/** * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author David Sehnal <david.sehnal@gmail.com> */ import { OrderedSet } from 'mol-data/int'; import { StructureQualityReport } from 'mol-model-props/pdbe/structure-quality-report'; import { StructureQualityReportColorTheme } from 'mol-model-props/pdbe/themes/structure-quality-report'; import { Loci } from 'mol-model/loci'; import { StructureElement } from 'mol-model/structure'; import { CustomPropertyRegistry } from 'mol-plugin/util/custom-prop-registry'; import { ParamDefinition as PD } from 'mol-util/param-definition'; import { PluginBehavior } from '../behavior'; export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: boolean }>({ name: 'pdbe-structure-quality-report-prop', display: { name: 'PDBe Structure Quality Report', group: 'Custom Props' }, ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> { private attach = StructureQualityReport.createAttachTask( m => `https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${m.label.toLowerCase()}`, this.ctx.fetch ); private provider: CustomPropertyRegistry.Provider = { option: [StructureQualityReport.Descriptor.name, 'PDBe Structure Quality Report'], descriptor: StructureQualityReport.Descriptor, defaultSelected: this.params.autoAttach, attachableTo: () => true, attach: this.attach } register(): void { this.ctx.customModelProperties.register(this.provider); this.ctx.lociLabels.addProvider(labelPDBeValidation); // TODO: support filtering of themes based on the input structure // in this case, it would check structure.models[0].customProperties.has(StructureQualityReport.Descriptor) this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.add('pdbe-structure-quality-report', { label: 'PDBe Structure Quality Report', factory: StructureQualityReportColorTheme, getParams: () => ({}), defaultValues: {} }) } update(p: { autoAttach: boolean }) { let updated = this.params.autoAttach !== p.autoAttach this.params.autoAttach = p.autoAttach; this.provider.defaultSelected = p.autoAttach; return updated; } unregister() { this.ctx.customModelProperties.unregister(StructureQualityReport.Descriptor.name); this.ctx.lociLabels.removeProvider(labelPDBeValidation); this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.remove('pdbe-structure-quality-report') } }, params: () => ({ autoAttach: PD.Boolean(false) }) }); function labelPDBeValidation(loci: Loci): string | undefined { switch (loci.kind) { case 'element-loci': const e = loci.elements[0]; const u = e.unit; if (!u.model.customProperties.has(StructureQualityReport.Descriptor)) return void 0; const se = StructureElement.create(u, u.elements[OrderedSet.getAt(e.indices, 0)]); const issues = StructureQualityReport.getIssues(se); if (issues.length === 0) return 'PDBe Validation: No Issues'; return `PDBe Validation: ${issues.join(', ')}`; default: return void 0; } }