From 7a7efca36affa3ec3b76d39bb45abe7b2293c7dc Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Mon, 25 Sep 2023 08:40:56 +0200 Subject: [PATCH] Rerun catalog generation --- .../generate_haddock3_catalog.py | 5 ++ .../public/catalog/haddock3.easy.yaml | 31 ++++---- .../public/catalog/haddock3.expert.yaml | 73 ++++++++++++++----- .../public/catalog/haddock3.guru.yaml | 73 ++++++++++++++----- 4 files changed, 128 insertions(+), 54 deletions(-) diff --git a/packages/haddock3_catalog/generate_haddock3_catalog.py b/packages/haddock3_catalog/generate_haddock3_catalog.py index 3e4ea6fa..221bf1a9 100755 --- a/packages/haddock3_catalog/generate_haddock3_catalog.py +++ b/packages/haddock3_catalog/generate_haddock3_catalog.py @@ -326,6 +326,11 @@ def config2schema(config): prop['items'] = { "type": "number" } + elif k == 'ligand_chains': + prop['items'] = { + "type": "string", + "format": "chain" + } else: raise ValueError(f"Don't know how to determine type of items of {v}") else: diff --git a/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml b/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml index ea79aa4d..874ef813 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml @@ -10,7 +10,7 @@ categories: description: HADDOCK3 actions referring to refinement. collapsed: false - name: scoring - description: HADDOCK3 modules to score modules. + description: HADDOCK3 modules to score models. collapsed: false - name: analysis description: HADDOCK3 modules related to model analysis. @@ -917,7 +917,7 @@ nodes: description: Performs Ligand RMSD calculations. $comment: Calculates the Ligand Root Mean Square Deviation. This calculation is done by superimposing the receptors (defined by the receptor_chain parameter) - and then evaluating the RMSD on the ligands (defined by the ligand_chain + and then evaluating the RMSD on the ligands (defined by the ligand_chains parameter). Superposition and RMSD calculations are done on backbone heavy atoms. type: boolean @@ -929,7 +929,7 @@ nodes: calculation is done by superimposing the model and the target on the interface backbone atoms of the receptor (defined by the receptor_chain parameter) and calculating the RMSD on all heavy atoms of the ligand (defined by the - ligand_chain parameter). + ligand_chains parameter). type: boolean dockq: default: true @@ -970,17 +970,20 @@ nodes: minLength: 1 maxLength: 1 format: chain - ligand_chain: - default: B - title: Ligand ChainID - description: Ligand ChainID to be considered for the RMSD calculations. - $comment: Ligand ChainID to be considered for the RMSD calculations. This - determines which chain will be treated as the ligand for the L-RMSD and + ligand_chains: + default: + - B + title: Ligand ChainIDs + description: Ligand ChainIDs to be considered for the RMSD calculations. + $comment: Ligand ChainIDs to be considered for the RMSD calculations. This + determines which chains will be treated as the ligand for the L-RMSD and for I-L-RMSD. - type: string - minLength: 1 - maxLength: 1 - format: chain + type: array + minItems: 0 + maxItems: 100 + items: + type: string + format: chain sortby: default: score title: Sort the structures/clusters in the output file by this value @@ -1056,7 +1059,7 @@ nodes: ui:group: analysis receptor_chain: ui:group: analysis - ligand_chain: + ligand_chains: ui:group: analysis sortby: ui:group: analysis diff --git a/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml b/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml index 2dba4c2d..b9b3ea0b 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml @@ -10,7 +10,7 @@ categories: description: HADDOCK3 actions referring to refinement. collapsed: false - name: scoring - description: HADDOCK3 modules to score modules. + description: HADDOCK3 modules to score models. collapsed: false - name: analysis description: HADDOCK3 modules related to model analysis. @@ -854,7 +854,7 @@ nodes: title: Boolean condition on the previous ambiguous distance restraints file description: Boolean condition on the previous ambiguous distance restraints file. If true, use the the restraint information coming from the previous - CNS module. If False, don't use previous information. + CNS module. If false, don't use previous information. $comment: Boolean condition on the ambiguous distance restraints file. If true, use the restraint information coming from the previous CNS module, as long as an ambig_fname is not defined for the current module. If False, @@ -1987,7 +1987,15 @@ nodes: 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: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 10000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 50000 minimum: 1 solvent: default: water @@ -2736,6 +2744,8 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling + max_nmodels: + ui:group: sampling nemsteps: ui:group: sampling waterheatsteps: @@ -4195,10 +4205,18 @@ nodes: sampling_factor: default: 1 title: Sampling factor for each starting model - description: This paramater control how many times a model will be refined. - $comment: This paramater control how many times a model will be refined. + description: This paramater controls how many times a model will be refined. + $comment: This paramater controls how many times a model will be refined. type: number - maximum: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 10000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 50000 minimum: 1 nemsteps: default: 200 @@ -4978,6 +4996,8 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling + max_nmodels: + ui:group: sampling nemsteps: ui:group: sampling mdsteps_rigid: @@ -6253,7 +6273,15 @@ nodes: of restraints is turned on. If not then the energy minimisation will lead to the same final conformation. type: number - maximum: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 50000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 100000 minimum: 1 nemsteps: default: 200 @@ -6952,6 +6980,8 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling + max_nmodels: + ui:group: sampling nemsteps: ui:group: sampling tolerance: @@ -7209,7 +7239,7 @@ nodes: description: Performs Ligand RMSD calculations. $comment: Calculates the Ligand Root Mean Square Deviation. This calculation is done by superimposing the receptors (defined by the receptor_chain parameter) - and then evaluating the RMSD on the ligands (defined by the ligand_chain + and then evaluating the RMSD on the ligands (defined by the ligand_chains parameter). Superposition and RMSD calculations are done on backbone heavy atoms. type: boolean @@ -7221,7 +7251,7 @@ nodes: calculation is done by superimposing the model and the target on the interface backbone atoms of the receptor (defined by the receptor_chain parameter) and calculating the RMSD on all heavy atoms of the ligand (defined by the - ligand_chain parameter). + ligand_chains parameter). type: boolean dockq: default: true @@ -7262,17 +7292,20 @@ nodes: minLength: 1 maxLength: 1 format: chain - ligand_chain: - default: B - title: Ligand ChainID - description: Ligand ChainID to be considered for the RMSD calculations. - $comment: Ligand ChainID to be considered for the RMSD calculations. This - determines which chain will be treated as the ligand for the L-RMSD and + ligand_chains: + default: + - B + title: Ligand ChainIDs + description: Ligand ChainIDs to be considered for the RMSD calculations. + $comment: Ligand ChainIDs to be considered for the RMSD calculations. This + determines which chains will be treated as the ligand for the L-RMSD and for I-L-RMSD. - type: string - minLength: 1 - maxLength: 1 - format: chain + type: array + minItems: 0 + maxItems: 100 + items: + type: string + format: chain sortby: default: score title: Sort the structures/clusters in the output file by this value @@ -7348,7 +7381,7 @@ nodes: ui:group: analysis receptor_chain: ui:group: analysis - ligand_chain: + ligand_chains: ui:group: analysis sortby: ui:group: analysis diff --git a/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml b/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml index e637ffb5..801fb44f 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml @@ -10,7 +10,7 @@ categories: description: HADDOCK3 actions referring to refinement. collapsed: false - name: scoring - description: HADDOCK3 modules to score modules. + description: HADDOCK3 modules to score models. collapsed: false - name: analysis description: HADDOCK3 modules related to model analysis. @@ -952,7 +952,7 @@ nodes: title: Boolean condition on the previous ambiguous distance restraints file description: Boolean condition on the previous ambiguous distance restraints file. If true, use the the restraint information coming from the previous - CNS module. If False, don't use previous information. + CNS module. If false, don't use previous information. $comment: Boolean condition on the ambiguous distance restraints file. If true, use the restraint information coming from the previous CNS module, as long as an ambig_fname is not defined for the current module. If False, @@ -2085,7 +2085,15 @@ nodes: 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: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 10000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 50000 minimum: 1 solvent: default: water @@ -2870,6 +2878,8 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling + max_nmodels: + ui:group: sampling nemsteps: ui:group: sampling timestep: @@ -4337,10 +4347,18 @@ nodes: sampling_factor: default: 1 title: Sampling factor for each starting model - description: This paramater control how many times a model will be refined. - $comment: This paramater control how many times a model will be refined. + description: This paramater controls how many times a model will be refined. + $comment: This paramater controls how many times a model will be refined. type: number - maximum: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 10000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 50000 minimum: 1 nemsteps: default: 200 @@ -5299,6 +5317,8 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling + max_nmodels: + ui:group: sampling nemsteps: ui:group: sampling mdsteps_rigid: @@ -6608,7 +6628,15 @@ nodes: of restraints is turned on. If not then the energy minimisation will lead to the same final conformation. type: number - maximum: 1 + maximum: 200 + minimum: 1 + max_nmodels: + default: 50000 + title: Maximum number of models to refine + description: This paramater controls the maximum number of models to refine. + $comment: This paramater controls the maximum number of models to refine. + type: number + maximum: 100000 minimum: 1 nemsteps: default: 200 @@ -7335,6 +7363,8 @@ nodes: ui:group: force field sampling_factor: ui:group: sampling + max_nmodels: + ui:group: sampling nemsteps: ui:group: sampling iniseed: @@ -7598,7 +7628,7 @@ nodes: description: Performs Ligand RMSD calculations. $comment: Calculates the Ligand Root Mean Square Deviation. This calculation is done by superimposing the receptors (defined by the receptor_chain parameter) - and then evaluating the RMSD on the ligands (defined by the ligand_chain + and then evaluating the RMSD on the ligands (defined by the ligand_chains parameter). Superposition and RMSD calculations are done on backbone heavy atoms. type: boolean @@ -7610,7 +7640,7 @@ nodes: calculation is done by superimposing the model and the target on the interface backbone atoms of the receptor (defined by the receptor_chain parameter) and calculating the RMSD on all heavy atoms of the ligand (defined by the - ligand_chain parameter). + ligand_chains parameter). type: boolean dockq: default: true @@ -7651,17 +7681,20 @@ nodes: minLength: 1 maxLength: 1 format: chain - ligand_chain: - default: B - title: Ligand ChainID - description: Ligand ChainID to be considered for the RMSD calculations. - $comment: Ligand ChainID to be considered for the RMSD calculations. This - determines which chain will be treated as the ligand for the L-RMSD and + ligand_chains: + default: + - B + title: Ligand ChainIDs + description: Ligand ChainIDs to be considered for the RMSD calculations. + $comment: Ligand ChainIDs to be considered for the RMSD calculations. This + determines which chains will be treated as the ligand for the L-RMSD and for I-L-RMSD. - type: string - minLength: 1 - maxLength: 1 - format: chain + type: array + minItems: 0 + maxItems: 100 + items: + type: string + format: chain sortby: default: score title: Sort the structures/clusters in the output file by this value @@ -7737,7 +7770,7 @@ nodes: ui:group: analysis receptor_chain: ui:group: analysis - ligand_chain: + ligand_chains: ui:group: analysis sortby: ui:group: analysis