_1: + fle_sta_7_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend7_1: + fle_end_7_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8869,18 +9727,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta8_1: + fle_sta_8_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend8_1: + fle_end_8_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8893,18 +9751,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta9_1: + fle_sta_9_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend9_1: + fle_end_9_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8917,18 +9775,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta10_1: + fle_sta_10_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend10_1: + fle_end_10_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8941,18 +9799,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta11_1: + fle_sta_11_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend11_1: + fle_end_11_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8965,18 +9823,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta12_1: + fle_sta_12_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend12_1: + fle_end_12_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -8989,18 +9847,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta13_1: + fle_sta_13_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend13_1: + fle_end_13_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9013,18 +9871,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta14_1: + fle_sta_14_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend14_1: + fle_end_14_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9037,18 +9895,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta15_1: + fle_sta_15_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend15_1: + fle_end_15_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9061,18 +9919,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta16_1: + fle_sta_16_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend16_1: + fle_end_16_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9085,18 +9943,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta17_1: + fle_sta_17_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend17_1: + fle_end_17_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9109,18 +9967,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta18_1: + fle_sta_18_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend18_1: + fle_end_18_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9133,18 +9991,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta19_1: + fle_sta_19_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend19_1: + fle_end_19_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9157,18 +10015,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta20_1: + fle_sta_20_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend20_1: + fle_end_20_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -9178,85 +10036,85 @@ nodes: required: [] additionalProperties: false uiSchema: - fix_origin_1: + mol_fix_origin_1: ui:group: molecule - fix_origin_2: + mol_fix_origin_2: ui:group: molecule - fix_origin_3: + mol_fix_origin_3: ui:group: molecule - fix_origin_4: + mol_fix_origin_4: ui:group: molecule - fix_origin_5: + mol_fix_origin_5: ui:group: molecule - fix_origin_6: + mol_fix_origin_6: ui:group: molecule - fix_origin_7: + mol_fix_origin_7: ui:group: molecule - fix_origin_8: + mol_fix_origin_8: ui:group: molecule - fix_origin_9: + mol_fix_origin_9: ui:group: molecule - fix_origin_10: + mol_fix_origin_10: ui:group: molecule - fix_origin_11: + mol_fix_origin_11: ui:group: molecule - fix_origin_12: + mol_fix_origin_12: ui:group: molecule - fix_origin_13: + mol_fix_origin_13: ui:group: molecule - fix_origin_14: + mol_fix_origin_14: ui:group: molecule - fix_origin_15: + mol_fix_origin_15: ui:group: molecule - fix_origin_16: + mol_fix_origin_16: ui:group: molecule - fix_origin_17: + mol_fix_origin_17: ui:group: molecule - fix_origin_18: + mol_fix_origin_18: ui:group: molecule - fix_origin_19: + mol_fix_origin_19: ui:group: molecule - fix_origin_20: + mol_fix_origin_20: ui:group: molecule - shape_1: + mol_shape_1: ui:group: molecule - shape_2: + mol_shape_2: ui:group: molecule - shape_3: + mol_shape_3: ui:group: molecule - shape_4: + mol_shape_4: ui:group: molecule - shape_5: + mol_shape_5: ui:group: molecule - shape_6: + mol_shape_6: ui:group: molecule - shape_7: + mol_shape_7: ui:group: molecule - shape_8: + mol_shape_8: ui:group: molecule - shape_9: + mol_shape_9: ui:group: molecule - shape_10: + mol_shape_10: ui:group: molecule - shape_11: + mol_shape_11: ui:group: molecule - shape_12: + mol_shape_12: ui:group: molecule - shape_13: + mol_shape_13: ui:group: molecule - shape_14: + mol_shape_14: ui:group: molecule - shape_15: + mol_shape_15: ui:group: molecule - shape_16: + mol_shape_16: ui:group: molecule - shape_17: + mol_shape_17: ui:group: molecule - shape_18: + mol_shape_18: ui:group: molecule - shape_19: + mol_shape_19: ui:group: molecule - shape_20: + mol_shape_20: ui:group: molecule ambig_fname: ui:widget: file @@ -9501,8 +10359,6 @@ nodes: ui:group: force field epsilon: ui:group: force field - sampling: - ui:group: sampling sampling_factor: ui:group: sampling nemsteps: @@ -9525,243 +10381,243 @@ nodes: ui:group: module nseg1: ui:group: flexibility - segsta1_1: + seg_sta_1_1: ui:group: flexibility - segend1_1: + seg_end_1_1: ui:group: flexibility nseg2: ui:group: flexibility - segsta2_1: + seg_sta_2_1: ui:group: flexibility - segend2_1: + seg_end_2_1: ui:group: flexibility nseg3: ui:group: flexibility - segsta3_1: + seg_sta_3_1: ui:group: flexibility - segend3_1: + seg_end_3_1: ui:group: flexibility nseg4: ui:group: flexibility - segsta4_1: + seg_sta_4_1: ui:group: flexibility - segend4_1: + seg_end_4_1: ui:group: flexibility nseg5: ui:group: flexibility - segsta5_1: + seg_sta_5_1: ui:group: flexibility - segend5_1: + seg_end_5_1: ui:group: flexibility nseg6: ui:group: flexibility - segsta6_1: + seg_sta_6_1: ui:group: flexibility - segend6_1: + seg_end_6_1: ui:group: flexibility nseg7: ui:group: flexibility - segsta7_1: + seg_sta_7_1: ui:group: flexibility - segend7_1: + seg_end_7_1: ui:group: flexibility nseg8: ui:group: flexibility - segsta8_1: + seg_sta_8_1: ui:group: flexibility - segend8_1: + seg_end_8_1: ui:group: flexibility nseg9: ui:group: flexibility - segsta9_1: + seg_sta_9_1: ui:group: flexibility - segend9_1: + seg_end_9_1: ui:group: flexibility nseg10: ui:group: flexibility - segsta10_1: + seg_sta_10_1: ui:group: flexibility - segend10_1: + seg_end_10_1: ui:group: flexibility nseg11: ui:group: flexibility - segsta11_1: + seg_sta_11_1: ui:group: flexibility - segend11_1: + seg_end_11_1: ui:group: flexibility nseg12: ui:group: flexibility - segsta12_1: + seg_sta_12_1: ui:group: flexibility - segend12_1: + seg_end_12_1: ui:group: flexibility nseg13: ui:group: flexibility - segsta13_1: + seg_sta_13_1: ui:group: flexibility - segend13_1: + seg_end_13_1: ui:group: flexibility nseg14: ui:group: flexibility - segsta14_1: + seg_sta_14_1: ui:group: flexibility - segend14_1: + seg_end_14_1: ui:group: flexibility nseg15: ui:group: flexibility - segsta15_1: + seg_sta_15_1: ui:group: flexibility - segend15_1: + seg_end_15_1: ui:group: flexibility nseg16: ui:group: flexibility - segsta16_1: + seg_sta_16_1: ui:group: flexibility - segend16_1: + seg_end_16_1: ui:group: flexibility nseg17: ui:group: flexibility - segsta17_1: + seg_sta_17_1: ui:group: flexibility - segend17_1: + seg_end_17_1: ui:group: flexibility nseg18: ui:group: flexibility - segsta18_1: + seg_sta_18_1: ui:group: flexibility - segend18_1: + seg_end_18_1: ui:group: flexibility nseg19: ui:group: flexibility - segsta19_1: + seg_sta_19_1: ui:group: flexibility - segend19_1: + seg_end_19_1: ui:group: flexibility nseg20: ui:group: flexibility - segsta20_1: + seg_sta_20_1: ui:group: flexibility - segend20_1: + seg_end_20_1: ui:group: flexibility nfle1: ui:group: flexibility - flesta1_1: + fle_sta_1_1: ui:group: flexibility - fleend1_1: + fle_end_1_1: ui:group: flexibility nfle2: ui:group: flexibility - flesta2_1: + fle_sta_2_1: ui:group: flexibility - fleend2_1: + fle_end_2_1: ui:group: flexibility nfle3: ui:group: flexibility - flesta3_1: + fle_sta_3_1: ui:group: flexibility - fleend3_1: + fle_end_3_1: ui:group: flexibility nfle4: ui:group: flexibility - flesta4_1: + fle_sta_4_1: ui:group: flexibility - fleend4_1: + fle_end_4_1: ui:group: flexibility nfle5: ui:group: flexibility - flesta5_1: + fle_sta_5_1: ui:group: flexibility - fleend5_1: + fle_end_5_1: ui:group: flexibility nfle6: ui:group: flexibility - flesta6_1: + fle_sta_6_1: ui:group: flexibility - fleend6_1: + fle_end_6_1: ui:group: flexibility nfle7: ui:group: flexibility - flesta7_1: + fle_sta_7_1: ui:group: flexibility - fleend7_1: + fle_end_7_1: ui:group: flexibility nfle8: ui:group: flexibility - flesta8_1: + fle_sta_8_1: ui:group: flexibility - fleend8_1: + fle_end_8_1: ui:group: flexibility nfle9: ui:group: flexibility - flesta9_1: + fle_sta_9_1: ui:group: flexibility - fleend9_1: + fle_end_9_1: ui:group: flexibility nfle10: ui:group: flexibility - flesta10_1: + fle_sta_10_1: ui:group: flexibility - fleend10_1: + fle_end_10_1: ui:group: flexibility nfle11: ui:group: flexibility - flesta11_1: + fle_sta_11_1: ui:group: flexibility - fleend11_1: + fle_end_11_1: ui:group: flexibility nfle12: ui:group: flexibility - flesta12_1: + fle_sta_12_1: ui:group: flexibility - fleend12_1: + fle_end_12_1: ui:group: flexibility nfle13: ui:group: flexibility - flesta13_1: + fle_sta_13_1: ui:group: flexibility - fleend13_1: + fle_end_13_1: ui:group: flexibility nfle14: ui:group: flexibility - flesta14_1: + fle_sta_14_1: ui:group: flexibility - fleend14_1: + fle_end_14_1: ui:group: flexibility nfle15: ui:group: flexibility - flesta15_1: + fle_sta_15_1: ui:group: flexibility - fleend15_1: + fle_end_15_1: ui:group: flexibility nfle16: ui:group: flexibility - flesta16_1: + fle_sta_16_1: ui:group: flexibility - fleend16_1: + fle_end_16_1: ui:group: flexibility nfle17: ui:group: flexibility - flesta17_1: + fle_sta_17_1: ui:group: flexibility - fleend17_1: + fle_end_17_1: ui:group: flexibility nfle18: ui:group: flexibility - flesta18_1: + fle_sta_18_1: ui:group: flexibility - fleend18_1: + fle_end_18_1: ui:group: flexibility nfle19: ui:group: flexibility - flesta19_1: + fle_sta_19_1: ui:group: flexibility - fleend19_1: + fle_end_19_1: ui:group: flexibility nfle20: ui:group: flexibility - flesta20_1: + fle_sta_20_1: ui:group: flexibility - fleend20_1: + fle_end_20_1: ui:group: flexibility - id: emref category: refinement @@ -9770,241 +10626,241 @@ nodes: schema: type: object properties: - fix_origin_1: + mol_fix_origin_1: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_2: + mol_fix_origin_2: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_3: + mol_fix_origin_3: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_4: + mol_fix_origin_4: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_5: + mol_fix_origin_5: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_6: + mol_fix_origin_6: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_7: + mol_fix_origin_7: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_8: + mol_fix_origin_8: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_9: + mol_fix_origin_9: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_10: + mol_fix_origin_10: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_11: + mol_fix_origin_11: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_12: + mol_fix_origin_12: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_13: + mol_fix_origin_13: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_14: + mol_fix_origin_14: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_15: + mol_fix_origin_15: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_16: + mol_fix_origin_16: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_17: + mol_fix_origin_17: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_18: + mol_fix_origin_18: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_19: + mol_fix_origin_19: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - fix_origin_20: + mol_fix_origin_20: default: false title: Fix molecule description: Fixes the molecule in its original position. $comment: Fixes the molecule in its original position. type: boolean - shape_1: + mol_shape_1: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_2: + mol_shape_2: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_3: + mol_shape_3: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_4: + mol_shape_4: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_5: + mol_shape_5: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_6: + mol_shape_6: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_7: + mol_shape_7: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_8: + mol_shape_8: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_9: + mol_shape_9: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_10: + mol_shape_10: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_11: + mol_shape_11: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_12: + mol_shape_12: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_13: + mol_shape_13: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_14: + mol_shape_14: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_15: + mol_shape_15: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_16: + mol_shape_16: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_17: + mol_shape_17: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_18: + mol_shape_18: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_19: + mol_shape_19: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. $comment: Defines a molecule as a shape, which is a collection of beads. type: boolean - shape_20: + mol_shape_20: default: false title: Is the molecule a shape? description: Defines a molecule as a shape. @@ -11018,14 +11874,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta1_1: + seg_sta_1_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend1_1: + seg_end_1_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11047,14 +11903,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta2_1: + seg_sta_2_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend2_1: + seg_end_2_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11076,14 +11932,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta3_1: + seg_sta_3_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend3_1: + seg_end_3_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11105,14 +11961,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta4_1: + seg_sta_4_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend4_1: + seg_end_4_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11134,14 +11990,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta5_1: + seg_sta_5_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend5_1: + seg_end_5_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11163,14 +12019,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta6_1: + seg_sta_6_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend6_1: + seg_end_6_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11192,14 +12048,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta7_1: + seg_sta_7_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend7_1: + seg_end_7_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11221,14 +12077,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta8_1: + seg_sta_8_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend8_1: + seg_end_8_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11250,14 +12106,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta9_1: + seg_sta_9_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend9_1: + seg_end_9_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11279,14 +12135,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta10_1: + seg_sta_10_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend10_1: + seg_end_10_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11308,14 +12164,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta11_1: + seg_sta_11_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend11_1: + seg_end_11_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11337,14 +12193,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta12_1: + seg_sta_12_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend12_1: + seg_end_12_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11366,14 +12222,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta13_1: + seg_sta_13_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend13_1: + seg_end_13_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11395,14 +12251,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta14_1: + seg_sta_14_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend14_1: + seg_end_14_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11424,14 +12280,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta15_1: + seg_sta_15_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend15_1: + seg_end_15_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11453,14 +12309,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta16_1: + seg_sta_16_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend16_1: + seg_end_16_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11482,14 +12338,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta17_1: + seg_sta_17_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend17_1: + seg_end_17_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11511,14 +12367,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta18_1: + seg_sta_18_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend18_1: + seg_end_18_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11540,14 +12396,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta19_1: + seg_sta_19_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend19_1: + seg_end_19_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11569,14 +12425,14 @@ nodes: type: number maximum: 1000 minimum: -1 - segsta20_1: + seg_sta_20_1: title: Starting residue number description: Residue number defining the start of the semi-flexible segment. $comment: Residue number defining the start of the semi-flexible segment. type: number maximum: 9999 minimum: -9999 - segend20_1: + seg_end_20_1: title: Ending residue number description: Residue number defining the end of the semi-flexible segment. $comment: Residue number defining the end of the semi-flexible segment. @@ -11589,18 +12445,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta1_1: + fle_sta_1_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend1_1: + fle_end_1_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11613,18 +12469,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta2_1: + fle_sta_2_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend2_1: + fle_end_2_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11637,18 +12493,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta3_1: + fle_sta_3_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend3_1: + fle_end_3_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11661,18 +12517,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta4_1: + fle_sta_4_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend4_1: + fle_end_4_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11685,18 +12541,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta5_1: + fle_sta_5_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend5_1: + fle_end_5_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11709,18 +12565,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta6_1: + fle_sta_6_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend6_1: + fle_end_6_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11733,18 +12589,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta7_1: + fle_sta_7_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend7_1: + fle_end_7_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11757,18 +12613,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta8_1: + fle_sta_8_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend8_1: + fle_end_8_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11781,18 +12637,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta9_1: + fle_sta_9_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend9_1: + fle_end_9_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11805,18 +12661,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta10_1: + fle_sta_10_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend10_1: + fle_end_10_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11829,18 +12685,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta11_1: + fle_sta_11_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend11_1: + fle_end_11_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11853,18 +12709,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta12_1: + fle_sta_12_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend12_1: + fle_end_12_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11877,18 +12733,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta13_1: + fle_sta_13_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend13_1: + fle_end_13_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11901,18 +12757,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta14_1: + fle_sta_14_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend14_1: + fle_end_14_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11925,18 +12781,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta15_1: + fle_sta_15_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend15_1: + fle_end_15_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11949,18 +12805,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta16_1: + fle_sta_16_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend16_1: + fle_end_16_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11973,18 +12829,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta17_1: + fle_sta_17_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend17_1: + fle_end_17_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -11997,18 +12853,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta18_1: + fle_sta_18_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend18_1: + fle_end_18_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -12021,18 +12877,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta19_1: + fle_sta_19_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend19_1: + fle_end_19_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -12045,18 +12901,18 @@ nodes: description: This defines the number of fully flexible segments. $comment: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with - starting and end residue numbers in the flesta and fleend variables. + starting and end residue numbers in the fle_sta_ and fle_end_ variables. type: number maximum: 1000 minimum: 0 - flesta20_1: + fle_sta_20_1: title: Starting residue number description: Residue number defining the start of the fully flexible segment. $comment: Residue number defining the start of the fully flexible segment. type: number maximum: 9999 minimum: -9999 - fleend20_1: + fle_end_20_1: title: End residue number description: Residue number defining the end of the fully flexible segment. $comment: Residue number defining the end of the fully flexible segment. @@ -12066,85 +12922,85 @@ nodes: required: [] additionalProperties: false uiSchema: - fix_origin_1: + mol_fix_origin_1: ui:group: molecule - fix_origin_2: + mol_fix_origin_2: ui:group: molecule - fix_origin_3: + mol_fix_origin_3: ui:group: molecule - fix_origin_4: + mol_fix_origin_4: ui:group: molecule - fix_origin_5: + mol_fix_origin_5: ui:group: molecule - fix_origin_6: + mol_fix_origin_6: ui:group: molecule - fix_origin_7: + mol_fix_origin_7: ui:group: molecule - fix_origin_8: + mol_fix_origin_8: ui:group: molecule - fix_origin_9: + mol_fix_origin_9: ui:group: molecule - fix_origin_10: + mol_fix_origin_10: ui:group: molecule - fix_origin_11: + mol_fix_origin_11: ui:group: molecule - fix_origin_12: + mol_fix_origin_12: ui:group: molecule - fix_origin_13: + mol_fix_origin_13: ui:group: molecule - fix_origin_14: + mol_fix_origin_14: ui:group: molecule - fix_origin_15: + mol_fix_origin_15: ui:group: molecule - fix_origin_16: + mol_fix_origin_16: ui:group: molecule - fix_origin_17: + mol_fix_origin_17: ui:group: molecule - fix_origin_18: + mol_fix_origin_18: ui:group: molecule - fix_origin_19: + mol_fix_origin_19: ui:group: molecule - fix_origin_20: + mol_fix_origin_20: ui:group: molecule - shape_1: + mol_shape_1: ui:group: molecule - shape_2: + mol_shape_2: ui:group: molecule - shape_3: + mol_shape_3: ui:group: molecule - shape_4: + mol_shape_4: ui:group: molecule - shape_5: + mol_shape_5: ui:group: molecule - shape_6: + mol_shape_6: ui:group: molecule - shape_7: + mol_shape_7: ui:group: molecule - shape_8: + mol_shape_8: ui:group: molecule - shape_9: + mol_shape_9: ui:group: molecule - shape_10: + mol_shape_10: ui:group: molecule - shape_11: + mol_shape_11: ui:group: molecule - shape_12: + mol_shape_12: ui:group: molecule - shape_13: + mol_shape_13: ui:group: molecule - shape_14: + mol_shape_14: ui:group: molecule - shape_15: + mol_shape_15: ui:group: molecule - shape_16: + mol_shape_16: ui:group: molecule - shape_17: + mol_shape_17: ui:group: molecule - shape_18: + mol_shape_18: ui:group: molecule - shape_19: + mol_shape_19: ui:group: molecule - shape_20: + mol_shape_20: ui:group: molecule ambig_fname: ui:widget: file @@ -12399,243 +13255,243 @@ nodes: ui:group: module nseg1: ui:group: flexibility - segsta1_1: + seg_sta_1_1: ui:group: flexibility - segend1_1: + seg_end_1_1: ui:group: flexibility nseg2: ui:group: flexibility - segsta2_1: + seg_sta_2_1: ui:group: flexibility - segend2_1: + seg_end_2_1: ui:group: flexibility nseg3: ui:group: flexibility - segsta3_1: + seg_sta_3_1: ui:group: flexibility - segend3_1: + seg_end_3_1: ui:group: flexibility nseg4: ui:group: flexibility - segsta4_1: + seg_sta_4_1: ui:group: flexibility - segend4_1: + seg_end_4_1: ui:group: flexibility nseg5: ui:group: flexibility - segsta5_1: + seg_sta_5_1: ui:group: flexibility - segend5_1: + seg_end_5_1: ui:group: flexibility nseg6: ui:group: flexibility - segsta6_1: + seg_sta_6_1: ui:group: flexibility - segend6_1: + seg_end_6_1: ui:group: flexibility nseg7: ui:group: flexibility - segsta7_1: + seg_sta_7_1: ui:group: flexibility - segend7_1: + seg_end_7_1: ui:group: flexibility nseg8: ui:group: flexibility - segsta8_1: + seg_sta_8_1: ui:group: flexibility - segend8_1: + seg_end_8_1: ui:group: flexibility nseg9: ui:group: flexibility - segsta9_1: + seg_sta_9_1: ui:group: flexibility - segend9_1: + seg_end_9_1: ui:group: flexibility nseg10: ui:group: flexibility - segsta10_1: + seg_sta_10_1: ui:group: flexibility - segend10_1: + seg_end_10_1: ui:group: flexibility nseg11: ui:group: flexibility - segsta11_1: + seg_sta_11_1: ui:group: flexibility - segend11_1: + seg_end_11_1: ui:group: flexibility nseg12: ui:group: flexibility - segsta12_1: + seg_sta_12_1: ui:group: flexibility - segend12_1: + seg_end_12_1: ui:group: flexibility nseg13: ui:group: flexibility - segsta13_1: + seg_sta_13_1: ui:group: flexibility - segend13_1: + seg_end_13_1: ui:group: flexibility nseg14: ui:group: flexibility - segsta14_1: + seg_sta_14_1: ui:group: flexibility - segend14_1: + seg_end_14_1: ui:group: flexibility nseg15: ui:group: flexibility - segsta15_1: + seg_sta_15_1: ui:group: flexibility - segend15_1: + seg_end_15_1: ui:group: flexibility nseg16: ui:group: flexibility - segsta16_1: + seg_sta_16_1: ui:group: flexibility - segend16_1: + seg_end_16_1: ui:group: flexibility nseg17: ui:group: flexibility - segsta17_1: + seg_sta_17_1: ui:group: flexibility - segend17_1: + seg_end_17_1: ui:group: flexibility nseg18: ui:group: flexibility - segsta18_1: + seg_sta_18_1: ui:group: flexibility - segend18_1: + seg_end_18_1: ui:group: flexibility nseg19: ui:group: flexibility - segsta19_1: + seg_sta_19_1: ui:group: flexibility - segend19_1: + seg_end_19_1: ui:group: flexibility nseg20: ui:group: flexibility - segsta20_1: + seg_sta_20_1: ui:group: flexibility - segend20_1: + seg_end_20_1: ui:group: flexibility nfle1: ui:group: flexibility - flesta1_1: + fle_sta_1_1: ui:group: flexibility - fleend1_1: + fle_end_1_1: ui:group: flexibility nfle2: ui:group: flexibility - flesta2_1: + fle_sta_2_1: ui:group: flexibility - fleend2_1: + fle_end_2_1: ui:group: flexibility nfle3: ui:group: flexibility - flesta3_1: + fle_sta_3_1: ui:group: flexibility - fleend3_1: + fle_end_3_1: ui:group: flexibility nfle4: ui:group: flexibility - flesta4_1: + fle_sta_4_1: ui:group: flexibility - fleend4_1: + fle_end_4_1: ui:group: flexibility nfle5: ui:group: flexibility - flesta5_1: + fle_sta_5_1: ui:group: flexibility - fleend5_1: + fle_end_5_1: ui:group: flexibility nfle6: ui:group: flexibility - flesta6_1: + fle_sta_6_1: ui:group: flexibility - fleend6_1: + fle_end_6_1: ui:group: flexibility nfle7: ui:group: flexibility - flesta7_1: + fle_sta_7_1: ui:group: flexibility - fleend7_1: + fle_end_7_1: ui:group: flexibility nfle8: ui:group: flexibility - flesta8_1: + fle_sta_8_1: ui:group: flexibility - fleend8_1: + fle_end_8_1: ui:group: flexibility nfle9: ui:group: flexibility - flesta9_1: + fle_sta_9_1: ui:group: flexibility - fleend9_1: + fle_end_9_1: ui:group: flexibility nfle10: ui:group: flexibility - flesta10_1: + fle_sta_10_1: ui:group: flexibility - fleend10_1: + fle_end_10_1: ui:group: flexibility nfle11: ui:group: flexibility - flesta11_1: + fle_sta_11_1: ui:group: flexibility - fleend11_1: + fle_end_11_1: ui:group: flexibility nfle12: ui:group: flexibility - flesta12_1: + fle_sta_12_1: ui:group: flexibility - fleend12_1: + fle_end_12_1: ui:group: flexibility nfle13: ui:group: flexibility - flesta13_1: + fle_sta_13_1: ui:group: flexibility - fleend13_1: + fle_end_13_1: ui:group: flexibility nfle14: ui:group: flexibility - flesta14_1: + fle_sta_14_1: ui:group: flexibility - fleend14_1: + fle_end_14_1: ui:group: flexibility nfle15: ui:group: flexibility - flesta15_1: + fle_sta_15_1: ui:group: flexibility - fleend15_1: + fle_end_15_1: ui:group: flexibility nfle16: ui:group: flexibility - flesta16_1: + fle_sta_16_1: ui:group: flexibility - fleend16_1: + fle_end_16_1: ui:group: flexibility nfle17: ui:group: flexibility - flesta17_1: + fle_sta_17_1: ui:group: flexibility - fleend17_1: + fle_end_17_1: ui:group: flexibility nfle18: ui:group: flexibility - flesta18_1: + fle_sta_18_1: ui:group: flexibility - fleend18_1: + fle_end_18_1: ui:group: flexibility nfle19: ui:group: flexibility - flesta19_1: + fle_sta_19_1: ui:group: flexibility - fleend19_1: + fle_end_19_1: ui:group: flexibility nfle20: ui:group: flexibility - flesta20_1: + fle_sta_20_1: ui:group: flexibility - fleend20_1: + fle_end_20_1: ui:group: flexibility examples: docking-protein-ligand: /examples/docking-protein-ligand.zip From 15e046718672fed825c945f0f4ec372b9eea8ab9 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Tue, 1 Mar 2022 13:22:55 +0100 Subject: [PATCH 2/7] After form submission remove all parameters which are equal to their default value Fixes #24 --- src/pruner.test.ts | 518 +++++++++++++++++++++++++++++++++++++++++++++ src/pruner.ts | 45 ++++ src/store.ts | 5 +- 3 files changed, 566 insertions(+), 2 deletions(-) create mode 100644 src/pruner.test.ts create mode 100644 src/pruner.ts diff --git a/src/pruner.test.ts b/src/pruner.test.ts new file mode 100644 index 00000000..f47a3079 --- /dev/null +++ b/src/pruner.test.ts @@ -0,0 +1,518 @@ +import { expect, describe, it } from 'vitest' +import { JSONSchema7 } from 'json-schema' +import { pruneDefaults } from './pruner' + +describe('pruneDefaults()', () => { + describe('given empty parameters', () => { + it('should return unchanged', () => { + const parameters = {} + const schema: JSONSchema7 = { + type: 'object', + properties: {}, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + expect(result).toEqual(parameters) + }) + }) + + describe('given parameters which has no default', () => { + it('should return unchanged', () => { + const parameters = { + prop1: 'something' + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'string' + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + expect(result).toEqual(parameters) + }) + }) + + describe('given parameters which is set to non-default', () => { + it('should return unchanged', () => { + const parameters = { + prop1: 'something' + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'string', + default: 'somethingelse' + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + expect(result).toEqual(parameters) + }) + }) + + describe('given a string and is set to default', () => { + it('should not include prop', () => { + const parameters = { + prop1: 'something' + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'string', + default: 'something' + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = {} + expect(result).toEqual(expected) + }) + }) + + describe('given an empty string and is set to default', () => { + it('should not include prop', () => { + const parameters = { + prop1: '' + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'string', + default: '' + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = {} + expect(result).toEqual(expected) + }) + }) + + describe('given a integer and is set to default', () => { + it('should not include prop', () => { + const parameters = { + prop1: 8 + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'number', + default: 8 + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = {} + expect(result).toEqual(expected) + }) + }) + + describe('given a float and is set to default', () => { + it('should not include prop', () => { + const parameters = { + prop1: 3.14 + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'number', + default: 3.14 + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = {} + expect(result).toEqual(expected) + }) + }) + + describe('given false and is set to default', () => { + it('should not include prop', () => { + const parameters = { + prop1: false + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'boolean', + default: false + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = {} + expect(result).toEqual(expected) + }) + }) + + describe('given true and is set to default', () => { + it('should not include prop', () => { + const parameters = { + prop1: true + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'boolean', + default: true + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = {} + expect(result).toEqual(expected) + }) + }) + + describe('given prop inside object is set to default', () => { + it('should not include object', () => { + const parameters = { + prop1: { + prop2: 'something' + } + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'object', + properties: { + prop2: { + type: 'string', + default: 'something' + } + } + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = {} + expect(result).toEqual(expected) + }) + }) + + describe('given prop is set to default and second prop without default', () => { + it('should not include object', () => { + const parameters = { + prop1: 'something', + prop2: 42 + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'string', + default: 'something' + }, + prop2: { + type: 'number' + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = { + prop2: 42 + } + expect(result).toEqual(expected) + }) + }) + + describe('given [] and is set to default', () => { + it('should not include prop', () => { + const parameters = { + prop1: [] + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'array', + default: [] + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = {} + expect(result).toEqual(expected) + }) + }) + + describe('given prop inside object is set to default and second prop inside object', () => { + it('should not include object', () => { + const parameters = { + prop1: { + prop2: 'something', + prop3: 42 + } + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'object', + properties: { + prop2: { + type: 'string', + default: 'something' + }, + prop3: { + type: 'number' + } + } + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = { + prop1: { + prop3: 42 + } + } + expect(result).toEqual(expected) + }) + }) +}) + +describe('given array items is string and has default', () => { + it('should not include prop', () => { + const parameters = { + prop1: ['something'] + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'array', + items: { + type: 'string', + default: 'something' + } + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = {} + expect(result).toEqual(expected) + }) +}) + +describe('given array items is string and has item equal to default and item which is non-default', () => { + it('should not include prop', () => { + const parameters = { + prop1: ['something', 'somethingelse'] + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'array', + items: { + type: 'string', + default: 'something' + } + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = { + prop1: ['somethingelse'] + } + expect(result).toEqual(expected) + }) +}) + +describe('given array items is object and has nested prop equal to default and another item with same prop with non-default value', () => { + it('should not include prop', () => { + const parameters = { + prop1: [{ prop2: 'something' }, { prop2: 'somethingelse' }] + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'array', + items: { + type: 'object', + properties: { + prop2: { + type: 'string', + default: 'something' + } + }, + additionalProperties: false + } + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = { + prop1: [{ prop2: 'somethingelse' }] + } + expect(result).toEqual(expected) + }) +}) + +describe('given array items is object and has nested prop equal to default and other nested prop not equal to default', () => { + it('should not include prop', () => { + const parameters = { + prop1: [{ prop2: 'something', prop3: 42 }, { prop2: 'somethingelse', prop3: 0 }] + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'array', + items: { + type: 'object', + properties: { + prop2: { + type: 'string', + default: 'something' + }, + prop3: { + type: 'number', + default: 0 + } + }, + additionalProperties: false + } + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = { + prop1: [{ prop3: 42 }, { prop2: 'somethingelse' }] + } + expect(result).toEqual(expected) + }) +}) + +describe('given array items is object and has nested prop equal to default and other nested prop also equal to default', () => { + it('should not include prop', () => { + const parameters = { + prop1: [{ prop2: 'something', prop3: 42 }, { prop2: 'somethingelse', prop3: 0 }] + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'array', + items: { + type: 'object', + properties: { + prop2: { + type: 'string', + default: 'something' + }, + prop3: { + type: 'number', + default: 42 + } + }, + additionalProperties: false + } + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = { + prop1: [{ prop2: 'somethingelse', prop3: 0 }] + } + expect(result).toEqual(expected) + }) +}) + +describe('given array items is object and has nested prop equal to default', () => { + it('should not include prop', () => { + const parameters = { + prop1: [{ prop2: 'something' }] + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'array', + items: { + type: 'object', + properties: { + prop2: { + type: 'string', + default: 'something' + } + }, + additionalProperties: false + } + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = { + } + expect(result).toEqual(expected) + }) +}) diff --git a/src/pruner.ts b/src/pruner.ts new file mode 100644 index 00000000..d87b4931 --- /dev/null +++ b/src/pruner.ts @@ -0,0 +1,45 @@ +import { JSONSchema7 } from 'json-schema' +import { IParameters } from './types' + +/** + * Any parameter whose value is same as the default defined in the schema will be pruned and not returned. + */ +export function pruneDefaults (parameters: IParameters, schema: JSONSchema7): IParameters { + const newParameters: IParameters = {} + Object.entries(parameters).forEach(([k, v]) => { + if (schema.properties !== undefined && k in schema.properties) { + const schemaOfK = schema.properties[k] as JSONSchema7 + if (v === schemaOfK.default) { + // skip it + } else if (schemaOfK.type === 'object') { + const prunedV = pruneDefaults(v as IParameters, schemaOfK) + if (Object.keys(prunedV).length > 0) { + newParameters[k] = prunedV + } + } else if (schemaOfK.type === 'array' && Array.isArray(v)) { + if (Array.isArray(schemaOfK.default) && schemaOfK.default.length === 0 && v.length === 0) { + // if default=[] and v=[] then skip it + } else if ('items' in schemaOfK) { + const schemaOfItem = schemaOfK.items as JSONSchema7 + const prunedV = v.map(v2 => { + const schemaOfItemAsObject: JSONSchema7 = { + type: 'object', + properties: { + a: schemaOfItem + } + } + return pruneDefaults({ a: v2 }, schemaOfItemAsObject).a + }).filter(v2 => v2 !== undefined) + if (prunedV.length > 0) { + newParameters[k] = prunedV + } + } + // TODO handle defaults in prefixItems, see https://json-schema.org/understanding-json-schema/reference/array.html#id7 + // but do not have catalog which uses tuples yet, so can delay it + } else { + newParameters[k] = v + } + } + }) + return newParameters +} diff --git a/src/store.ts b/src/store.ts index 72c99ec0..0b8d4d33 100644 --- a/src/store.ts +++ b/src/store.ts @@ -9,6 +9,7 @@ import { fetchCatalogIndex, fetchCatalog } from './catalog' import { catalogIndexURL } from './constants' import { removeItemAtIndex, replaceItemAtIndex, moveItem, swapItem, removeAllItems } from './utils/array' import { groupParameters, unGroupParameters } from './grouper' +import { pruneDefaults } from './pruner' const catalogIndexState = selector({ key: 'catalogIndex', @@ -115,7 +116,7 @@ const globalFormDataState = selector({ if (inlinedParameters instanceof DefaultValue) { parameters = {} } else { - parameters = externalizeDataUrls(unGroupParameters(inlinedParameters, catalog.global.uiSchema), newFiles) + parameters = pruneDefaults(externalizeDataUrls(unGroupParameters(inlinedParameters, catalog.global.uiSchema), newFiles), catalog.global.schema) } const nodes = get(workflowNodesState) const newUsedFiles = dropUnusedFiles(parameters, nodes, newFiles) @@ -193,7 +194,7 @@ const selectedNodeFormDataState = selector({ if (inlinedParameters instanceof DefaultValue) { parameters = {} } else { - parameters = externalizeDataUrls(unGroupParameters(inlinedParameters, catalogNode.uiSchema), newFiles) + parameters = pruneDefaults(externalizeDataUrls(unGroupParameters(inlinedParameters, catalogNode.uiSchema), newFiles), catalogNode.schema) } const nodes = get(workflowNodesState) const selectedNodeIndex = get(selectedNodeIndexState) From 0c6ea62690099a674a43520573076da07e559f3a Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 17 Mar 2022 15:19:57 +0100 Subject: [PATCH 3/7] Copy when array schema does not have items --- src/pruner.test.ts | 24 ++++++++++++++++++++++++ src/pruner.ts | 8 +++++--- 2 files changed, 29 insertions(+), 3 deletions(-) diff --git a/src/pruner.test.ts b/src/pruner.test.ts index f47a3079..76d31bac 100644 --- a/src/pruner.test.ts +++ b/src/pruner.test.ts @@ -346,6 +346,30 @@ describe('given array items is string and has default', () => { }) }) +describe('given array item is untyped and has default', () => { + it('should include prop', () => { + const parameters = { + prop1: ['something'] + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'array' + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = { + prop1: ['something'] + } + expect(result).toEqual(expected) + }) +}) + describe('given array items is string and has item equal to default and item which is non-default', () => { it('should not include prop', () => { const parameters = { diff --git a/src/pruner.ts b/src/pruner.ts index d87b4931..c8dd60f7 100644 --- a/src/pruner.ts +++ b/src/pruner.ts @@ -16,7 +16,7 @@ export function pruneDefaults (parameters: IParameters, schema: JSONSchema7): IP if (Object.keys(prunedV).length > 0) { newParameters[k] = prunedV } - } else if (schemaOfK.type === 'array' && Array.isArray(v)) { + } else if (Array.isArray(v)) { if (Array.isArray(schemaOfK.default) && schemaOfK.default.length === 0 && v.length === 0) { // if default=[] and v=[] then skip it } else if ('items' in schemaOfK) { @@ -33,9 +33,11 @@ export function pruneDefaults (parameters: IParameters, schema: JSONSchema7): IP if (prunedV.length > 0) { newParameters[k] = prunedV } + } else { + // TODO handle defaults in prefixItems, see https://json-schema.org/understanding-json-schema/reference/array.html#id7 + // but do not have catalog which uses tuples yet, so can delay it + newParameters[k] = v } - // TODO handle defaults in prefixItems, see https://json-schema.org/understanding-json-schema/reference/array.html#id7 - // but do not have catalog which uses tuples yet, so can delay it } else { newParameters[k] = v } From 7d6360cbb56b076975645bba5fba3fc3790e09a4 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 17 Mar 2022 15:37:50 +0100 Subject: [PATCH 4/7] Dont call triple nested function on single line --- src/store.ts | 36 ++++++++++++++++++++++++++---------- 1 file changed, 26 insertions(+), 10 deletions(-) diff --git a/src/store.ts b/src/store.ts index 0b8d4d33..dc7be35e 100644 --- a/src/store.ts +++ b/src/store.ts @@ -1,4 +1,6 @@ import { atom, DefaultValue, selector, SetterOrUpdater, useRecoilState, useRecoilValue, useSetRecoilState } from 'recoil' +import { JSONSchema7 } from 'json-schema' +import { UiSchema } from '@rjsf/core' import { externalizeDataUrls, internalizeDataUrls } from './dataurls' import { saveArchive } from './archive' @@ -11,6 +13,7 @@ import { removeItemAtIndex, replaceItemAtIndex, moveItem, swapItem, removeAllIte import { groupParameters, unGroupParameters } from './grouper' import { pruneDefaults } from './pruner' + const catalogIndexState = selector({ key: 'catalogIndex', get: async () => { @@ -96,27 +99,40 @@ const filesState = atom({ default: {} }) +function formData2parameters(formData: IParameters, newFiles: IFiles, schema: JSONSchema7, uiSchema: UiSchema): IParameters { + const ungrouped = unGroupParameters(formData, uiSchema) + const externailized = externalizeDataUrls(ungrouped, newFiles) + const pruned = pruneDefaults(externailized, schema) + return pruned +} + +function parameters2formData(parameters: IParameters, files: IFiles, uiSchema: UiSchema): IParameters { + const internalized = internalizeDataUrls(parameters, files) + const grouped = groupParameters(internalized, uiSchema) + return grouped +} + const globalFormDataState = selector({ key: 'globalFormData', get: ({ get }) => { const parameters = get(globalParametersState) const files = get(filesState) const catalog = get(catalogState) - const formData = groupParameters(internalizeDataUrls(parameters, files), catalog.global.uiSchema) + const formData = parameters2formData(parameters, files, catalog.global.uiSchema) return formData }, - set: ({ get, set }, inlinedParameters) => { - if (inlinedParameters === undefined) { + set: ({ get, set }, formData) => { + if (formData === undefined) { return } const files = get(filesState) const newFiles = { ...files } const catalog = get(catalogState) let parameters: IParameters - if (inlinedParameters instanceof DefaultValue) { + if (formData instanceof DefaultValue) { parameters = {} } else { - parameters = pruneDefaults(externalizeDataUrls(unGroupParameters(inlinedParameters, catalog.global.uiSchema), newFiles), catalog.global.schema) + parameters = formData2parameters(formData, newFiles, catalog.global.schema, catalog.global.uiSchema) } const nodes = get(workflowNodesState) const newUsedFiles = dropUnusedFiles(parameters, nodes, newFiles) @@ -177,11 +193,11 @@ const selectedNodeFormDataState = selector({ return undefined } const files = get(filesState) - const formData = groupParameters(internalizeDataUrls(node.parameters, files), catalogNode.uiSchema) + const formData = parameters2formData(node.parameters, files, catalogNode.uiSchema) return formData }, - set: ({ set, get }, inlinedParameters) => { - if (inlinedParameters === undefined) { + set: ({ set, get }, formData) => { + if (formData === undefined) { return } const catalogNode = get(selectedCatalogNodeState) @@ -191,10 +207,10 @@ const selectedNodeFormDataState = selector({ const files = get(filesState) const newFiles = { ...files } let parameters: IParameters - if (inlinedParameters instanceof DefaultValue) { + if (formData instanceof DefaultValue) { parameters = {} } else { - parameters = pruneDefaults(externalizeDataUrls(unGroupParameters(inlinedParameters, catalogNode.uiSchema), newFiles), catalogNode.schema) + parameters = formData2parameters(formData, newFiles, catalogNode.schema, catalogNode.uiSchema) } const nodes = get(workflowNodesState) const selectedNodeIndex = get(selectedNodeIndexState) From 05ca475bbfc7b7a5271dfc87044bf4892518abb9 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 18 Mar 2022 09:55:35 +0100 Subject: [PATCH 5/7] Lint fix --- src/store.ts | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/store.ts b/src/store.ts index dc7be35e..f38cadb1 100644 --- a/src/store.ts +++ b/src/store.ts @@ -13,7 +13,6 @@ import { removeItemAtIndex, replaceItemAtIndex, moveItem, swapItem, removeAllIte import { groupParameters, unGroupParameters } from './grouper' import { pruneDefaults } from './pruner' - const catalogIndexState = selector({ key: 'catalogIndex', get: async () => { @@ -99,14 +98,14 @@ const filesState = atom({ default: {} }) -function formData2parameters(formData: IParameters, newFiles: IFiles, schema: JSONSchema7, uiSchema: UiSchema): IParameters { +function formData2parameters (formData: IParameters, newFiles: IFiles, schema: JSONSchema7, uiSchema: UiSchema): IParameters { const ungrouped = unGroupParameters(formData, uiSchema) const externailized = externalizeDataUrls(ungrouped, newFiles) const pruned = pruneDefaults(externailized, schema) return pruned } -function parameters2formData(parameters: IParameters, files: IFiles, uiSchema: UiSchema): IParameters { +function parameters2formData (parameters: IParameters, files: IFiles, uiSchema: UiSchema): IParameters { const internalized = internalizeDataUrls(parameters, files) const grouped = groupParameters(internalized, uiSchema) return grouped From 64deb68f55a3d46375930f397bce8dd05089e73f Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 18 Mar 2022 10:03:40 +0100 Subject: [PATCH 6/7] Added test for value empty string and default is some string --- src/pruner.test.ts | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/src/pruner.test.ts b/src/pruner.test.ts index 76d31bac..71b83f0a 100644 --- a/src/pruner.test.ts +++ b/src/pruner.test.ts @@ -107,6 +107,31 @@ describe('pruneDefaults()', () => { }) }) + describe('given an empty string and default is something', () => { + it('should include prop', () => { + const parameters = { + prop1: '' + } + const schema: JSONSchema7 = { + type: 'object', + properties: { + prop1: { + type: 'string', + default: 'something' + } + }, + additionalProperties: false + } + + const result = pruneDefaults(parameters, schema) + + const expected = { + prop1: '' + } + expect(result).toEqual(expected) + }) + }) + describe('given a integer and is set to default', () => { it('should not include prop', () => { const parameters = { From d73b885ecc9fb4ec1d1d6816b04c20edd05782ab Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 18 Mar 2022 11:28:39 +0100 Subject: [PATCH 7/7] Remove unneeded newline --- src/pruner.test.ts | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/pruner.test.ts b/src/pruner.test.ts index 71b83f0a..0ac8f233 100644 --- a/src/pruner.test.ts +++ b/src/pruner.test.ts @@ -560,8 +560,7 @@ describe('given array items is object and has nested prop equal to default', () const result = pruneDefaults(parameters, schema) - const expected = { - } + const expected = {} expect(result).toEqual(expected) }) })