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molstar

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A comprehensive macromolecular library.

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"use strict"; /** * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author David Sehnal <david.sehnal@gmail.com> * @author Alexander Rose <alexander.rose@weirdbyte.de> */ Object.defineProperty(exports, "__esModule", { value: true }); exports.StructureQualityReportProvider = exports.StructureQualityReportParams = exports.StructureQualityReport = void 0; const db_1 = require("../../../mol-data/db"); const schema_1 = require("../../../mol-io/reader/cif/schema"); const mmcif_extras_1 = require("../../../mol-io/reader/cif/schema/mmcif-extras"); const cif_1 = require("../../../mol-io/writer/cif"); const structure_1 = require("../../../mol-model/structure"); const atom_site_1 = require("../../../mol-model/structure/export/categories/atom_site"); const symbol_1 = require("../../../mol-script/language/symbol"); const type_1 = require("../../../mol-script/language/type"); const compiler_1 = require("../../../mol-script/runtime/query/compiler"); const param_definition_1 = require("../../../mol-util/param-definition"); const array_1 = require("../../../mol-util/array"); const mmcif_1 = require("../../../mol-model-formats/structure/mmcif"); const wrapper_1 = require("../../../mol-model-props/common/wrapper"); const custom_model_property_1 = require("../../../mol-model-props/common/custom-model-property"); const assets_1 = require("../../../mol-util/assets"); const custom_property_1 = require("../../../mol-model/custom-property"); var StructureQualityReport; (function (StructureQualityReport) { StructureQualityReport.DefaultServerUrl = 'https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/'; function getEntryUrl(pdbId, serverUrl) { return `${serverUrl}/${pdbId.toLowerCase()}`; } StructureQualityReport.getEntryUrl = getEntryUrl; function isApplicable(model) { return !!model && structure_1.Model.hasPdbId(model); } StructureQualityReport.isApplicable = isApplicable; StructureQualityReport.Schema = { pdbe_structure_quality_report: { updated_datetime_utc: db_1.Column.Schema.str }, pdbe_structure_quality_report_issues: { id: db_1.Column.Schema.int, ...mmcif_extras_1.mmCIF_residueId_schema, pdbx_PDB_model_num: db_1.Column.Schema.int, issue_type_group_id: db_1.Column.Schema.int }, pdbe_structure_quality_report_issue_types: { group_id: db_1.Column.Schema.int, issue_type: db_1.Column.Schema.str } }; function fromJson(model, data) { const info = wrapper_1.PropertyWrapper.createInfo(); const issueMap = createIssueMapFromJson(model, data); return { info, data: issueMap }; } StructureQualityReport.fromJson = fromJson; async function fromServer(ctx, model, props) { const url = assets_1.Asset.getUrlAsset(ctx.assetManager, getEntryUrl(model.entryId, props.serverUrl)); const json = await ctx.assetManager.resolve(url, 'json').runInContext(ctx.runtime); const data = json.data[model.entryId.toLowerCase()]; if (!data) throw new Error('missing data'); return { value: fromJson(model, data), assets: [json] }; } StructureQualityReport.fromServer = fromServer; function fromCif(ctx, model, props) { const info = wrapper_1.PropertyWrapper.tryGetInfoFromCif('pdbe_structure_quality_report', model); if (!info) return; const data = getCifData(model); const issueMap = createIssueMapFromCif(model, data.residues, data.groups); return { info, data: issueMap }; } StructureQualityReport.fromCif = fromCif; async function fromCifOrServer(ctx, model, props) { const cif = fromCif(ctx, model, props); return cif ? { value: cif } : fromServer(ctx, model, props); } StructureQualityReport.fromCifOrServer = fromCifOrServer; const _emptyArray = []; function getIssues(e) { if (!structure_1.Unit.isAtomic(e.unit)) return _emptyArray; const prop = exports.StructureQualityReportProvider.get(e.unit.model).value; if (!prop || !prop.data) return _emptyArray; const rI = e.unit.residueIndex[e.element]; return prop.data.issues.has(rI) ? prop.data.issues.get(rI) : _emptyArray; } StructureQualityReport.getIssues = getIssues; function getIssueTypes(structure) { if (!structure) return _emptyArray; const prop = exports.StructureQualityReportProvider.get(structure.models[0]).value; if (!prop || !prop.data) return _emptyArray; return prop.data.issueTypes; } StructureQualityReport.getIssueTypes = getIssueTypes; function getCifData(model) { if (!mmcif_1.MmcifFormat.is(model.sourceData)) throw new Error('Data format must be mmCIF.'); return { residues: (0, schema_1.toTable)(StructureQualityReport.Schema.pdbe_structure_quality_report_issues, model.sourceData.data.frame.categories.pdbe_structure_quality_report_issues), groups: (0, schema_1.toTable)(StructureQualityReport.Schema.pdbe_structure_quality_report_issue_types, model.sourceData.data.frame.categories.pdbe_structure_quality_report_issue_types), }; } })(StructureQualityReport || (exports.StructureQualityReport = StructureQualityReport = {})); exports.StructureQualityReportParams = { serverUrl: param_definition_1.ParamDefinition.Text(StructureQualityReport.DefaultServerUrl, { description: 'JSON API Server URL' }) }; exports.StructureQualityReportProvider = custom_model_property_1.CustomModelProperty.createProvider({ label: 'Structure Quality Report', descriptor: (0, custom_property_1.CustomPropertyDescriptor)({ name: 'pdbe_structure_quality_report', cifExport: { prefix: 'pdbe', context(ctx) { return createExportContext(ctx); }, categories: [ wrapper_1.PropertyWrapper.defaultInfoCategory('pdbe_structure_quality_report', ctx => ctx.info), { name: 'pdbe_structure_quality_report_issues', instance(ctx) { return { fields: _structure_quality_report_issues_fields, source: ctx.models.map(data => ({ data, rowCount: data.elements.length })) }; } }, { name: 'pdbe_structure_quality_report_issue_types', instance(ctx) { return cif_1.CifWriter.Category.ofTable(ctx.issueTypes); } } ] }, symbols: { issueCount: compiler_1.QuerySymbolRuntime.Dynamic((0, symbol_1.CustomPropSymbol)('pdbe', 'structure-quality.issue-count', type_1.Type.Num), ctx => StructureQualityReport.getIssues(ctx.element).length), // TODO: add (hasIssue :: IssueType(extends string) -> boolean) symbol } }), type: 'static', defaultParams: exports.StructureQualityReportParams, getParams: (data) => exports.StructureQualityReportParams, isApplicable: (data) => StructureQualityReport.isApplicable(data), obtain: async (ctx, data, props) => { const p = { ...param_definition_1.ParamDefinition.getDefaultValues(exports.StructureQualityReportParams), ...props }; return await StructureQualityReport.fromCifOrServer(ctx, data, p); } }); const _structure_quality_report_issues_fields = cif_1.CifWriter.fields() .index('id') .many((0, atom_site_1.residueIdFields)((i, d) => d.elements[i], { includeModelNum: true })) .int('issue_type_group_id', (i, d) => d.groupId[i]) .getFields(); function createExportContext(ctx) { const groupMap = new Map(); const models = []; const group_id = [], issue_type = []; let info = wrapper_1.PropertyWrapper.createInfo(); for (const s of ctx.structures) { const prop = exports.StructureQualityReportProvider.get(s.model).value; if (prop) info = prop.info; if (!prop || !prop.data) continue; const { elements, property } = prop.data.issues.getElements(s); if (elements.length === 0) continue; const elementGroupId = []; for (let i = 0; i < elements.length; i++) { const issues = property(i); const key = issues.join(','); if (!groupMap.has(key)) { const idx = groupMap.size + 1; groupMap.set(key, idx); for (const issue of issues) { group_id.push(idx); issue_type.push(issue); } } elementGroupId[i] = groupMap.get(key); } models.push({ elements, groupId: elementGroupId }); } return { info, models, issueTypes: db_1.Table.ofArrays(StructureQualityReport.Schema.pdbe_structure_quality_report_issue_types, { group_id, issue_type }) }; } function createIssueMapFromJson(modelData, data) { const ret = new Map(); if (!data.molecules) return; const issueTypes = []; for (const entity of data.molecules) { const entity_id = entity.entity_id.toString(); for (const chain of entity.chains) { const asym_id = chain.struct_asym_id.toString(); for (const model of chain.models) { const model_id = model.model_id.toString(); if (+model_id !== modelData.modelNum) continue; for (const residue of model.residues) { const auth_seq_id = residue.author_residue_number, ins_code = residue.author_insertion_code || ''; const idx = modelData.atomicHierarchy.index.findResidue(entity_id, asym_id, auth_seq_id, ins_code); ret.set(idx, residue.outlier_types); for (const t of residue.outlier_types) { (0, array_1.arraySetAdd)(issueTypes, t); } } } } } return { issues: structure_1.IndexedCustomProperty.fromResidueMap(ret), issueTypes }; } function createIssueMapFromCif(modelData, residueData, groupData) { const ret = new Map(); const { label_entity_id, label_asym_id, auth_seq_id, pdbx_PDB_ins_code, issue_type_group_id, pdbx_PDB_model_num, _rowCount } = residueData; const groups = parseIssueTypes(groupData); for (let i = 0; i < _rowCount; i++) { if (pdbx_PDB_model_num.value(i) !== modelData.modelNum) continue; const idx = modelData.atomicHierarchy.index.findResidue(label_entity_id.value(i), label_asym_id.value(i), auth_seq_id.value(i), pdbx_PDB_ins_code.value(i)); ret.set(idx, groups.get(issue_type_group_id.value(i))); } const issueTypes = []; groups.forEach(issues => { for (const t of issues) { (0, array_1.arraySetAdd)(issueTypes, t); } }); return { issues: structure_1.IndexedCustomProperty.fromResidueMap(ret), issueTypes }; } function parseIssueTypes(groupData) { const ret = new Map(); const { group_id, issue_type } = groupData; for (let i = 0; i < groupData._rowCount; i++) { let group; const id = group_id.value(i); if (ret.has(id)) group = ret.get(id); else { group = []; ret.set(id, group); } group.push(issue_type.value(i)); } return ret; }