molstar 3.0.0-dev.3 → 3.0.0-dev.7

package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts

@@ -0,0 +1,68 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
+import { StructureRepresentationPresetProvider } from '../../../mol-plugin-state/builder/structure/representation-preset';
+export declare const MAQualityAssessment: import("../../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
+    autoAttach: boolean;
+    showTooltip: boolean;
+}>;
+export declare const QualityAssessmentPLDDTPreset: StructureRepresentationPresetProvider<{
+    ignoreHydrogens: boolean | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    theme: PD.Normalize<{
+        globalName: any;
+        carbonColor: any;
+        symmetryColor: any;
+        focus: any;
+    }> | undefined;
+}, {
+    components?: undefined;
+    representations?: undefined;
+} | {
+    components: {
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+    };
+    representations: {
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+    };
+} | {
+    components: {
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        branched: undefined;
+    };
+    representations: {
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+    };
+}>;
+export declare const QualityAssessmentQmeanPreset: StructureRepresentationPresetProvider<{
+    ignoreHydrogens: boolean | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    theme: PD.Normalize<{
+        globalName: any;
+        carbonColor: any;
+        symmetryColor: any;
+        focus: any;
+    }> | undefined;
+}, {
+    components?: undefined;
+    representations?: undefined;
+} | {
+    components: {
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+    };
+    representations: {
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+    };
+} | {
+    components: {
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        branched: undefined;
+    };
+    representations: {
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+    };
+}>;

package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js

@@ -0,0 +1,236 @@
+"use strict";
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.QualityAssessmentQmeanPreset = exports.QualityAssessmentPLDDTPreset = exports.MAQualityAssessment = void 0;
+var tslib_1 = require("tslib");
+var param_definition_1 = require("../../../mol-util/param-definition");
+var behavior_1 = require("../../../mol-plugin/behavior/behavior");
+var compiler_1 = require("../../../mol-script/runtime/query/compiler");
+var plddt_1 = require("./color/plddt");
+var prop_1 = require("./prop");
+var structure_selection_query_1 = require("../../../mol-plugin-state/helpers/structure-selection-query");
+var builder_1 = require("../../../mol-script/language/builder");
+var int_1 = require("../../../mol-data/int");
+var util_1 = require("../../../mol-data/util");
+var qmean_1 = require("./color/qmean");
+var representation_preset_1 = require("../../../mol-plugin-state/builder/structure/representation-preset");
+var mol_state_1 = require("../../../mol-state");
+exports.MAQualityAssessment = behavior_1.PluginBehavior.create({
+    name: 'ma-quality-assessment-prop',
+    category: 'custom-props',
+    display: {
+        name: 'Quality Assessment',
+        description: 'Data included in Model Archive files.'
+    },
+    ctor: /** @class */ (function (_super) {
+        (0, tslib_1.__extends)(class_1, _super);
+        function class_1() {
+            var _this = _super !== null && _super.apply(this, arguments) || this;
+            _this.provider = prop_1.QualityAssessmentProvider;
+            _this.labelProvider = {
+                label: function (loci) {
+                    if (!_this.params.showTooltip)
+                        return;
+                    return [
+                        plddtLabel(loci),
+                        qmeanLabel(loci),
+                    ].filter(function (l) { return !!l; }).join('</br>');
+                }
+            };
+            return _this;
+        }
+        class_1.prototype.register = function () {
+            compiler_1.DefaultQueryRuntimeTable.addCustomProp(this.provider.descriptor);
+            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
+            this.ctx.managers.lociLabels.addProvider(this.labelProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(plddt_1.PLDDTConfidenceColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(qmean_1.QmeanScoreColorThemeProvider);
+            this.ctx.query.structure.registry.add(confidentPLDDT);
+            this.ctx.builders.structure.representation.registerPreset(exports.QualityAssessmentPLDDTPreset);
+            this.ctx.builders.structure.representation.registerPreset(exports.QualityAssessmentQmeanPreset);
+        };
+        class_1.prototype.update = function (p) {
+            var updated = this.params.autoAttach !== p.autoAttach;
+            this.params.autoAttach = p.autoAttach;
+            this.params.showTooltip = p.showTooltip;
+            this.ctx.customStructureProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
+            return updated;
+        };
+        class_1.prototype.unregister = function () {
+            compiler_1.DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
+            this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
+            this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(plddt_1.PLDDTConfidenceColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(qmean_1.QmeanScoreColorThemeProvider);
+            this.ctx.query.structure.registry.remove(confidentPLDDT);
+            this.ctx.builders.structure.representation.unregisterPreset(exports.QualityAssessmentPLDDTPreset);
+            this.ctx.builders.structure.representation.unregisterPreset(exports.QualityAssessmentQmeanPreset);
+        };
+        return class_1;
+    }(behavior_1.PluginBehavior.Handler)),
+    params: function () { return ({
+        autoAttach: param_definition_1.ParamDefinition.Boolean(false),
+        showTooltip: param_definition_1.ParamDefinition.Boolean(true),
+    }); }
+});
+//
+function plddtCategory(score) {
+    if (score > 50 && score <= 70)
+        return 'Low';
+    if (score > 70 && score <= 90)
+        return 'Confident';
+    if (score > 90)
+        return 'Very high';
+    return 'Very low';
+}
+function plddtLabel(loci) {
+    return metricLabel(loci, 'pLDDT', function (scoreAvg, countInfo) { return "pLDDT Score ".concat(countInfo, ": ").concat(scoreAvg.toFixed(2), " <small>(").concat(plddtCategory(scoreAvg), ")</small>"); });
+}
+function qmeanLabel(loci) {
+    return metricLabel(loci, 'qmean', function (scoreAvg, countInfo) { return "QMEAN Score ".concat(countInfo, ": ").concat(scoreAvg.toFixed(2)); });
+}
+function metricLabel(loci, name, label) {
+    var _a;
+    if (loci.kind === 'element-loci') {
+        if (loci.elements.length === 0)
+            return;
+        var seen_1 = new Set();
+        var scoreSeen_1 = new Set();
+        var scoreSum_1 = 0;
+        var _loop_1 = function (indices, unit) {
+            var metric = (_a = prop_1.QualityAssessmentProvider.get(unit.model).value) === null || _a === void 0 ? void 0 : _a[name];
+            if (!metric)
+                return "continue";
+            var residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index;
+            var elements = unit.elements;
+            int_1.OrderedSet.forEach(indices, function (idx) {
+                var _a;
+                var eI = elements[idx];
+                var rI = residueIndex[eI];
+                var residueKey = (0, util_1.cantorPairing)(rI, unit.id);
+                if (!seen_1.has(residueKey)) {
+                    var score = (_a = metric.get(residueIndex[eI])) !== null && _a !== void 0 ? _a : -1;
+                    if (score !== -1) {
+                        scoreSum_1 += score;
+                        scoreSeen_1.add(residueKey);
+                    }
+                    seen_1.add(residueKey);
+                }
+            });
+        };
+        for (var _i = 0, _b = loci.elements; _i < _b.length; _i++) {
+            var _c = _b[_i], indices = _c.indices, unit = _c.unit;
+            _loop_1(indices, unit);
+        }
+        if (seen_1.size === 0)
+            return;
+        var summary = [];
+        if (scoreSeen_1.size) {
+            var countInfo = "<small>(".concat(scoreSeen_1.size, " ").concat(scoreSeen_1.size > 1 ? 'Residues avg.' : 'Residue', ")</small>");
+            var scoreAvg = scoreSum_1 / scoreSeen_1.size;
+            summary.push(label(scoreAvg, countInfo));
+        }
+        if (summary.length) {
+            return summary.join('</br>');
+        }
+    }
+}
+//
+var confidentPLDDT = (0, structure_selection_query_1.StructureSelectionQuery)('Confident pLDDT (> 70)', builder_1.MolScriptBuilder.struct.modifier.union([
+    builder_1.MolScriptBuilder.struct.modifier.wholeResidues([
+        builder_1.MolScriptBuilder.struct.modifier.union([
+            builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
+                'residue-test': builder_1.MolScriptBuilder.core.rel.gr([prop_1.QualityAssessment.symbols.pLDDT.symbol(), 70]),
+            })
+        ])
+    ])
+]), {
+    description: 'Select residues with a pLDDT > 70 (confident).',
+    category: structure_selection_query_1.StructureSelectionCategory.Validation,
+    ensureCustomProperties: function (ctx, structure) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+        var _i, _a, m;
+        return (0, tslib_1.__generator)(this, function (_b) {
+            switch (_b.label) {
+                case 0:
+                    _i = 0, _a = structure.models;
+                    _b.label = 1;
+                case 1:
+                    if (!(_i < _a.length)) return [3 /*break*/, 4];
+                    m = _a[_i];
+                    return [4 /*yield*/, prop_1.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*/];
+            }
+        });
+    }); }
+});
+//
+exports.QualityAssessmentPLDDTPreset = (0, representation_preset_1.StructureRepresentationPresetProvider)({
+    id: 'preset-structure-representation-ma-quality-assessment-plddt',
+    display: {
+        name: 'Quality Assessment (pLDDT)', group: 'Annotation',
+        description: 'Color structure based on pLDDT Confidence.'
+    },
+    isApplicable: function (a) {
+        return !!a.data.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'pLDDT'); });
+    },
+    params: function () { return representation_preset_1.StructureRepresentationPresetProvider.CommonParams; },
+    apply: function (ref, params, plugin) {
+        var _a;
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var structureCell, structure, colorTheme;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+                        structure = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data;
+                        if (!structureCell || !structure)
+                            return [2 /*return*/, {}];
+                        colorTheme = plddt_1.PLDDTConfidenceColorThemeProvider.name;
+                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { theme: { globalName: colorTheme, focus: { name: colorTheme } } }), plugin)];
+                    case 1: return [2 /*return*/, _b.sent()];
+                }
+            });
+        });
+    }
+});
+exports.QualityAssessmentQmeanPreset = (0, representation_preset_1.StructureRepresentationPresetProvider)({
+    id: 'preset-structure-representation-ma-quality-assessment-qmean',
+    display: {
+        name: 'Quality Assessment (QMEAN)', group: 'Annotation',
+        description: 'Color structure based on QMEAN Score.'
+    },
+    isApplicable: function (a) {
+        return !!a.data.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'qmean'); });
+    },
+    params: function () { return representation_preset_1.StructureRepresentationPresetProvider.CommonParams; },
+    apply: function (ref, params, plugin) {
+        var _a;
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var structureCell, structure, colorTheme;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+                        structure = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data;
+                        if (!structureCell || !structure)
+                            return [2 /*return*/, {}];
+                        colorTheme = qmean_1.QmeanScoreColorThemeProvider.name;
+                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { theme: { globalName: colorTheme, focus: { name: colorTheme } } }), plugin)];
+                    case 1: return [2 /*return*/, _b.sent()];
+                }
+            });
+        });
+    }
+});
+//# sourceMappingURL=behavior.js.map

package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.d.ts

@@ -0,0 +1,14 @@
+/**
+ * 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 { ColorTheme } from '../../../../mol-theme/color';
+import { ThemeDataContext } from '../../../../mol-theme/theme';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+export declare function getPLDDTConfidenceColorThemeParams(ctx: ThemeDataContext): {};
+export declare type PLDDTConfidenceColorThemeParams = ReturnType<typeof getPLDDTConfidenceColorThemeParams>;
+export declare function PLDDTConfidenceColorTheme(ctx: ThemeDataContext, props: PD.Values<PLDDTConfidenceColorThemeParams>): ColorTheme<PLDDTConfidenceColorThemeParams>;
+export declare const PLDDTConfidenceColorThemeProvider: ColorTheme.Provider<PLDDTConfidenceColorThemeParams, 'plddt-confidence'>;

package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js

@@ -0,0 +1,125 @@
+"use strict";
+/**
+ * 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>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.PLDDTConfidenceColorThemeProvider = exports.PLDDTConfidenceColorTheme = exports.getPLDDTConfidenceColorThemeParams = void 0;
+var tslib_1 = require("tslib");
+var prop_1 = require("../prop");
+var structure_1 = require("../../../../mol-model/structure");
+var color_1 = require("../../../../mol-util/color");
+var param_definition_1 = require("../../../../mol-util/param-definition");
+var legend_1 = require("../../../../mol-util/legend");
+var DefaultColor = (0, color_1.Color)(0xaaaaaa);
+var 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)
+};
+var ConfidenceColorLegend = (0, legend_1.TableLegend)(Object.entries(ConfidenceColors));
+function getPLDDTConfidenceColorThemeParams(ctx) {
+    return {};
+}
+exports.getPLDDTConfidenceColorThemeParams = getPLDDTConfidenceColorThemeParams;
+function PLDDTConfidenceColorTheme(ctx, props) {
+    var color = function () { return DefaultColor; };
+    if (ctx.structure) {
+        var l_1 = structure_1.StructureElement.Location.create(ctx.structure.root);
+        var getColor_1 = function (location) {
+            var _a, _b;
+            var unit = location.unit, element = location.element;
+            if (!structure_1.Unit.isAtomic(unit))
+                return DefaultColor;
+            var qualityAssessment = prop_1.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 (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 = function (location) {
+            if (structure_1.StructureElement.Location.is(location)) {
+                return getColor_1(location);
+            }
+            else if (structure_1.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
+    };
+}
+exports.PLDDTConfidenceColorTheme = PLDDTConfidenceColorTheme;
+exports.PLDDTConfidenceColorThemeProvider = {
+    name: 'plddt-confidence',
+    label: 'pLDDT Confidence',
+    category: "Validation" /* Validation */,
+    factory: PLDDTConfidenceColorTheme,
+    getParams: getPLDDTConfidenceColorThemeParams,
+    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(getPLDDTConfidenceColorThemeParams({})),
+    isApplicable: function (ctx) { var _a; return !!((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'pLDDT'); })); },
+    ensureCustomProperties: {
+        attach: function (ctx, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+            var _i, _a, m;
+            return (0, tslib_1.__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*/, prop_1.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 (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+            var _i, _a, m;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                if (data.structure) {
+                    for (_i = 0, _a = data.structure.models; _i < _a.length; _i++) {
+                        m = _a[_i];
+                        prop_1.QualityAssessmentProvider.ref(m, false);
+                    }
+                }
+                return [2 /*return*/];
+            });
+        }); }
+    }
+};
+//# sourceMappingURL=plddt.js.map

package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.d.ts

@@ -0,0 +1,12 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { ColorTheme } from '../../../../mol-theme/color';
+import { ThemeDataContext } from '../../../../mol-theme/theme';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+export declare function getQmeanScoreColorThemeParams(ctx: ThemeDataContext): {};
+export declare type QmeanScoreColorThemeParams = ReturnType<typeof getQmeanScoreColorThemeParams>;
+export declare function QmeanScoreColorTheme(ctx: ThemeDataContext, props: PD.Values<QmeanScoreColorThemeParams>): ColorTheme<QmeanScoreColorThemeParams>;
+export declare const QmeanScoreColorThemeProvider: ColorTheme.Provider<QmeanScoreColorThemeParams, 'qmean-score'>;

package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js

@@ -0,0 +1,111 @@
+"use strict";
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.QmeanScoreColorThemeProvider = exports.QmeanScoreColorTheme = exports.getQmeanScoreColorThemeParams = void 0;
+var tslib_1 = require("tslib");
+var prop_1 = require("../prop");
+var structure_1 = require("../../../../mol-model/structure");
+var color_1 = require("../../../../mol-util/color");
+var param_definition_1 = require("../../../../mol-util/param-definition");
+var DefaultColor = (0, color_1.Color)(0xaaaaaa);
+function getQmeanScoreColorThemeParams(ctx) {
+    return {};
+}
+exports.getQmeanScoreColorThemeParams = getQmeanScoreColorThemeParams;
+function QmeanScoreColorTheme(ctx, props) {
+    var color = function () { return DefaultColor; };
+    var scale = color_1.ColorScale.create({
+        domain: [0, 1],
+        listOrName: [
+            [(0, color_1.Color)(0xFF5000), 0.5], [(0, color_1.Color)(0x025AFD), 1.0]
+        ]
+    });
+    if (ctx.structure) {
+        var l_1 = structure_1.StructureElement.Location.create(ctx.structure.root);
+        var getColor_1 = function (location) {
+            var _a, _b;
+            var unit = location.unit, element = location.element;
+            if (!structure_1.Unit.isAtomic(unit))
+                return DefaultColor;
+            var qualityAssessment = prop_1.QualityAssessmentProvider.get(unit.model).value;
+            var score = (_b = (_a = qualityAssessment === null || qualityAssessment === void 0 ? void 0 : qualityAssessment.qmean) === 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 {
+                return scale.color(score);
+            }
+        };
+        color = function (location) {
+            if (structure_1.StructureElement.Location.is(location)) {
+                return getColor_1(location);
+            }
+            else if (structure_1.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: QmeanScoreColorTheme,
+        granularity: 'group',
+        preferSmoothing: true,
+        color: color,
+        props: props,
+        description: 'Assigns residue colors according to the QMEAN score.',
+        legend: scale.legend
+    };
+}
+exports.QmeanScoreColorTheme = QmeanScoreColorTheme;
+exports.QmeanScoreColorThemeProvider = {
+    name: 'qmean-score',
+    label: 'QMEAN Score',
+    category: "Validation" /* Validation */,
+    factory: QmeanScoreColorTheme,
+    getParams: getQmeanScoreColorThemeParams,
+    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(getQmeanScoreColorThemeParams({})),
+    isApplicable: function (ctx) { var _a; return !!((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'qmean'); })); },
+    ensureCustomProperties: {
+        attach: function (ctx, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+            var _i, _a, m;
+            return (0, tslib_1.__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*/, prop_1.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 (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+            var _i, _a, m;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                if (data.structure) {
+                    for (_i = 0, _a = data.structure.models; _i < _a.length; _i++) {
+                        m = _a[_i];
+                        prop_1.QualityAssessmentProvider.ref(m, false);
+                    }
+                }
+                return [2 /*return*/];
+            });
+        }); }
+    }
+};
+//# sourceMappingURL=qmean.js.map

package/lib/commonjs/extensions/model-archive/quality-assessment/prop.d.ts

@@ -0,0 +1,28 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
+import { Model, ResidueIndex } from '../../../mol-model/structure/model';
+import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
+export { QualityAssessment };
+interface QualityAssessment {
+    localMetrics: Map<string, Map<ResidueIndex, number>>;
+    pLDDT?: Map<ResidueIndex, number>;
+    qmean?: Map<ResidueIndex, number>;
+}
+declare namespace QualityAssessment {
+    function isApplicable(model?: Model, localMetricName?: 'pLDDT' | 'qmean'): boolean;
+    function obtain(ctx: CustomProperty.Context, model: Model, props: QualityAssessmentProps): Promise<CustomProperty.Data<QualityAssessment>>;
+    const symbols: {
+        pLDDT: QuerySymbolRuntime;
+        qmean: QuerySymbolRuntime;
+    };
+}
+export declare const QualityAssessmentParams: {};
+export declare type QualityAssessmentParams = typeof QualityAssessmentParams;
+export declare type QualityAssessmentProps = PD.Values<QualityAssessmentParams>;
+export declare const QualityAssessmentProvider: CustomModelProperty.Provider<QualityAssessmentParams, QualityAssessment>;