molstar
Version:
A comprehensive macromolecular library.
113 lines (112 loc) • 5.15 kB
JavaScript
;
/**
* Copyright (c) 2021-2025 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>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.PLDDTConfidenceColorThemeProvider = void 0;
exports.getPLDDTConfidenceColorThemeParams = getPLDDTConfidenceColorThemeParams;
exports.PLDDTConfidenceColorTheme = PLDDTConfidenceColorTheme;
const prop_1 = require("../prop");
const structure_1 = require("../../../../mol-model/structure");
const color_1 = require("../../../../mol-util/color");
const param_definition_1 = require("../../../../mol-util/param-definition");
const legend_1 = require("../../../../mol-util/legend");
const categories_1 = require("../../../../mol-theme/color/categories");
const DefaultColor = (0, color_1.Color)(0xaaaaaa);
const ConfidenceColors = {
'No Score': DefaultColor,
'Very Low': (0, color_1.Color)(0xff7d45),
'Low': (0, color_1.Color)(0xffdb13),
'Confident': (0, color_1.Color)(0x65cbf3),
'Very High': (0, color_1.Color)(0x0053d6)
};
const ConfidenceColorLegend = (0, legend_1.TableLegend)(Object.entries(ConfidenceColors));
function getPLDDTConfidenceColorThemeParams(ctx) {
var _a;
return {
metricId: prop_1.QualityAssessment.getLocalOptions((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models[0], 'pLDDT'),
};
}
function PLDDTConfidenceColorTheme(ctx, props) {
let color = () => DefaultColor;
if (ctx.structure) {
const l = structure_1.StructureElement.Location.create(ctx.structure.root);
const getColor = (location) => {
var _a, _b;
const { unit, element } = location;
if (!structure_1.Unit.isAtomic(unit))
return DefaultColor;
const qualityAssessment = prop_1.QualityAssessmentProvider.get(unit.model).value;
const metric = (_b = (_a = qualityAssessment === null || qualityAssessment === void 0 ? void 0 : qualityAssessment.localMap.get(props.metricId)) === null || _a === void 0 ? void 0 : _a.values) !== null && _b !== void 0 ? _b : qualityAssessment === null || qualityAssessment === void 0 ? void 0 : qualityAssessment.pLDDT;
let score = metric === null || metric === void 0 ? void 0 : metric.get(unit.model.atomicHierarchy.residueAtomSegments.index[element]);
if (typeof score !== 'number') {
score = unit.model.atomicConformation.B_iso_or_equiv.value(element);
}
if (score < 0) {
return DefaultColor;
}
else if (score <= 50) {
return (0, color_1.Color)(0xff7d45);
}
else if (score <= 70) {
return (0, color_1.Color)(0xffdb13);
}
else if (score <= 90) {
return (0, color_1.Color)(0x65cbf3);
}
else {
return (0, color_1.Color)(0x0053d6);
}
};
color = (location) => {
if (structure_1.StructureElement.Location.is(location)) {
return getColor(location);
}
else if (structure_1.Bond.isLocation(location)) {
l.unit = location.aUnit;
l.element = location.aUnit.elements[location.aIndex];
return getColor(l);
}
return DefaultColor;
};
}
return {
factory: PLDDTConfidenceColorTheme,
granularity: 'group',
preferSmoothing: true,
color,
props,
description: 'Assigns residue colors according to the pLDDT Confidence score. If no Model Archive quality assessment score is available, the B-factor value is used instead.',
legend: ConfidenceColorLegend
};
}
exports.PLDDTConfidenceColorThemeProvider = {
name: 'plddt-confidence',
label: 'pLDDT Confidence',
category: categories_1.ColorThemeCategory.Validation,
factory: PLDDTConfidenceColorTheme,
getParams: getPLDDTConfidenceColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(getPLDDTConfidenceColorThemeParams({})),
isApplicable: (ctx) => { var _a; return !!((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models.some(m => prop_1.QualityAssessment.isApplicable(m, 'pLDDT') || (m.atomicConformation.B_iso_or_equiv.isDefined && !structure_1.Model.isExperimental(m)))); },
ensureCustomProperties: {
attach: async (ctx, data) => {
if (data.structure) {
for (const m of data.structure.models) {
await prop_1.QualityAssessmentProvider.attach(ctx, m, void 0, true);
}
}
},
detach: async (data) => {
if (data.structure) {
for (const m of data.structure.models) {
prop_1.QualityAssessmentProvider.ref(m, false);
}
}
}
}
};