diff --git a/.github/workflows/node.js.yml b/.github/workflows/node.js.yml index 0d67da4..54100ef 100644 --- a/.github/workflows/node.js.yml +++ b/.github/workflows/node.js.yml @@ -15,7 +15,7 @@ jobs: steps: - uses: actions/checkout@v2 - name: Use Node.js - uses: actions/setup-node@v2 + uses: actions/setup-node@v6 with: node-version: 18.x cache: 'yarn' diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml index c6d28dd..1dd582e 100644 --- a/.github/workflows/pages.yml +++ b/.github/workflows/pages.yml @@ -31,7 +31,7 @@ jobs: - name: Checkout uses: actions/checkout@v3 - name: Use Node.js - uses: actions/setup-node@v2 + uses: actions/setup-node@v6 with: node-version: 18.x cache: "yarn" diff --git a/apps/haddock3-download/integration-tests/dupheader.spec.ts b/apps/haddock3-download/integration-tests/dupheader.spec.ts index 88bd06f..36e8197 100644 --- a/apps/haddock3-download/integration-tests/dupheader.spec.ts +++ b/apps/haddock3-download/integration-tests/dupheader.spec.ts @@ -27,7 +27,7 @@ test.describe('given an uploaded archive with a workflow.cfg file with a duplica test('it should show uplaoded file', async ({ page }) => { // Click Files tab - await page.locator('text=Files').click() + await page.locator('button:has-text("Files")').click() // validate file button is present await page.waitForSelector('button:has-text("some.pdb")') }) diff --git a/apps/haddock3-download/integration-tests/syntaxhighlighter.spec.ts b/apps/haddock3-download/integration-tests/syntaxhighlighter.spec.ts index 59aa63a..99de0cd 100644 --- a/apps/haddock3-download/integration-tests/syntaxhighlighter.spec.ts +++ b/apps/haddock3-download/integration-tests/syntaxhighlighter.spec.ts @@ -10,7 +10,7 @@ test('Verify that [object Object] bug does not show up (issue #74)', async ({ pa await page.locator('text=docking-protein-ligand').click() // validate that file is used - await page.locator('text=Files').click() + await page.locator('button:has-text("Files")').click() await page.waitForSelector('button:has-text("data/target.pdb")') // change to 'text' tab diff --git a/apps/haddock3-download/integration-tests/topoaamol.spec.ts b/apps/haddock3-download/integration-tests/topoaamol.spec.ts index 5b4ab47..4a45c24 100644 --- a/apps/haddock3-download/integration-tests/topoaamol.spec.ts +++ b/apps/haddock3-download/integration-tests/topoaamol.spec.ts @@ -74,7 +74,7 @@ test.describe('given 1 molecule and a topoaa node', () => { .setInputFiles({ name: 'workflow.zip', mimeType: 'application/zip', buffer: file1 }) // ensure file is uploaded - await page.locator('text=Files').click() + await page.locator('button:has-text("Files")').click() await page.waitForSelector('button:has-text("e2a-hpr_1GGR.pdb")') }) diff --git a/apps/haddock3-download/package.json b/apps/haddock3-download/package.json index ca70f20..635236c 100644 --- a/apps/haddock3-download/package.json +++ b/apps/haddock3-download/package.json @@ -18,7 +18,7 @@ "react-dom": "^17.0.0" }, "devDependencies": { - "@playwright/test": "^1.22.1", + "@playwright/test": "^1.45.0", "@types/adm-zip": "^0.5.0", "@types/node": "16", "@types/react": "^17.0.0", diff --git a/apps/haddock3-download/tsconfig.json b/apps/haddock3-download/tsconfig.json index f26181b..af6b9e8 100644 --- a/apps/haddock3-download/tsconfig.json +++ b/apps/haddock3-download/tsconfig.json @@ -4,7 +4,7 @@ "useDefineForClassFields": true, "lib": ["DOM", "DOM.Iterable", "ESNext"], "allowJs": false, - "skipLibCheck": false, + "skipLibCheck": true, "esModuleInterop": false, "allowSyntheticDefaultImports": true, "strict": true, diff --git a/packages/haddock3_catalog/generate_haddock3_catalog.py b/packages/haddock3_catalog/generate_haddock3_catalog.py index 2fa268e..1c63567 100755 --- a/packages/haddock3_catalog/generate_haddock3_catalog.py +++ b/packages/haddock3_catalog/generate_haddock3_catalog.py @@ -392,12 +392,18 @@ def config2schema(config): prop['items'] = { "type": "number" } - elif k == 'ligand_chains': + elif k == 'ligand_chains' or k == 'chains': prop['items'] = { "type": "string", "format": "chain" } prop['default'] = v['default'] + elif k == 'interface_combinations': + # For emscoring module + prop['items'] = { + "type": "string" + } + prop['default'] = v['default'] 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 d7bf7bb..eaddc96 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml @@ -59,6 +59,15 @@ global: used to plot the results of a HADDOCK3 workflow. If this option, this command is automatically executed at the end of the workflow (on the caprieval folders). type: boolean + gen_archive: + default: false + title: Generates an archive of the run and of the analysis. + description: If true, executes haddock3-analyse in self_contained mode and + generates archives of the run_directory and of the analysis in two separated + tgz files. + $comment: If true, executes haddock3-analyse in self_contained mode and generates + archives of the run_directory and of the analysis in two separated tgz files. + type: boolean cns_exec: title: Path to the CNS executable description: If not provided, HADDOCK3 will use the cns path configured during @@ -229,13 +238,19 @@ nodes: type: number maximum: 20.0 minimum: 1.0 - output: + output_bfactor: 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. + title: Dump the input models with the rescaled delta_score written in the + b-factor column. + description: Dump the input models with the rescaled delta_score written in + the b-factor column. + $comment: Dump the input models with the rescaled delta_score written in the + b-factor column. Those files do not contain the mutations, but rather will + display the normalized (between 0 and 100) delta HADDOCK score (100 * (delta_score + - min_score) / (max_score - min_score)) in the b-factor column. The higher + the b-factor, the more favourable (or less unfavourable) the mutation. You + can color the PDB files according to this attribute (in pymol, type "spectrum + b") type: boolean scan_residue: default: ALA @@ -290,23 +305,71 @@ nodes: - TOP - TYP - TYS + - CIR plot: default: false title: Plot scanning data. description: Plot scanning data. $comment: Plot scanning data. type: boolean + chains: + default: [] + title: ChainIDs to be considered for the scanning. + description: ChainIDs to be considered for the scanning. + $comment: ChainIDs to be considered for the scanning. If empty, all the chains + will be considered. If not empty, only residues part of the specified chains + will be mutated. Do not use this parameter if you are using the resdic_* + parameter. + type: array + minItems: 0 + maxItems: 10 + items: + type: string + format: chain + output_mutants: + default: false + title: Dump the mutated, energy-minimized PDB files. + description: Dump the mutated, energy-minimized PDB files. + $comment: Dump the mutated, energy-minimized PDB files. As the number of mutants + can be very large, this option is allowed only when a single model is provided + in input. + type: boolean + ligand_param_fname: + title: Custom ligand parameter file + description: Ligand parameter file in CNS format + $comment: Ligand parameter file in CNS format, for any ligand/residues/molecules + 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 required: [] additionalProperties: false uiSchema: int_cutoff: ui:group: analysis - output: + output_bfactor: ui:group: analysis scan_residue: ui:group: analysis plot: ui:group: analysis + chains: + ui:group: analysis + output_mutants: + ui:group: analysis + ligand_param_fname: + ui:widget: file + ui:group: force field + ligand_top_fname: + ui:widget: file + ui:group: force field tomlSchema: {} - id: caprieval category: analysis @@ -483,6 +546,14 @@ nodes: $comment: Atoms to be considered during the analysis. If false (default), only backbone atoms will be considered, otherwise all the heavy-atoms. type: boolean + keep_hetatm: + default: false + title: HETATM to be considered during the analysis. + description: HETATM to be considered during the analysis. + $comment: HETATM to be considered during the analysis. If false (default), + only ATOM coordinates lines will be used, otherwise the HETATM from reference + will also be used. + type: boolean required: [] additionalProperties: false uiSchema: @@ -521,10 +592,12 @@ nodes: ui:group: analysis allatoms: ui:group: analysis + keep_hetatm: + ui:group: analysis tomlSchema: {} - id: clustfcc category: analysis - label: Cluster modules with FCC. + label: Fraction of Common Contacts (FCC) clustering module. description: HADDOCK3 module for clustering with FCC. schema: type: object @@ -962,6 +1035,28 @@ nodes: elecflag: ui:group: force field tomlSchema: {} +- id: filter + category: analysis + label: Filter models based on their score. + description: HADDOCK3 module to select top cluster/model. + schema: + type: object + properties: + threshold: + default: 0.0 + title: Threshold value to filter models. + description: Threshold value to filter models based on their score. + $comment: Threshold value to filter models based on their score. Models having + higher score than the threshold value will be filtered out. + type: number + maximum: 99999.99 + minimum: -99999.99 + required: [] + additionalProperties: false + uiSchema: + threshold: + ui:group: analysis + tomlSchema: {} - id: flexref category: refinement label: Flexible refinement with CNS. @@ -1127,23 +1222,6 @@ nodes: tomlSchema: mol_shape: indexed: true -- id: gdock - category: sampling - label: gdock integration sampling module. - description: HADDOCK3 gdock module. - schema: - type: object - properties: - ambig_fname: - type: string - format: uri-reference - required: [] - additionalProperties: false - uiSchema: - ambig_fname: - ui:widget: file - ui:group: distance restraints - tomlSchema: {} - id: ilrmsdmatrix category: analysis label: ilRMSD matrix module. @@ -1601,7 +1679,7 @@ nodes: tomlSchema: {} - id: openmm category: refinement - label: OpenMM refinement module for HADDOCK3. + label: OpenMM Molecular Dynamics refinement module for HADDOCK3. description: HADDOCK3 OpenMM module. schema: type: object @@ -1793,6 +1871,127 @@ nodes: solv_equilibration: ui:group: sampling tomlSchema: {} +- id: prodigyligand + category: scoring + label: PRODIGY-ligand scoring module. + description: HADDOCK3 module to perform energy minimization scoring. + schema: + type: object + properties: + receptor_chain: + default: A + title: Chain ID of the receptor. + description: Chain ID of the receptor. + $comment: Chain ID of the receptor. Used to know what chain should be considered + as receptor interacting with the ligand. + type: string + minLength: 1 + maxLength: 1 + format: chain + ligand_chain: + default: B + title: Chain ID of the ligand. + description: Chain ID of the ligand. + $comment: Chain of the ligand to score. Used to know in which chain the ligand + is found. + type: string + minLength: 1 + maxLength: 1 + format: chain + ligand_resname: + default: UNK + title: Residue name of the ligand. + description: Residue name of the ligand. + $comment: Residue name of the ligand to score. Must be present in the ligand + chain. + type: string + minLength: 1 + maxLength: 3 + temperature: + default: 25.0 + title: "Temperature (\xB0C) at which to perform the conversion to pKd." + description: "Temperature (\xB0C) at which to perform the conversion from\ + \ deltaG (kcal.mol-1) to pKd." + $comment: "Temperature (\xB0C) at which to perform the conversion from deltaG\ + \ (kcal.mol-1) to pKd." + type: number + maximum: 95.0 + minimum: -273.15 + to_pkd: + default: true + title: Converts binding affinity values to pKd. + description: Converts binding affinity values to pKd. + $comment: By default, prodigy-lig results in deltaG (kcal.mol-1), but this + parameter allows to convert results to pKd. + type: boolean + required: [] + additionalProperties: false + uiSchema: + receptor_chain: + ui:group: scoring + ligand_chain: + ui:group: scoring + ligand_resname: + ui:group: scoring + temperature: + ui:group: conversion + to_pkd: + ui:group: conversion + tomlSchema: {} +- id: prodigyprotein + category: scoring + label: PRODIGY protein complex scoring module + description: HADDOCK3 module to perform energy minimization scoring. + schema: + type: object + properties: + chains: + default: [] + title: Chains to be scored. + description: List of chains to be scored. If empty/unspecified, all inter-chains + contacts will be considered for the final prediction. + $comment: List of chains to be scored. If empty/unspecified, all inter-chains + contacts will be considered for the final prediction. In specific cases, + for example antibody-antigen complexes, some chains should be considered + as a single molecule. Use the chains parameter to provide a list of chains + that should be considered for the calculation. Use commas to include multiple + chains as part of a single group. ["A", "B"] => Contacts calculated + (only) between chains A and B. ["A,B", "C"] => Contacts calculated (only) + between chains A and C; and B and C. ["A", "B", "C"] => Contacts calculated + (only) between chains A and B; B and C; and A and C. + type: array + minItems: 0 + maxItems: 20 + items: + type: string + format: chain + temperature: + default: 25.0 + title: "Temperature (\xB0C) at which to perform the conversion to pKd." + description: "Temperature (\xB0C) at which to perform the conversion from\ + \ deltaG (kcal.mol-1) to pKd." + $comment: "Temperature (\xB0C) at which to perform the conversion from deltaG\ + \ (kcal.mol-1) to pKd." + type: number + maximum: 95.0 + minimum: -273.15 + to_pkd: + default: true + title: Converts binding affinity values to pKd. + description: Converts binding affinity values to pKd. + $comment: By default, prodigy-lig results in deltaG (kcal.mol-1), but this + parameter allows to convert results to pKd. + type: boolean + required: [] + additionalProperties: false + uiSchema: + chains: + ui:group: scoring + temperature: + ui:group: conversion + to_pkd: + ui:group: conversion + tomlSchema: {} - id: rigidbody category: sampling label: Rigid-body docking sampling module @@ -2051,7 +2250,7 @@ nodes: schema: type: object properties: - top_cluster: + top_clusters: default: 1000 title: Number of clusters to consider description: Number of clusters to consider (ranked by score) @@ -2087,7 +2286,7 @@ nodes: required: [] additionalProperties: false uiSchema: - top_cluster: + top_clusters: ui:group: analysis top_models: ui:group: analysis @@ -2146,6 +2345,30 @@ nodes: are within 2A. This cutoff can be changed in the generate-topology.cns script. type: boolean + charged_nter: + default: false + title: N-ter topology + description: Define if N-terminus should be charged or uncharged + $comment: This option defines how N-terminus residue should be. If false + (default), N-ter will be an uncharged NH, as it would be in a peptide + bond. If true, N-ter will be a charged NH3+. + type: boolean + charged_cter: + default: false + title: C-ter topology + description: Define if C-terminus should be charged or uncharged + $comment: This option defines how N-terminus residue should be. If false + (default), C-ter will be an uncharged CO, as it would be in a peptide + bond. If true, C-ter will be a charged COO-. + type: boolean + 5_phosphate: + default: false + title: Nucleic Acids 5' topology + description: Define if 5' end should be phosphate or not. + $comment: This option defines how nucleic acid 5' residue should be. + If false (default), 5' end will be an OH. If true, 5' end will be + a phosphate. + type: boolean required: [] additionalProperties: false maxItemsFrom: molecules diff --git a/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml b/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml index 3c564f1..572b9af 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml @@ -59,6 +59,15 @@ global: used to plot the results of a HADDOCK3 workflow. If this option, this command is automatically executed at the end of the workflow (on the caprieval folders). type: boolean + gen_archive: + default: false + title: Generates an archive of the run and of the analysis. + description: If true, executes haddock3-analyse in self_contained mode and + generates archives of the run_directory and of the analysis in two separated + tgz files. + $comment: If true, executes haddock3-analyse in self_contained mode and generates + archives of the run_directory and of the analysis in two separated tgz files. + type: boolean cns_exec: title: Path to the CNS executable description: If not provided, HADDOCK3 will use the cns path configured during @@ -263,13 +272,19 @@ nodes: type: number maximum: 20.0 minimum: 1.0 - output: + output_bfactor: 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. + title: Dump the input models with the rescaled delta_score written in the + b-factor column. + description: Dump the input models with the rescaled delta_score written in + the b-factor column. + $comment: Dump the input models with the rescaled delta_score written in the + b-factor column. Those files do not contain the mutations, but rather will + display the normalized (between 0 and 100) delta HADDOCK score (100 * (delta_score + - min_score) / (max_score - min_score)) in the b-factor column. The higher + the b-factor, the more favourable (or less unfavourable) the mutation. You + can color the PDB files according to this attribute (in pymol, type "spectrum + b") type: boolean scan_residue: default: ALA @@ -324,12 +339,50 @@ nodes: - TOP - TYP - TYS + - CIR plot: default: false title: Plot scanning data. description: Plot scanning data. $comment: Plot scanning data. type: boolean + chains: + default: [] + title: ChainIDs to be considered for the scanning. + description: ChainIDs to be considered for the scanning. + $comment: ChainIDs to be considered for the scanning. If empty, all the chains + will be considered. If not empty, only residues part of the specified chains + will be mutated. Do not use this parameter if you are using the resdic_* + parameter. + type: array + minItems: 0 + maxItems: 10 + items: + type: string + format: chain + output_mutants: + default: false + title: Dump the mutated, energy-minimized PDB files. + description: Dump the mutated, energy-minimized PDB files. + $comment: Dump the mutated, energy-minimized PDB files. As the number of mutants + can be very large, this option is allowed only when a single model is provided + in input. + type: boolean + ligand_param_fname: + title: Custom ligand parameter file + description: Ligand parameter file in CNS format + $comment: Ligand parameter file in CNS format, for any ligand/residues/molecules + 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 required: [] additionalProperties: false uiSchema: @@ -337,12 +390,22 @@ nodes: ui:group: analysis int_cutoff: ui:group: analysis - output: + output_bfactor: ui:group: analysis scan_residue: ui:group: analysis plot: ui:group: analysis + chains: + ui:group: analysis + output_mutants: + ui:group: analysis + ligand_param_fname: + ui:widget: file + ui:group: force field + ligand_top_fname: + ui:widget: file + ui:group: force field tomlSchema: resdic: indexed: true @@ -521,6 +584,14 @@ nodes: $comment: Atoms to be considered during the analysis. If false (default), only backbone atoms will be considered, otherwise all the heavy-atoms. type: boolean + keep_hetatm: + default: false + title: HETATM to be considered during the analysis. + description: HETATM to be considered during the analysis. + $comment: HETATM to be considered during the analysis. If false (default), + only ATOM coordinates lines will be used, otherwise the HETATM from reference + will also be used. + type: boolean required: [] additionalProperties: false uiSchema: @@ -559,10 +630,12 @@ nodes: ui:group: analysis allatoms: ui:group: analysis + keep_hetatm: + ui:group: analysis tomlSchema: {} - id: clustfcc category: analysis - label: Cluster modules with FCC. + label: Fraction of Common Contacts (FCC) clustering module. description: HADDOCK3 module for clustering with FCC. schema: type: object @@ -1942,7 +2015,7 @@ nodes: number might be smaller if the minimisation converges earlier. type: number maximum: 10000 - minimum: 1 + minimum: 0 tolerance: default: 5 title: Failure tolerance percentage @@ -2538,6 +2611,25 @@ nodes: terms) and their components (Eelec, Evdw, Edesol, BSA) will be written to the header of each PDB file. type: boolean + interface_combinations: + default: [] + title: Chains to be scored. + description: List of chains to be scored. Use this parameter to provide a + list of chain pairs (coma separated) that should be considered for the calculation. + If empty/unspecified, all inter-chains contacts will be considered for the + final prediction. + $comment: List of chains to be scored. If empty/unspecified, all inter-chains + contacts will be considered for the final prediction. In specific cases, + for example antibody-antigen complexes, some chains should be considered + as a single molecule. Use this parameter to provide a list of chain pairs + (separated by coma) that should be considered for the calculation. [] => + Compute all interface scores ["A,H", "A,L"] => Compute sum of per-interface + scores between chains A and H; A and L + type: array + minItems: 0 + maxItems: 20 + items: + type: string w_air: default: 0.0 title: Weight of the distance restraint energy @@ -2662,7 +2754,7 @@ nodes: number might be smaller if the minimisation converges earlier. type: number maximum: 10000 - minimum: 1 + minimum: 0 tolerance: default: 5 title: Failure tolerance percentage @@ -2676,6 +2768,8 @@ nodes: uiSchema: per_interface_scoring: ui:group: scoring + interface_combinations: + ui:group: scoring w_air: ui:group: scoring w_bsa: @@ -2709,6 +2803,28 @@ nodes: tolerance: ui:group: module tomlSchema: {} +- id: filter + category: analysis + label: Filter models based on their score. + description: HADDOCK3 module to select top cluster/model. + schema: + type: object + properties: + threshold: + default: 0.0 + title: Threshold value to filter models. + description: Threshold value to filter models based on their score. + $comment: Threshold value to filter models based on their score. Models having + higher score than the threshold value will be filtered out. + type: number + maximum: 99999.99 + minimum: -99999.99 + required: [] + additionalProperties: false + uiSchema: + threshold: + ui:group: analysis + tomlSchema: {} - id: flexref category: refinement label: Flexible refinement with CNS. @@ -3987,7 +4103,7 @@ nodes: be smaller if the minimisation converges earlier. type: number maximum: 10000 - minimum: 1 + minimum: 0 mdsteps_rigid: default: 500 title: Hot phase SA MD steps @@ -4657,23 +4773,6 @@ nodes: indexed: true items: flatten: true -- id: gdock - category: sampling - label: gdock integration sampling module. - description: HADDOCK3 gdock module. - schema: - type: object - properties: - ambig_fname: - type: string - format: uri-reference - required: [] - additionalProperties: false - uiSchema: - ambig_fname: - ui:widget: file - ui:group: distance restraints - tomlSchema: {} - id: ilrmsdmatrix category: analysis label: ilRMSD matrix module. @@ -5994,7 +6093,7 @@ nodes: be smaller if the minimisation converges earlier. type: number maximum: 10000 - minimum: 1 + minimum: 0 waterheatsteps: default: 100 title: Number of MD steps for the heating @@ -6631,6 +6730,25 @@ nodes: terms) and their components (Eelec, Evdw, Edesol, BSA) will be written to the header of each PDB file. type: boolean + interface_combinations: + default: [] + title: Chains to be scored. + description: List of chains to be scored. Use this parameter to provide a + list of chain pairs (coma separated) that should be considered for the calculation. + If empty/unspecified, all inter-chains contacts will be considered for the + final prediction. + $comment: List of chains to be scored. If empty/unspecified, all inter-chains + contacts will be considered for the final prediction. In specific cases, + for example antibody-antigen complexes, some chains should be considered + as a single molecule. Use this parameter to provide a list of chain pairs + (separated by coma) that should be considered for the calculation. [] => + Compute all interface scores ["A,H", "A,L"] => Compute sum of per-interface + scores between chains A and H; A and L + type: array + minItems: 0 + maxItems: 20 + items: + type: string w_bsa: default: 0.0 title: Weight of the buried surface area term @@ -6822,7 +6940,7 @@ nodes: be smaller if the minimisation converges earlier. type: number maximum: 10000 - minimum: 1 + minimum: 0 waterheatsteps: default: 100 title: Number of MD steps for the heating @@ -6865,6 +6983,8 @@ nodes: uiSchema: per_interface_scoring: ui:group: scoring + interface_combinations: + ui:group: scoring w_bsa: ui:group: scoring w_cdih: @@ -6914,7 +7034,7 @@ nodes: tomlSchema: {} - id: openmm category: refinement - label: OpenMM refinement module for HADDOCK3. + label: OpenMM Molecular Dynamics refinement module for HADDOCK3. description: HADDOCK3 OpenMM module. schema: type: object @@ -7025,7 +7145,7 @@ nodes: - AllBonds - HAngles equilibration_timesteps: - default: 3000 + default: 2000 title: Equilibration timesteps. description: Equilibration timesteps performed without saving the simulation state. @@ -7148,27 +7268,6 @@ nodes: type: number maximum: 4 minimum: 0.5 - solv_eq_timesteps: - default: 500 - title: Number of timesteps to be performed during solvent equilibration phase. - description: Number of timesteps to be performed during solvent equilibration - phase. - $comment: Number of timesteps to be performed during solvent equilibration - phase. - type: number - maximum: 10000 - minimum: 10 - solv_eq_spring_constant: - default: 20.0 - title: Spring constant (k) used to restrain protein coordinates during solvent - equilibration phase. - description: Spring constant (k) used to restrain protein coordintes during - solvent equilibration phase. - $comment: Spring constant (k) used to restrain protein coordinates during - solvent equilibration phase. - type: number - maximum: 10000 - minimum: 0 required: [] additionalProperties: false uiSchema: @@ -7218,10 +7317,172 @@ nodes: ui:group: sampling solv_eq_stepsize_fs: ui:group: sampling - solv_eq_timesteps: - ui:group: sampling - solv_eq_spring_constant: - ui:group: sampling + tomlSchema: {} +- id: prodigyligand + category: scoring + label: PRODIGY-ligand scoring module. + description: HADDOCK3 module to perform energy minimization scoring. + schema: + type: object + properties: + receptor_chain: + default: A + title: Chain ID of the receptor. + description: Chain ID of the receptor. + $comment: Chain ID of the receptor. Used to know what chain should be considered + as receptor interacting with the ligand. + type: string + minLength: 1 + maxLength: 1 + format: chain + ligand_chain: + default: B + title: Chain ID of the ligand. + description: Chain ID of the ligand. + $comment: Chain of the ligand to score. Used to know in which chain the ligand + is found. + type: string + minLength: 1 + maxLength: 1 + format: chain + ligand_resname: + default: UNK + title: Residue name of the ligand. + description: Residue name of the ligand. + $comment: Residue name of the ligand to score. Must be present in the ligand + chain. + type: string + minLength: 1 + maxLength: 3 + temperature: + default: 25.0 + title: "Temperature (\xB0C) at which to perform the conversion to pKd." + description: "Temperature (\xB0C) at which to perform the conversion from\ + \ deltaG (kcal.mol-1) to pKd." + $comment: "Temperature (\xB0C) at which to perform the conversion from deltaG\ + \ (kcal.mol-1) to pKd." + type: number + maximum: 95.0 + minimum: -273.15 + electrostatics: + default: true + title: Use the electrostatic component. + description: Use the electrostatic component from the input model to make + the prediction. + $comment: Use the electrostatic component from the input model to make the + prediction, if available. The electroststics must have been computed by + HADDOCK and written in the REMARK of the model. + type: boolean + to_pkd: + default: true + title: Converts binding affinity values to pKd. + description: Converts binding affinity values to pKd. + $comment: By default, prodigy-lig results in deltaG (kcal.mol-1), but this + parameter allows to convert results to pKd. + type: boolean + distance_cutoff: + default: 10.5 + title: "Distance cutoff (\xC5) to extract amino-acids from the receptor." + description: "Distance cutoff (\xC5) to extract amino-acids from the receptor." + $comment: "Distance cutoff (\xC5) to extract amino-acids from the receptor\ + \ in contact with the ligand." + type: number + maximum: 100.0 + minimum: 1.0 + required: [] + additionalProperties: false + uiSchema: + receptor_chain: + ui:group: scoring + ligand_chain: + ui:group: scoring + ligand_resname: + ui:group: scoring + temperature: + ui:group: conversion + electrostatics: + ui:group: scoring + to_pkd: + ui:group: conversion + distance_cutoff: + ui:group: scoring + tomlSchema: {} +- id: prodigyprotein + category: scoring + label: PRODIGY protein complex scoring module + description: HADDOCK3 module to perform energy minimization scoring. + schema: + type: object + properties: + chains: + default: [] + title: Chains to be scored. + description: List of chains to be scored. If empty/unspecified, all inter-chains + contacts will be considered for the final prediction. + $comment: List of chains to be scored. If empty/unspecified, all inter-chains + contacts will be considered for the final prediction. In specific cases, + for example antibody-antigen complexes, some chains should be considered + as a single molecule. Use the chains parameter to provide a list of chains + that should be considered for the calculation. Use commas to include multiple + chains as part of a single group. ["A", "B"] => Contacts calculated + (only) between chains A and B. ["A,B", "C"] => Contacts calculated (only) + between chains A and C; and B and C. ["A", "B", "C"] => Contacts calculated + (only) between chains A and B; B and C; and A and C. + type: array + minItems: 0 + maxItems: 20 + items: + type: string + format: chain + distance_cutoff: + default: 5.5 + title: "Distance cutoff (\xC5) to extract amino-acids in contact between the\ + \ two chains." + description: "Distance cutoff (\xC5) to extract amino-acids in contact between\ + \ the two chains." + $comment: "Distance cutoff (\xC5) to extract amino-acids in contact between\ + \ the two chains." + type: number + maximum: 100.0 + minimum: 1.0 + accessibility_cutoff: + default: 0.05 + title: Accessibility threshold for BSA analysis. + description: Accessibility threshold for BSA analysis. + $comment: Accessibility threshold for BSA analysis. + type: number + maximum: 1.0 + minimum: 0.0 + temperature: + default: 25.0 + title: "Temperature (\xB0C) at which to perform the conversion to pKd." + description: "Temperature (\xB0C) at which to perform the conversion from\ + \ deltaG (kcal.mol-1) to pKd." + $comment: "Temperature (\xB0C) at which to perform the conversion from deltaG\ + \ (kcal.mol-1) to pKd." + type: number + maximum: 95.0 + minimum: -273.15 + to_pkd: + default: true + title: Converts binding affinity values to pKd. + description: Converts binding affinity values to pKd. + $comment: By default, prodigy-lig results in deltaG (kcal.mol-1), but this + parameter allows to convert results to pKd. + type: boolean + required: [] + additionalProperties: false + uiSchema: + chains: + ui:group: scoring + distance_cutoff: + ui:group: scoring + accessibility_cutoff: + ui:group: scoring + temperature: + ui:group: conversion + to_pkd: + ui:group: conversion tomlSchema: {} - id: rigidbody category: sampling @@ -8723,7 +8984,7 @@ nodes: schema: type: object properties: - top_cluster: + top_clusters: default: 1000 title: Number of clusters to consider description: Number of clusters to consider (ranked by score) @@ -8759,7 +9020,7 @@ nodes: required: [] additionalProperties: false uiSchema: - top_cluster: + top_clusters: ui:group: analysis top_models: ui:group: analysis @@ -8898,6 +9159,30 @@ nodes: maximum: 9999 minimum: -9999 format: residue + charged_nter: + default: false + title: N-ter topology + description: Define if N-terminus should be charged or uncharged + $comment: This option defines how N-terminus residue should be. If false + (default), N-ter will be an uncharged NH, as it would be in a peptide + bond. If true, N-ter will be a charged NH3+. + type: boolean + charged_cter: + default: false + title: C-ter topology + description: Define if C-terminus should be charged or uncharged + $comment: This option defines how N-terminus residue should be. If false + (default), C-ter will be an uncharged CO, as it would be in a peptide + bond. If true, C-ter will be a charged COO-. + type: boolean + 5_phosphate: + default: false + title: Nucleic Acids 5' topology + description: Define if 5' end should be phosphate or not. + $comment: This option defines how nucleic acid 5' residue should be. + If false (default), 5' end will be an OH. If true, 5' end will be + a phosphate. + type: boolean required: [] additionalProperties: false maxItemsFrom: molecules diff --git a/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml b/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml index 087d26b..42509a1 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml @@ -59,6 +59,15 @@ global: used to plot the results of a HADDOCK3 workflow. If this option, this command is automatically executed at the end of the workflow (on the caprieval folders). type: boolean + gen_archive: + default: false + title: Generates an archive of the run and of the analysis. + description: If true, executes haddock3-analyse in self_contained mode and + generates archives of the run_directory and of the analysis in two separated + tgz files. + $comment: If true, executes haddock3-analyse in self_contained mode and generates + archives of the run_directory and of the analysis in two separated tgz files. + type: boolean cns_exec: title: Path to the CNS executable description: If not provided, HADDOCK3 will use the cns path configured during @@ -275,13 +284,19 @@ nodes: type: number maximum: 20.0 minimum: 1.0 - output: + output_bfactor: 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. + title: Dump the input models with the rescaled delta_score written in the + b-factor column. + description: Dump the input models with the rescaled delta_score written in + the b-factor column. + $comment: Dump the input models with the rescaled delta_score written in the + b-factor column. Those files do not contain the mutations, but rather will + display the normalized (between 0 and 100) delta HADDOCK score (100 * (delta_score + - min_score) / (max_score - min_score)) in the b-factor column. The higher + the b-factor, the more favourable (or less unfavourable) the mutation. You + can color the PDB files according to this attribute (in pymol, type "spectrum + b") type: boolean scan_residue: default: ALA @@ -336,12 +351,50 @@ nodes: - TOP - TYP - TYS + - CIR plot: default: false title: Plot scanning data. description: Plot scanning data. $comment: Plot scanning data. type: boolean + chains: + default: [] + title: ChainIDs to be considered for the scanning. + description: ChainIDs to be considered for the scanning. + $comment: ChainIDs to be considered for the scanning. If empty, all the chains + will be considered. If not empty, only residues part of the specified chains + will be mutated. Do not use this parameter if you are using the resdic_* + parameter. + type: array + minItems: 0 + maxItems: 10 + items: + type: string + format: chain + output_mutants: + default: false + title: Dump the mutated, energy-minimized PDB files. + description: Dump the mutated, energy-minimized PDB files. + $comment: Dump the mutated, energy-minimized PDB files. As the number of mutants + can be very large, this option is allowed only when a single model is provided + in input. + type: boolean + ligand_param_fname: + title: Custom ligand parameter file + description: Ligand parameter file in CNS format + $comment: Ligand parameter file in CNS format, for any ligand/residues/molecules + 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 required: [] additionalProperties: false uiSchema: @@ -349,12 +402,22 @@ nodes: ui:group: analysis int_cutoff: ui:group: analysis - output: + output_bfactor: ui:group: analysis scan_residue: ui:group: analysis plot: ui:group: analysis + chains: + ui:group: analysis + output_mutants: + ui:group: analysis + ligand_param_fname: + ui:widget: file + ui:group: force field + ligand_top_fname: + ui:widget: file + ui:group: force field tomlSchema: resdic: indexed: true @@ -533,6 +596,14 @@ nodes: $comment: Atoms to be considered during the analysis. If false (default), only backbone atoms will be considered, otherwise all the heavy-atoms. type: boolean + keep_hetatm: + default: false + title: HETATM to be considered during the analysis. + description: HETATM to be considered during the analysis. + $comment: HETATM to be considered during the analysis. If false (default), + only ATOM coordinates lines will be used, otherwise the HETATM from reference + will also be used. + type: boolean required: [] additionalProperties: false uiSchema: @@ -571,10 +642,12 @@ nodes: ui:group: analysis allatoms: ui:group: analysis + keep_hetatm: + ui:group: analysis tomlSchema: {} - id: clustfcc category: analysis - label: Cluster modules with FCC. + label: Fraction of Common Contacts (FCC) clustering module. description: HADDOCK3 module for clustering with FCC. schema: type: object @@ -1954,7 +2027,7 @@ nodes: number might be smaller if the minimisation converges earlier. type: number maximum: 10000 - minimum: 1 + minimum: 0 iniseed: default: 917 title: Random seed @@ -2584,6 +2657,25 @@ nodes: terms) and their components (Eelec, Evdw, Edesol, BSA) will be written to the header of each PDB file. type: boolean + interface_combinations: + default: [] + title: Chains to be scored. + description: List of chains to be scored. Use this parameter to provide a + list of chain pairs (coma separated) that should be considered for the calculation. + If empty/unspecified, all inter-chains contacts will be considered for the + final prediction. + $comment: List of chains to be scored. If empty/unspecified, all inter-chains + contacts will be considered for the final prediction. In specific cases, + for example antibody-antigen complexes, some chains should be considered + as a single molecule. Use this parameter to provide a list of chain pairs + (separated by coma) that should be considered for the calculation. [] => + Compute all interface scores ["A,H", "A,L"] => Compute sum of per-interface + scores between chains A and H; A and L + type: array + minItems: 0 + maxItems: 20 + items: + type: string w_air: default: 0.0 title: Weight of the distance restraint energy @@ -2708,7 +2800,7 @@ nodes: number might be smaller if the minimisation converges earlier. type: number maximum: 10000 - minimum: 1 + minimum: 0 tolerance: default: 5 title: Failure tolerance percentage @@ -2736,6 +2828,8 @@ nodes: uiSchema: per_interface_scoring: ui:group: scoring + interface_combinations: + ui:group: scoring w_air: ui:group: scoring w_bsa: @@ -2771,6 +2865,28 @@ nodes: log_level: ui:group: module tomlSchema: {} +- id: filter + category: analysis + label: Filter models based on their score. + description: HADDOCK3 module to select top cluster/model. + schema: + type: object + properties: + threshold: + default: 0.0 + title: Threshold value to filter models. + description: Threshold value to filter models based on their score. + $comment: Threshold value to filter models based on their score. Models having + higher score than the threshold value will be filtered out. + type: number + maximum: 99999.99 + minimum: -99999.99 + required: [] + additionalProperties: false + uiSchema: + threshold: + ui:group: analysis + tomlSchema: {} - id: flexref category: refinement label: Flexible refinement with CNS. @@ -4049,7 +4165,7 @@ nodes: be smaller if the minimisation converges earlier. type: number maximum: 10000 - minimum: 1 + minimum: 0 mdsteps_rigid: default: 500 title: Hot phase SA MD steps @@ -4941,23 +5057,6 @@ nodes: indexed: true items: flatten: true -- id: gdock - category: sampling - label: gdock integration sampling module. - description: HADDOCK3 gdock module. - schema: - type: object - properties: - ambig_fname: - type: string - format: uri-reference - required: [] - additionalProperties: false - uiSchema: - ambig_fname: - ui:widget: file - ui:group: distance restraints - tomlSchema: {} - id: ilrmsdmatrix category: analysis label: ilRMSD matrix module. @@ -6291,7 +6390,7 @@ nodes: be smaller if the minimisation converges earlier. type: number maximum: 10000 - minimum: 1 + minimum: 0 timestep: default: 0.002 title: MD integrating time step @@ -6972,6 +7071,25 @@ nodes: terms) and their components (Eelec, Evdw, Edesol, BSA) will be written to the header of each PDB file. type: boolean + interface_combinations: + default: [] + title: Chains to be scored. + description: List of chains to be scored. Use this parameter to provide a + list of chain pairs (coma separated) that should be considered for the calculation. + If empty/unspecified, all inter-chains contacts will be considered for the + final prediction. + $comment: List of chains to be scored. If empty/unspecified, all inter-chains + contacts will be considered for the final prediction. In specific cases, + for example antibody-antigen complexes, some chains should be considered + as a single molecule. Use this parameter to provide a list of chain pairs + (separated by coma) that should be considered for the calculation. [] => + Compute all interface scores ["A,H", "A,L"] => Compute sum of per-interface + scores between chains A and H; A and L + type: array + minItems: 0 + maxItems: 20 + items: + type: string w_bsa: default: 0.0 title: Weight of the buried surface area term @@ -7163,7 +7281,7 @@ nodes: be smaller if the minimisation converges earlier. type: number maximum: 10000 - minimum: 1 + minimum: 0 timestep: default: 0.002 title: MD integrating time step @@ -7242,6 +7360,8 @@ nodes: uiSchema: per_interface_scoring: ui:group: scoring + interface_combinations: + ui:group: scoring w_bsa: ui:group: scoring w_cdih: @@ -7299,7 +7419,7 @@ nodes: tomlSchema: {} - id: openmm category: refinement - label: OpenMM refinement module for HADDOCK3. + label: OpenMM Molecular Dynamics refinement module for HADDOCK3. description: HADDOCK3 OpenMM module. schema: type: object @@ -7410,7 +7530,7 @@ nodes: - AllBonds - HAngles equilibration_timesteps: - default: 3000 + default: 2000 title: Equilibration timesteps. description: Equilibration timesteps performed without saving the simulation state. @@ -7541,7 +7661,7 @@ nodes: $comment: Number of timesteps to be performed during solvent equilibration phase. type: number - maximum: 10000 + maximum: 50000 minimum: 10 solv_eq_spring_constant: default: 20.0 @@ -7608,6 +7728,172 @@ nodes: solv_eq_spring_constant: ui:group: sampling tomlSchema: {} +- id: prodigyligand + category: scoring + label: PRODIGY-ligand scoring module. + description: HADDOCK3 module to perform energy minimization scoring. + schema: + type: object + properties: + receptor_chain: + default: A + title: Chain ID of the receptor. + description: Chain ID of the receptor. + $comment: Chain ID of the receptor. Used to know what chain should be considered + as receptor interacting with the ligand. + type: string + minLength: 1 + maxLength: 1 + format: chain + ligand_chain: + default: B + title: Chain ID of the ligand. + description: Chain ID of the ligand. + $comment: Chain of the ligand to score. Used to know in which chain the ligand + is found. + type: string + minLength: 1 + maxLength: 1 + format: chain + ligand_resname: + default: UNK + title: Residue name of the ligand. + description: Residue name of the ligand. + $comment: Residue name of the ligand to score. Must be present in the ligand + chain. + type: string + minLength: 1 + maxLength: 3 + temperature: + default: 25.0 + title: "Temperature (\xB0C) at which to perform the conversion to pKd." + description: "Temperature (\xB0C) at which to perform the conversion from\ + \ deltaG (kcal.mol-1) to pKd." + $comment: "Temperature (\xB0C) at which to perform the conversion from deltaG\ + \ (kcal.mol-1) to pKd." + type: number + maximum: 95.0 + minimum: -273.15 + electrostatics: + default: true + title: Use the electrostatic component. + description: Use the electrostatic component from the input model to make + the prediction. + $comment: Use the electrostatic component from the input model to make the + prediction, if available. The electroststics must have been computed by + HADDOCK and written in the REMARK of the model. + type: boolean + to_pkd: + default: true + title: Converts binding affinity values to pKd. + description: Converts binding affinity values to pKd. + $comment: By default, prodigy-lig results in deltaG (kcal.mol-1), but this + parameter allows to convert results to pKd. + type: boolean + distance_cutoff: + default: 10.5 + title: "Distance cutoff (\xC5) to extract amino-acids from the receptor." + description: "Distance cutoff (\xC5) to extract amino-acids from the receptor." + $comment: "Distance cutoff (\xC5) to extract amino-acids from the receptor\ + \ in contact with the ligand." + type: number + maximum: 100.0 + minimum: 1.0 + required: [] + additionalProperties: false + uiSchema: + receptor_chain: + ui:group: scoring + ligand_chain: + ui:group: scoring + ligand_resname: + ui:group: scoring + temperature: + ui:group: conversion + electrostatics: + ui:group: scoring + to_pkd: + ui:group: conversion + distance_cutoff: + ui:group: scoring + tomlSchema: {} +- id: prodigyprotein + category: scoring + label: PRODIGY protein complex scoring module + description: HADDOCK3 module to perform energy minimization scoring. + schema: + type: object + properties: + chains: + default: [] + title: Chains to be scored. + description: List of chains to be scored. If empty/unspecified, all inter-chains + contacts will be considered for the final prediction. + $comment: List of chains to be scored. If empty/unspecified, all inter-chains + contacts will be considered for the final prediction. In specific cases, + for example antibody-antigen complexes, some chains should be considered + as a single molecule. Use the chains parameter to provide a list of chains + that should be considered for the calculation. Use commas to include multiple + chains as part of a single group. ["A", "B"] => Contacts calculated + (only) between chains A and B. ["A,B", "C"] => Contacts calculated (only) + between chains A and C; and B and C. ["A", "B", "C"] => Contacts calculated + (only) between chains A and B; B and C; and A and C. + type: array + minItems: 0 + maxItems: 20 + items: + type: string + format: chain + distance_cutoff: + default: 5.5 + title: "Distance cutoff (\xC5) to extract amino-acids in contact between the\ + \ two chains." + description: "Distance cutoff (\xC5) to extract amino-acids in contact between\ + \ the two chains." + $comment: "Distance cutoff (\xC5) to extract amino-acids in contact between\ + \ the two chains." + type: number + maximum: 100.0 + minimum: 1.0 + accessibility_cutoff: + default: 0.05 + title: Accessibility threshold for BSA analysis. + description: Accessibility threshold for BSA analysis. + $comment: Accessibility threshold for BSA analysis. + type: number + maximum: 1.0 + minimum: 0.0 + temperature: + default: 25.0 + title: "Temperature (\xB0C) at which to perform the conversion to pKd." + description: "Temperature (\xB0C) at which to perform the conversion from\ + \ deltaG (kcal.mol-1) to pKd." + $comment: "Temperature (\xB0C) at which to perform the conversion from deltaG\ + \ (kcal.mol-1) to pKd." + type: number + maximum: 95.0 + minimum: -273.15 + to_pkd: + default: true + title: Converts binding affinity values to pKd. + description: Converts binding affinity values to pKd. + $comment: By default, prodigy-lig results in deltaG (kcal.mol-1), but this + parameter allows to convert results to pKd. + type: boolean + required: [] + additionalProperties: false + uiSchema: + chains: + ui:group: scoring + distance_cutoff: + ui:group: scoring + accessibility_cutoff: + ui:group: scoring + temperature: + ui:group: conversion + to_pkd: + ui:group: conversion + tomlSchema: {} - id: rigidbody category: sampling label: Rigid-body docking sampling module @@ -9151,7 +9437,7 @@ nodes: schema: type: object properties: - top_cluster: + top_clusters: default: 1000 title: Number of clusters to consider description: Number of clusters to consider (ranked by score) @@ -9187,7 +9473,7 @@ nodes: required: [] additionalProperties: false uiSchema: - top_cluster: + top_clusters: ui:group: analysis top_models: ui:group: analysis @@ -9368,6 +9654,30 @@ nodes: maximum: 9999 minimum: -9999 format: residue + charged_nter: + default: false + title: N-ter topology + description: Define if N-terminus should be charged or uncharged + $comment: This option defines how N-terminus residue should be. If false + (default), N-ter will be an uncharged NH, as it would be in a peptide + bond. If true, N-ter will be a charged NH3+. + type: boolean + charged_cter: + default: false + title: C-ter topology + description: Define if C-terminus should be charged or uncharged + $comment: This option defines how N-terminus residue should be. If false + (default), C-ter will be an uncharged CO, as it would be in a peptide + bond. If true, C-ter will be a charged COO-. + type: boolean + 5_phosphate: + default: false + title: Nucleic Acids 5' topology + description: Define if 5' end should be phosphate or not. + $comment: This option defines how nucleic acid 5' residue should be. + If false (default), 5' end will be an OH. If true, 5' end will be + a phosphate. + type: boolean required: [] additionalProperties: false maxItemsFrom: molecules diff --git a/yarn.lock b/yarn.lock index 4689c84..1f3ce49 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2256,7 +2256,7 @@ __metadata: resolution: "@i-vresse/haddock3-config-builder-download@workspace:apps/haddock3-download" dependencies: "@i-vresse/wb-core": "workspace:^" - "@playwright/test": ^1.22.1 + "@playwright/test": ^1.45.0 "@types/adm-zip": ^0.5.0 "@types/node": 16 "@types/react": ^17.0.0 @@ -2761,15 +2761,14 @@ __metadata: languageName: node linkType: hard -"@playwright/test@npm:^1.22.1": - version: 1.23.2 - resolution: "@playwright/test@npm:1.23.2" +"@playwright/test@npm:^1.45.0": + version: 1.58.2 + resolution: "@playwright/test@npm:1.58.2" dependencies: - "@types/node": "*" - playwright-core: 1.23.2 + playwright: 1.58.2 bin: playwright: cli.js - checksum: 3f01cc25d9e2095ee31a272cead11de859303f7c2e4ccdbd5a01985d51dd0d946da2b284b43fb0bcd6780e80939ef4b67215650572a3124a84339c760faa8460 + checksum: 4169d8484081d24de132d10e960bb83159a751dd81d00ed8b21ddf68266c024a51eaf5329c3943d5f023009d3af9c72649016d7a1919d634f787292e97a980f0 languageName: node linkType: hard @@ -10276,6 +10275,16 @@ __metadata: languageName: node linkType: hard +"fsevents@npm:2.3.2, fsevents@npm:^2.1.2, fsevents@npm:~2.3.2": + version: 2.3.2 + resolution: "fsevents@npm:2.3.2" + dependencies: + node-gyp: latest + checksum: 97ade64e75091afee5265e6956cb72ba34db7819b4c3e94c431d4be2b19b8bb7a2d4116da417950c3425f17c8fe693d25e20212cac583ac1521ad066b77ae31f + conditions: os=darwin + languageName: node + linkType: hard + "fsevents@npm:^1.2.7": version: 1.2.13 resolution: "fsevents@npm:1.2.13" @@ -10287,22 +10296,21 @@ __metadata: languageName: node linkType: hard -"fsevents@npm:^2.1.2, fsevents@npm:~2.3.2": - version: 2.3.2 - resolution: "fsevents@npm:2.3.2" +"fsevents@npm:~2.3.3": + version: 2.3.3 + resolution: "fsevents@npm:2.3.3" dependencies: node-gyp: latest - checksum: 97ade64e75091afee5265e6956cb72ba34db7819b4c3e94c431d4be2b19b8bb7a2d4116da417950c3425f17c8fe693d25e20212cac583ac1521ad066b77ae31f + checksum: 11e6ea6fea15e42461fc55b4b0e4a0a3c654faa567f1877dbd353f39156f69def97a69936d1746619d656c4b93de2238bf731f6085a03a50cabf287c9d024317 conditions: os=darwin languageName: node linkType: hard -"fsevents@npm:~2.3.3": - version: 2.3.3 - resolution: "fsevents@npm:2.3.3" +"fsevents@patch:fsevents@2.3.2#~builtin, fsevents@patch:fsevents@^2.1.2#~builtin, fsevents@patch:fsevents@~2.3.2#~builtin": + version: 2.3.2 + resolution: "fsevents@patch:fsevents@npm%3A2.3.2#~builtin::version=2.3.2&hash=18f3a7" dependencies: node-gyp: latest - checksum: 11e6ea6fea15e42461fc55b4b0e4a0a3c654faa567f1877dbd353f39156f69def97a69936d1746619d656c4b93de2238bf731f6085a03a50cabf287c9d024317 conditions: os=darwin languageName: node linkType: hard @@ -10317,15 +10325,6 @@ __metadata: languageName: node linkType: hard -"fsevents@patch:fsevents@^2.1.2#~builtin, fsevents@patch:fsevents@~2.3.2#~builtin": - version: 2.3.2 - resolution: "fsevents@patch:fsevents@npm%3A2.3.2#~builtin::version=2.3.2&hash=18f3a7" - dependencies: - node-gyp: latest - conditions: os=darwin - languageName: node - linkType: hard - "fsevents@patch:fsevents@~2.3.3#~builtin": version: 2.3.3 resolution: "fsevents@patch:fsevents@npm%3A2.3.3#~builtin::version=2.3.3&hash=18f3a7" @@ -14841,12 +14840,27 @@ __metadata: languageName: node linkType: hard -"playwright-core@npm:1.23.2": - version: 1.23.2 - resolution: "playwright-core@npm:1.23.2" +"playwright-core@npm:1.58.2": + version: 1.58.2 + resolution: "playwright-core@npm:1.58.2" + bin: + playwright-core: cli.js + checksum: fd8c4c6658b80f5db90af36db9f560e7bf461f704d0ffe706e8858570af0321312fff9c44a5ee49552df3e3cce981e1f8dd9e8b09e6d7bdd62e094639b68bddd + languageName: node + linkType: hard + +"playwright@npm:1.58.2": + version: 1.58.2 + resolution: "playwright@npm:1.58.2" + dependencies: + fsevents: 2.3.2 + playwright-core: 1.58.2 + dependenciesMeta: + fsevents: + optional: true bin: playwright: cli.js - checksum: 7e5c7adbc436c68e5de8535508746c2734393f77948c08ff1df7d21eaa518cd00d82f49c936b2776be6958dc2d7f18985582d72690ffeee7a59006267e22a391 + checksum: 3536138633135bdd62eb3aa63c653036b944fbb6fb2d57f4d936baaad9d706c11bde13ef11b307677fba061bad2f4ad68256f84978cc9280667437d1106d12e6 languageName: node linkType: hard