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@@ -0,0 +1,116 @@
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+/**
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+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
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+ *
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+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
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+ */
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+
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+import { CollapsableControls, CollapsableState } from 'molstar/lib/mol-plugin-ui/base';
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+import { StructureHierarchyManager } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy';
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+import { ValidationReport } from 'molstar/lib/extensions/rcsb/validation-report/prop';
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+import { ValidationReportGeometryQualityPreset } from 'molstar/lib/extensions/rcsb/validation-report/behavior';
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+import { ActionMenu } from 'molstar/lib/mol-plugin-ui/controls/action-menu';
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+import { Model } from 'molstar/lib/mol-model/structure/model';
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+import { MmcifFormat } from 'molstar/lib/mol-model-formats/structure/mmcif';
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+
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+interface ValidationReportState extends CollapsableState {
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+ errorStates: Set<string>
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+}
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+
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+const ValidationReportTag = 'validation-report';
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+
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+const _QualityIcon = <svg width='50px' height='50px' viewBox='0 0 38 47'>
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+ <g strokeWidth='4' fill='none'>
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+ <path d='m19 4.8c-3.7 3.6-9 5.8-15 5.8v4.3c0 25 14 29 14 29s16-4.5 16-29v-4.3c-6 0-11-2.3-15-5.8z' stroke='#000' strokeLinecap='square' strokeMiterlimit='10'/>
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+ <path d='m13 23 3.5 3.5 9.4-9.4' stroke='#000'/>
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+ </g>
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+</svg>;
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+export function QualityIconSvg() { return _QualityIcon; }
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+
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+/**
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+ * A high-level component that gives access to the validation report preset.
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+ */
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+export class ValidationReportControls extends CollapsableControls<{}, ValidationReportState> {
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+ protected defaultState() {
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+ return {
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+ header: 'Quality Assessment',
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+ isCollapsed: false,
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+ isHidden: true,
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+ errorStates: new Set<string>(),
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+ brand: { accent: 'cyan' as const, svg: QualityIconSvg }
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+ };
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+ }
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+
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+ componentDidMount() {
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+ this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, () => {
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+ const { errorStates, description } = this.state;
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+ const nextDescription = StructureHierarchyManager.getSelectedStructuresDescription(this.plugin);
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+ this.setState({
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+ isHidden: !this.canEnable(),
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+ // if structure is unchanged then keep old error states
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+ errorStates: nextDescription === description ? errorStates : new Set<string>(),
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+ description: nextDescription
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+ });
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+ });
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+ }
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+
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+ get pivot() {
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+ return this.plugin.managers.structure.hierarchy.selection.structures[0];
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+ }
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+
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+ canEnable() {
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+ const { selection } = this.plugin.managers.structure.hierarchy;
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+ if (selection.structures.length !== 1) return false;
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+ const pivot = this.pivot.cell;
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+ if (!pivot.obj) return false;
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+ return pivot.obj.data.models.length === 1 && ValidationReport.isApplicable(pivot.obj.data.models[0]);
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+ }
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+
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+ get noValidationReport() {
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+ const structure = this.pivot.cell.obj?.data;
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+ if (!structure || structure.models.length !== 1) return true;
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+ const model = structure.models[0];
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+ return !model || !this.isFromPdbArchive(model);
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+ }
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+
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+ isFromPdbArchive(model: Model) {
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+ if (!MmcifFormat.is(model.sourceData)) return false;
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+ return model.entryId.match(/^[1-9][a-z0-9]{3}$/i) !== null ||
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+ model.entryId.match(/^pdb_[0-9]{4}[1-9][a-z0-9]{3}$/i) !== null;
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+ }
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+
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+ requestValidationReportPreset = async () => {
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+ try {
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+ await ValidationReportGeometryQualityPreset.apply(this.pivot.cell, Object.create(null), this.plugin);
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+ } catch (err) {
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+ // happens e.g. for 2W4S
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+ this.setState(({ errorStates }) => {
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+ const errors = new Set(errorStates);
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+ errors.add(ValidationReportTag);
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+ return { errorStates: errors };
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+ });
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+ }
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+ }
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+
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+ get actions(): ActionMenu.Items {
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+ // TODO this could support other kinds of reports/validation like the AlphaFold confidence scores
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+ const noValidationReport = this.noValidationReport;
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+ const validationReportError = this.state.errorStates.has(ValidationReportTag);
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+ return [
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+ {
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+ kind: 'item',
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+ label: validationReportError ? 'Failed to Obtain Validation Report' : (noValidationReport ? 'No Validation Report Available' : 'RCSB PDB Validation Report'),
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+ value: this.requestValidationReportPreset,
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+ disabled: noValidationReport || validationReportError
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+ },
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+ ];
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+ }
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+
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+ selectAction: ActionMenu.OnSelect = item => {
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+ if (!item) return;
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+ (item?.value as any)();
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+ }
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+
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+ renderControls() {
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+ return <ActionMenu items={this.actions} onSelect={this.selectAction} />;
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+ }
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+}
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Sebastian Bittrich