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molstar

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A comprehensive macromolecular library.

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/** * 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> * @author Alexander Rose <alexander.rose@weirdbyte.de> */ import { __awaiter, __generator } from "tslib"; import { QualityAssessment, QualityAssessmentProvider } from '../prop'; import { Bond, StructureElement, Unit } from '../../../../mol-model/structure'; import { Color } from '../../../../mol-util/color'; import { ParamDefinition as PD } from '../../../../mol-util/param-definition'; import { TableLegend } from '../../../../mol-util/legend'; var DefaultColor = Color(0xaaaaaa); var ConfidenceColors = { 'No Score': DefaultColor, 'Very Low': Color(0xff7d45), 'Low': Color(0xffdb13), 'Confident': Color(0x65cbf3), 'Very High': Color(0x0053d6) }; var ConfidenceColorLegend = TableLegend(Object.entries(ConfidenceColors)); export function getPLDDTConfidenceColorThemeParams(ctx) { return {}; } export function PLDDTConfidenceColorTheme(ctx, props) { var color = function () { return DefaultColor; }; if (ctx.structure) { var l_1 = StructureElement.Location.create(ctx.structure.root); var getColor_1 = function (location) { var _a, _b; var unit = location.unit, element = location.element; if (!Unit.isAtomic(unit)) return DefaultColor; var qualityAssessment = QualityAssessmentProvider.get(unit.model).value; var score = (_b = (_a = qualityAssessment === null || qualityAssessment === void 0 ? void 0 : qualityAssessment.pLDDT) === null || _a === void 0 ? void 0 : _a.get(unit.model.atomicHierarchy.residueAtomSegments.index[element])) !== null && _b !== void 0 ? _b : -1; if (score < 0) { return DefaultColor; } else if (score <= 50) { return Color(0xff7d45); } else if (score <= 70) { return Color(0xffdb13); } else if (score <= 90) { return Color(0x65cbf3); } else { return Color(0x0053d6); } }; color = function (location) { if (StructureElement.Location.is(location)) { return getColor_1(location); } else if (Bond.isLocation(location)) { l_1.unit = location.aUnit; l_1.element = location.aUnit.elements[location.aIndex]; return getColor_1(l_1); } return DefaultColor; }; } return { factory: PLDDTConfidenceColorTheme, granularity: 'group', preferSmoothing: true, color: color, props: props, description: 'Assigns residue colors according to the pLDDT Confidence score.', legend: ConfidenceColorLegend }; } export var PLDDTConfidenceColorThemeProvider = { name: 'plddt-confidence', label: 'pLDDT Confidence', category: "Validation" /* ColorTheme.Category.Validation */, factory: PLDDTConfidenceColorTheme, getParams: getPLDDTConfidenceColorThemeParams, defaultValues: PD.getDefaultValues(getPLDDTConfidenceColorThemeParams({})), isApplicable: function (ctx) { var _a; return !!((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models.some(function (m) { return QualityAssessment.isApplicable(m, 'pLDDT'); })); }, ensureCustomProperties: { attach: function (ctx, data) { return __awaiter(void 0, void 0, void 0, function () { var _i, _a, m; return __generator(this, function (_b) { switch (_b.label) { case 0: if (!data.structure) return [3 /*break*/, 4]; _i = 0, _a = data.structure.models; _b.label = 1; case 1: if (!(_i < _a.length)) return [3 /*break*/, 4]; m = _a[_i]; return [4 /*yield*/, QualityAssessmentProvider.attach(ctx, m, void 0, true)]; case 2: _b.sent(); _b.label = 3; case 3: _i++; return [3 /*break*/, 1]; case 4: return [2 /*return*/]; } }); }); }, detach: function (data) { return __awaiter(void 0, void 0, void 0, function () { var _i, _a, m; return __generator(this, function (_b) { if (data.structure) { for (_i = 0, _a = data.structure.models; _i < _a.length; _i++) { m = _a[_i]; QualityAssessmentProvider.ref(m, false); } } return [2 /*return*/]; }); }); } } };