remove rcsb-molstar-internal pLDDT coloring

src/viewer/helpers/plddt-confidence/behavior.ts

@@ -1,70 +0,0 @@
-/**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Mandar Deshpande <mandar@ebi.ac.uk>
- */
-
-import { OrderedSet } from 'molstar/lib/mol-data/int';
-import { PLDDTConfidence, PLDDTConfidenceProvider } from './prop';
-import { PLDDTConfidenceColorThemeProvider } from './color';
-import { Loci } from 'molstar/lib/mol-model/loci';
-import { StructureElement } from 'molstar/lib/mol-model/structure';
-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
-import { PluginBehavior } from 'molstar/lib/mol-plugin/behavior/behavior';
-
-export const PLDDTConfidenceScore = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
-    name: 'plddt-confidence-prop',
-    category: 'custom-props',
-    display: {
-        name: 'pLDDT Confidence Score',
-        description: 'pLDDT Confidence Score.'
-    },
-    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
-        private provider = PLDDTConfidenceProvider;
-
-        private labelProvider = {
-            label: (loci: Loci): string | undefined => {
-                if (!this.params.showTooltip) return;
-
-                switch (loci.kind) {
-                    case 'element-loci':
-                        if (loci.elements.length === 0) return;
-                        const e = loci.elements[0];
-                        const u = e.unit;
-                        if (!u.model.customProperties.hasReference(PLDDTConfidenceProvider.descriptor)) return;
-
-                        const se = StructureElement.Location.create(loci.structure, u, u.elements[OrderedSet.getAt(e.indices, 0)]);
-                        const confidenceScore = PLDDTConfidence.getConfidenceScore(se);
-                        return confidenceScore ? `Confidence score: ${confidenceScore[0]} <small>( ${confidenceScore[1]} )</small>` : `No confidence score`;
-
-                    default: return;
-                }
-            }
-        };
-
-        register(): void {
-            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
-            this.ctx.managers.lociLabels.addProvider(this.labelProvider);
-
-            this.ctx.representation.structure.themes.colorThemeRegistry.add(PLDDTConfidenceColorThemeProvider);
-        }
-
-        update(p: { autoAttach: boolean, showTooltip: boolean }) {
-            const updated = this.params.autoAttach !== p.autoAttach;
-            this.params.autoAttach = p.autoAttach;
-            this.params.showTooltip = p.showTooltip;
-            this.ctx.customModelProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
-            return updated;
-        }
-
-        unregister() {
-            this.ctx.customModelProperties.unregister(PLDDTConfidenceProvider.descriptor.name);
-            this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
-            this.ctx.representation.structure.themes.colorThemeRegistry.remove(PLDDTConfidenceColorThemeProvider);
-        }
-    },
-    params: () => ({
-        autoAttach: PD.Boolean(false),
-        showTooltip: PD.Boolean(true)
-    })
-});

src/viewer/helpers/plddt-confidence/color.ts

@@ -1,95 +0,0 @@
-/**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Mandar Deshpande <mandar@ebi.ac.uk>
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- */
-
-import { PLDDTConfidence, PLDDTConfidenceProvider } from './prop';
-import { Location } from 'molstar/lib/mol-model/location';
-import { StructureElement } from 'molstar/lib/mol-model/structure';
-import { ColorTheme, LocationColor } from 'molstar/lib/mol-theme/color';
-import { ThemeDataContext } from 'molstar/lib/mol-theme/theme';
-import { Color } from 'molstar/lib/mol-util/color';
-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
-import { CustomProperty } from 'molstar/lib/mol-model-props/common/custom-property';
-import { TableLegend } from 'molstar/lib/mol-util/legend';
-
-const DefaultColor = Color(0xaaaaaa);
-const ConfidenceColors: { [k: string]: Color } = {
-    'No Score': DefaultColor,
-    'Very low': Color(0xff7d45),
-    'Low': Color(0xffdb13),
-    'Confident': Color(0x65cbf3),
-    'Very high': Color(0x0053d6)
-};
-
-const ConfidenceColorLegend = TableLegend(Object.entries(ConfidenceColors));
-
-export function getPLDDTConfidenceColorThemeParams(ctx: ThemeDataContext) {
-    const categories = PLDDTConfidence.getCategories(ctx.structure);
-    if (categories.length === 0) {
-        return {
-            type: PD.MappedStatic('score', {
-                'score': PD.Group({})
-            })
-        };
-    }
-
-    return {
-        type: PD.MappedStatic('score', {
-            'score': PD.Group({}),
-            'category': PD.Group({
-                kind: PD.Select(categories[0], PD.arrayToOptions(categories))
-            }, { isFlat: true })
-        })
-    };
-}
-export type PLDDTConfidenceColorThemeParams = ReturnType<typeof getPLDDTConfidenceColorThemeParams>
-
-export function PLDDTConfidenceColorTheme(ctx: ThemeDataContext, props: PD.Values<PLDDTConfidenceColorThemeParams>): ColorTheme<PLDDTConfidenceColorThemeParams> {
-    let color: LocationColor = () => DefaultColor;
-
-    if (ctx.structure && ctx.structure.models.length > 0 && ctx.structure.models[0].customProperties.has(PLDDTConfidenceProvider.descriptor)) {
-        const getColor = (location: StructureElement.Location): Color => {
-            const score: string = PLDDTConfidence.getConfidenceScore(location)[1];
-
-            if (props.type.name !== 'score') {
-                const categoryProp = props.type.params.kind;
-                if (score === categoryProp) return ConfidenceColors[score];
-            }
-
-            return ConfidenceColors[score];
-        };
-
-        color = (location: Location) => {
-            if (StructureElement.Location.is(location)) {
-                return getColor(location);
-            }
-            return DefaultColor;
-        };
-    }
-
-    return {
-        factory: PLDDTConfidenceColorTheme,
-        granularity: 'group',
-        color,
-        props,
-        description: 'Assigns residue colors according to the pLDDT Confidence score.',
-        legend: ConfidenceColorLegend
-    };
-}
-
-export const PLDDTConfidenceColorThemeProvider: ColorTheme.Provider<PLDDTConfidenceColorThemeParams, 'plddt-confidence'> = {
-    name: 'plddt-confidence',
-    label: 'pLDDT Confidence',
-    category: ColorTheme.Category.Validation,
-    factory: PLDDTConfidenceColorTheme,
-    getParams: getPLDDTConfidenceColorThemeParams,
-    defaultValues: PD.getDefaultValues(getPLDDTConfidenceColorThemeParams({})),
-    isApplicable: (ctx: ThemeDataContext) => PLDDTConfidence.isApplicable(ctx.structure?.models[0]),
-    ensureCustomProperties: {
-        attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? PLDDTConfidenceProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && PLDDTConfidenceProvider.ref(data.structure.models[0], false)
-    }
-};

src/viewer/helpers/plddt-confidence/prop.ts

@@ -1,154 +0,0 @@
-/**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Mandar Deshpande <mandar@ebi.ac.uk>
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- */
-
-import { Column, Table } from 'molstar/lib/mol-data/db';
-import { toTable } from 'molstar/lib/mol-io/reader/cif/schema';
-import { IndexedCustomProperty, Model, ResidueIndex, Unit } from 'molstar/lib/mol-model/structure';
-import { Structure, StructureElement } from 'molstar/lib/mol-model/structure/structure';
-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
-import { MmcifFormat } from 'molstar/lib/mol-model-formats/structure/mmcif';
-import { PropertyWrapper } from 'molstar/lib/mol-model-props/common/wrapper';
-import { CustomProperty } from 'molstar/lib/mol-model-props/common/custom-property';
-import { CustomModelProperty } from 'molstar/lib/mol-model-props/common/custom-model-property';
-import { CustomPropertyDescriptor } from 'molstar/lib/mol-model/custom-property';
-import { arraySetAdd } from 'molstar/lib/mol-util/array';
-import { dateToUtcString } from 'molstar/lib/mol-util/date';
-
-export type PLDDTConfidence = PropertyWrapper<{
-    score: IndexedCustomProperty.Residue<[number, string]>,
-    category: string[]
-}>
-
-export namespace PLDDTConfidence {
-    const AlphaFoldNamespace = 'AF-';
-    const BakerNamespace = 'MA-BAK-';
-
-    export function isApplicable(model?: Model): boolean {
-        if (!model || !MmcifFormat.is(model.sourceData)) return false;
-        const entryId = model.entryId.toUpperCase();
-        if (!entryId.startsWith(AlphaFoldNamespace) && !entryId.startsWith(BakerNamespace)) return false;
-        return model.sourceData.data.frame.categoryNames.includes('ma_qa_metric_local');
-    }
-
-    export interface Info {
-        timestamp_utc: string
-    }
-
-    export const Schema = {
-        local_metric_values: {
-            label_asym_id: Column.Schema.str,
-            label_comp_id: Column.Schema.str,
-            label_seq_id: Column.Schema.int,
-            metric_id: Column.Schema.int,
-            metric_value: Column.Schema.float,
-            model_id: Column.Schema.int,
-            ordinal_id: Column.Schema.int
-        }
-    };
-    export type Schema = typeof Schema;
-
-    function tryGetInfoFromCif(categoryName: string, model: Model): undefined | Info {
-        if (!MmcifFormat.is(model.sourceData) || !model.sourceData.data.frame.categoryNames.includes(categoryName)) {
-            return;
-        }
-
-        const timestampField = model.sourceData.data.frame.categories[categoryName].getField('metric_value');
-        if (!timestampField || timestampField.rowCount === 0) return;
-
-        return { timestamp_utc: timestampField.str(0) || dateToUtcString(new Date()) };
-    }
-
-
-    export function fromCif(ctx: CustomProperty.Context, model: Model): PLDDTConfidence | undefined {
-        const info = tryGetInfoFromCif('ma_qa_metric_local', model);
-        if (!info) return;
-        const data = getCifData(model);
-        const metricMap = createScoreMapFromCif(model, data.residues);
-        return { info, data: metricMap };
-    }
-
-    export async function obtain(ctx: CustomProperty.Context, model: Model, _props: PLDDTConfidenceProps): Promise<CustomProperty.Data<any>> {
-        const cif = fromCif(ctx, model);
-        return { value: cif };
-    }
-
-    export function getConfidenceScore(e: StructureElement.Location): [number, string] {
-        if (!Unit.isAtomic(e.unit)) return [-1, 'No Score'];
-        const prop = PLDDTConfidenceProvider.get(e.unit.model).value;
-        if (!prop || !prop.data) return [-1, 'No Score'];
-        const rI = e.unit.residueIndex[e.element];
-        return prop.data.score.has(rI) ? prop.data.score.get(rI)! : [-1, 'No Score'];
-    }
-
-    const _emptyArray: string[] = [];
-    export function getCategories(structure?: Structure) {
-        if (!structure) return _emptyArray;
-        const prop = PLDDTConfidenceProvider.get(structure.models[0]).value;
-        if (!prop || !prop.data) return _emptyArray;
-        return prop.data.category;
-    }
-
-    function getCifData(model: Model) {
-        if (!MmcifFormat.is(model.sourceData)) throw new Error('Data format must be mmCIF.');
-        return {
-            residues: toTable(Schema.local_metric_values, model.sourceData.data.frame.categories.ma_qa_metric_local),
-        };
-    }
-}
-
-export const PLDDTConfidenceParams = {};
-export type PLDDTConfidenceParams = typeof PLDDTConfidenceParams
-export type PLDDTConfidenceProps = PD.Values<PLDDTConfidenceParams>
-
-export const PLDDTConfidenceProvider: CustomModelProperty.Provider<PLDDTConfidenceParams, PLDDTConfidence> = CustomModelProperty.createProvider({
-    label: 'pLDDT Confidence Score',
-    descriptor: CustomPropertyDescriptor({
-        name: 'plddt_confidence_score'
-    }),
-    type: 'static',
-    defaultParams: PLDDTConfidenceParams,
-    getParams: () => PLDDTConfidenceParams,
-    isApplicable: (data: Model) => PLDDTConfidence.isApplicable(data),
-    obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<PLDDTConfidenceProps>) => {
-        const p = { ...PD.getDefaultValues(PLDDTConfidenceParams), ...props };
-        return await PLDDTConfidence.obtain(ctx, data, p);
-    }
-});
-
-function createScoreMapFromCif(modelData: Model, residueData: Table<typeof PLDDTConfidence.Schema.local_metric_values>): PLDDTConfidence['data'] {
-    const { label_asym_id, label_seq_id, metric_value, _rowCount } = residueData;
-
-    const ret = new Map<ResidueIndex, [number, string]>();
-    const categories: string[] = [];
-
-    const toCategory = (v: number): 'Very low' | 'Low' | 'Confident' | 'Very high' => {
-        if (v > 50 && v <= 70) return 'Low';
-        if (v > 70 && v <= 90) return 'Confident';
-        if (v > 90) return 'Very high';
-        return 'Very low';
-    };
-
-    const entityMap = new Map<string, string>();
-    for (let i = 0; i < _rowCount; i++) {
-        const confidenceScore = metric_value.value(i);
-        const labelAsymId = label_asym_id.value(i);
-        if (!entityMap.has(labelAsymId)) entityMap.set(labelAsymId, (modelData.atomicHierarchy.index.findEntity(labelAsymId) + 1).toString());
-        const entityId = entityMap.get(labelAsymId)!;
-        const idx = modelData.atomicHierarchy.index.findResidue(entityId, labelAsymId, label_seq_id.value(i));
-        const confidenceCategory = toCategory(confidenceScore);
-
-        ret.set(idx, [confidenceScore, confidenceCategory]);
-        arraySetAdd(categories, confidenceCategory);
-    }
-
-    return {
-        score: IndexedCustomProperty.fromResidueMap(ret),
-        category: categories
-    };
-}

src/viewer/index.html

@@ -607,12 +607,12 @@
                 {
                     id: 'AF-Q8W3K0-F1',
                     url: 'https://alphafold.ebi.ac.uk/files/AF-Q8W3K0-F1-model_v2.cif',
-                    info: 'confidence coloring: Probable disease resistance protein At1g58602'
+                    info: 'pLDDT coloring: Probable disease resistance protein At1g58602'
                 },
                 {
                     id: 'ma-bak-cepc-0003',
                     url: 'https://www.modelarchive.org/doi/10.5452/ma-bak-cepc-0003.cif',
-                    info: 'confidence coloring: Predicted interaction between Ribosome biogenesis protein ERB1 (Eukaryotic ribosome biogenesis protein 1) and Ribosome biogenesis protein BRX1'
+                    info: 'pLDDT coloring: Predicted interaction between Ribosome biogenesis protein ERB1 (Eukaryotic ribosome biogenesis protein 1) and Ribosome biogenesis protein BRX1'
                 }
             ];
 

src/viewer/ui/validation.tsx

@@ -11,8 +11,9 @@ import { ValidationReportGeometryQualityPreset } from 'molstar/lib/extensions/rc
 import { ActionMenu } from 'molstar/lib/mol-plugin-ui/controls/action-menu';
 import { Model } from 'molstar/lib/mol-model/structure/model';
 import { MmcifFormat } from 'molstar/lib/mol-model-formats/structure/mmcif';
-import { PLDDTConfidence } from '../helpers/plddt-confidence/prop';
-import { PLDDTConfidenceColorThemeProvider } from '../helpers/plddt-confidence/color';
+import { QualityAssessment } from 'molstar/lib/extensions/model-archive/quality-assessment/prop';
+import { PLDDTConfidenceColorThemeProvider } from 'molstar/lib/extensions/model-archive/quality-assessment/color/plddt';
+import { QmeanScoreColorThemeProvider } from 'molstar/lib/extensions/model-archive/quality-assessment/color/qmean';
 
 interface ValidationReportState extends CollapsableState {
     errorStates: Set<string>
@@ -66,7 +67,7 @@ export class ValidationReportControls extends CollapsableControls<{}, Validation
         if (!pivot.obj || pivot.obj.data.models.length !== 1) return false;
         const model = pivot.obj.data.models[0];
         // all supported options must be registered here
-        return ValidationReport.isApplicable(model) || PLDDTConfidence.isApplicable(model);
+        return ValidationReport.isApplicable(model) || QualityAssessment.isApplicable(model, 'pLDDT') || QualityAssessment.isApplicable(model, 'qmean');
     }
 
     get noValidationReport() {
@@ -80,7 +81,14 @@ export class ValidationReportControls extends CollapsableControls<{}, Validation
         const structure = this.pivot.cell.obj?.data;
         if (!structure || structure.models.length !== 1) return false;
         const model = structure.models[0];
-        return PLDDTConfidence.isApplicable(model);
+        return QualityAssessment.isApplicable(model, 'pLDDT');
+    }
+
+    get qmeanData() {
+        const structure = this.pivot.cell.obj?.data;
+        if (!structure || structure.models.length !== 1) return false;
+        const model = structure.models[0];
+        return QualityAssessment.isApplicable(model, 'qmean');
     }
 
     isFromPdbArchive(model: Model) {
@@ -106,6 +114,10 @@ export class ValidationReportControls extends CollapsableControls<{}, Validation
         await this.plugin.managers.structure.component.updateRepresentationsTheme(this.pivot.components, { color: PLDDTConfidenceColorThemeProvider.name as any });
     };
 
+    requestQmeanConfidenceColoring = async () => {
+        await this.plugin.managers.structure.component.updateRepresentationsTheme(this.pivot.components, { color: QmeanScoreColorThemeProvider.name as any });
+    };
+
     get actions(): ActionMenu.Items {
         const noValidationReport = this.noValidationReport;
         const validationReportError = this.state.errorStates.has(ValidationReportTag);
@@ -125,6 +137,13 @@ export class ValidationReportControls extends CollapsableControls<{}, Validation
                 value: this.requestPLDDTConfidenceColoring
             });
         }
+        if (this.qmeanData) {
+            out.push({
+                kind: 'item',
+                label: 'QMEAN Confidence Scores',
+                value: this.requestQmeanConfidenceColoring
+            });
+        }
 
         return out;
     }