From ec6e1f0fcdea9b28b2e6d89fbbeab3ce4c4193a1 Mon Sep 17 00:00:00 2001 From: sverhoeven Date: Fri, 3 Nov 2023 13:37:04 +0100 Subject: [PATCH] Regenerate catalogs From https://github.com/haddocking/haddock3/commit/7d2dfff3fb826db2962486193ade43014713a5a1 --- .../public/catalog/haddock3.easy.yaml | 100 ++++++++++++- .../public/catalog/haddock3.expert.yaml | 128 +++++++++++++++- .../public/catalog/haddock3.guru.yaml | 137 +++++++++++++++++- 3 files changed, 357 insertions(+), 8 deletions(-) diff --git a/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml b/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml index 34894f18..06c092f6 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml @@ -62,7 +62,7 @@ global: original input PDBs. type: boolean postprocess: - default: false + default: true title: Executes haddock3-analyse on the CAPRI folders at the end of the run description: If true, executes haddock3-analyse on the CAPRI folders at the end of the workflow @@ -148,7 +148,7 @@ global: maximum: 9999 minimum: 1 clean: - default: false + default: true title: Clean the module output files. description: Clean the module if run succeeds by compressing or removing output files. @@ -194,6 +194,102 @@ global: ui:group: clean tomlSchema: {} nodes: +- id: alascan + category: analysis + label: HADDOCK3 module for alanine scan. + description: HADDOCK3 module for alanine scan. + schema: + type: object + properties: + int_cutoff: + default: 5.0 + title: "Distance cutoff (\xC5) used to define interface contacts." + description: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." + $comment: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." + type: number + maximum: 20.0 + minimum: 1.0 + output: + default: false + title: Dump all the models in the output folder + description: Dump all the models in the output folder with the delta_score + written in the b-factor column. + $comment: Dump all the models in the output folder with the delta_score written + in the b-factor column. + type: boolean + scan_residue: + default: ALA + title: Residue to be used for the scanning + description: Residue to be used for the scanning. The default is alanine. + $comment: Residue to be used for the scanning. The default is alanine. Use + bigger residues at your own risk. + type: string + minLength: 3 + maxLength: 3 + enum: + - ALA + - ARG + - ASN + - ASP + - CYS + - GLN + - GLU + - GLY + - HIS + - ILE + - LEU + - LYS + - MET + - PHE + - PRO + - SER + - THR + - TRP + - TYR + - VAL + - ALY + - ASH + - CFE + - CSP + - CYC + - CYF + - CYM + - DDZ + - GLH + - HLY + - HY3 + - HYP + - M3L + - MLY + - MLZ + - MSE + - NEP + - PNS + - PTR + - SEP + - TOP + - TYP + - TYS + plot: + default: false + title: Plot scanning data. + description: Plot scanning data. + $comment: Plot scanning data. + type: boolean + required: [] + additionalProperties: false + uiSchema: + int_cutoff: + ui:group: analysis + output: + ui:group: analysis + scan_residue: + ui:group: analysis + plot: + ui:group: analysis + tomlSchema: {} - id: caprieval category: analysis label: Calculate CAPRI metrics. diff --git a/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml b/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml index 54f44841..70b04efd 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml @@ -62,7 +62,7 @@ global: original input PDBs. type: boolean postprocess: - default: false + default: true title: Executes haddock3-analyse on the CAPRI folders at the end of the run description: If true, executes haddock3-analyse on the CAPRI folders at the end of the workflow @@ -158,7 +158,7 @@ global: maximum: 9999 minimum: 1 clean: - default: false + default: true title: Clean the module output files. description: Clean the module if run succeeds by compressing or removing output files. @@ -206,6 +206,128 @@ global: ui:group: clean tomlSchema: {} nodes: +- id: alascan + category: analysis + label: HADDOCK3 module for alanine scan. + description: HADDOCK3 module for alanine scan. + schema: + type: object + properties: + resdic: + default: {} + title: List of residues to be mutated + description: List of residues to be mutated. By default all the interface + residues are mutated. + $comment: List of residues to be mutated. By default all the interface residues + are mutated. resdic_* is an expandable parameter. You can provide resdic_A, + resdic_B, resdic_C, etc, where the last capital letter is the chain identifier. + type: object + additionalProperties: + type: array + items: + type: number + format: residue + minItems: 0 + maxItems: 100 + uniqueItems: true + default: [] + propertyNames: + pattern: ^[A-Z]$ + format: chain + maxPropertiesFrom: molecules + int_cutoff: + default: 5.0 + title: "Distance cutoff (\xC5) used to define interface contacts." + description: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." + $comment: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." + type: number + maximum: 20.0 + minimum: 1.0 + output: + default: false + title: Dump all the models in the output folder + description: Dump all the models in the output folder with the delta_score + written in the b-factor column. + $comment: Dump all the models in the output folder with the delta_score written + in the b-factor column. + type: boolean + scan_residue: + default: ALA + title: Residue to be used for the scanning + description: Residue to be used for the scanning. The default is alanine. + $comment: Residue to be used for the scanning. The default is alanine. Use + bigger residues at your own risk. + type: string + minLength: 3 + maxLength: 3 + enum: + - ALA + - ARG + - ASN + - ASP + - CYS + - GLN + - GLU + - GLY + - HIS + - ILE + - LEU + - LYS + - MET + - PHE + - PRO + - SER + - THR + - TRP + - TYR + - VAL + - ALY + - ASH + - CFE + - CSP + - CYC + - CYF + - CYM + - DDZ + - GLH + - HLY + - HY3 + - HYP + - M3L + - MLY + - MLZ + - MSE + - NEP + - PNS + - PTR + - SEP + - TOP + - TYP + - TYS + plot: + default: false + title: Plot scanning data. + description: Plot scanning data. + $comment: Plot scanning data. + type: boolean + required: [] + additionalProperties: false + uiSchema: + resdic: + ui:group: analysis + int_cutoff: + ui:group: analysis + output: + ui:group: analysis + scan_residue: + ui:group: analysis + plot: + ui:group: analysis + tomlSchema: + resdic: + indexed: true - id: caprieval category: analysis label: Calculate CAPRI metrics. @@ -3973,7 +4095,7 @@ nodes: 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: 200 + maximum: 500 minimum: 1 max_nmodels: default: 10000 diff --git a/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml b/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml index a99f2b65..b0607af4 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml @@ -62,7 +62,7 @@ global: original input PDBs. type: boolean postprocess: - default: false + default: true title: Executes haddock3-analyse on the CAPRI folders at the end of the run description: If true, executes haddock3-analyse on the CAPRI folders at the end of the workflow @@ -168,7 +168,7 @@ global: purpose to allow to edit the scripts without touching the main installation. type: boolean clean: - default: false + default: true title: Clean the module output files. description: Clean the module if run succeeds by compressing or removing output files. @@ -218,6 +218,128 @@ global: ui:group: clean tomlSchema: {} nodes: +- id: alascan + category: analysis + label: HADDOCK3 module for alanine scan. + description: HADDOCK3 module for alanine scan. + schema: + type: object + properties: + resdic: + default: {} + title: List of residues to be mutated + description: List of residues to be mutated. By default all the interface + residues are mutated. + $comment: List of residues to be mutated. By default all the interface residues + are mutated. resdic_* is an expandable parameter. You can provide resdic_A, + resdic_B, resdic_C, etc, where the last capital letter is the chain identifier. + type: object + additionalProperties: + type: array + items: + type: number + format: residue + minItems: 0 + maxItems: 100 + uniqueItems: true + default: [] + propertyNames: + pattern: ^[A-Z]$ + format: chain + maxPropertiesFrom: molecules + int_cutoff: + default: 5.0 + title: "Distance cutoff (\xC5) used to define interface contacts." + description: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." + $comment: "Distance cutoff (\xC5) used to define interface contacts between\ + \ two interacting molecules." + type: number + maximum: 20.0 + minimum: 1.0 + output: + default: false + title: Dump all the models in the output folder + description: Dump all the models in the output folder with the delta_score + written in the b-factor column. + $comment: Dump all the models in the output folder with the delta_score written + in the b-factor column. + type: boolean + scan_residue: + default: ALA + title: Residue to be used for the scanning + description: Residue to be used for the scanning. The default is alanine. + $comment: Residue to be used for the scanning. The default is alanine. Use + bigger residues at your own risk. + type: string + minLength: 3 + maxLength: 3 + enum: + - ALA + - ARG + - ASN + - ASP + - CYS + - GLN + - GLU + - GLY + - HIS + - ILE + - LEU + - LYS + - MET + - PHE + - PRO + - SER + - THR + - TRP + - TYR + - VAL + - ALY + - ASH + - CFE + - CSP + - CYC + - CYF + - CYM + - DDZ + - GLH + - HLY + - HY3 + - HYP + - M3L + - MLY + - MLZ + - MSE + - NEP + - PNS + - PTR + - SEP + - TOP + - TYP + - TYS + plot: + default: false + title: Plot scanning data. + description: Plot scanning data. + $comment: Plot scanning data. + type: boolean + required: [] + additionalProperties: false + uiSchema: + resdic: + ui:group: analysis + int_cutoff: + ui:group: analysis + output: + ui:group: analysis + scan_residue: + ui:group: analysis + plot: + ui:group: analysis + tomlSchema: + resdic: + indexed: true - id: caprieval category: analysis label: Calculate CAPRI metrics. @@ -4035,7 +4157,7 @@ nodes: 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: 200 + maximum: 500 minimum: 1 max_nmodels: default: 10000 @@ -4095,6 +4217,13 @@ nodes: type: number maximum: 10000 minimum: 0 + randorien: + default: false + title: Randomize starting orientations + description: Randomize starting orientations + $comment: Randomize starting orientations by separating the molecules in space + and randomly rotating those + type: boolean timestep: default: 0.002 title: MD integrating time step @@ -5014,6 +5143,8 @@ nodes: ui:group: sampling mdsteps_cool3: ui:group: sampling + randorien: + ui:group: sampling timestep: ui:group: sampling tadfactor: