drugflow-molstar 0.2.1 → 0.2.2

package/lib/sifts-mapping.js

@@ -1,83 +1,83 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.SIFTSMapping = void 0;
-var tslib_1 = require("tslib");
-var mmcif_1 = require("Molstar/mol-model-formats/structure/mmcif");
-var custom_property_1 = require("Molstar/mol-model/custom-property");
-var custom_model_property_1 = require("Molstar/mol-model-props/common/custom-model-property");
-var SIFTSMapping;
-(function (SIFTSMapping) {
-    var _this = this;
-    SIFTSMapping.Provider = custom_model_property_1.CustomModelProperty.createProvider({
-        label: 'SIFTS Mapping',
-        descriptor: (0, custom_property_1.CustomPropertyDescriptor)({
-            name: 'sifts_sequence_mapping'
-        }),
-        type: 'static',
-        defaultParams: {},
-        getParams: function () { return ({}); },
-        isApplicable: function (data) { return isAvailable(data); },
-        obtain: function (ctx, data) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-            return tslib_1.__generator(this, function (_a) {
-                return [2 /*return*/, { value: fromCif(data) }];
-            });
-        }); }
-    });
-    function isAvailable(model) {
-        if (!mmcif_1.MmcifFormat.is(model.sourceData))
-            return false;
-        var _a = model.sourceData.data.db.atom_site, db_name = _a.pdbx_sifts_xref_db_name, db_acc = _a.pdbx_sifts_xref_db_acc, db_num = _a.pdbx_sifts_xref_db_num, db_res = _a.pdbx_sifts_xref_db_res;
-        return db_name.isDefined && db_acc.isDefined && db_num.isDefined && db_res.isDefined;
-    }
-    SIFTSMapping.isAvailable = isAvailable;
-    function getKey(loc) {
-        var model = loc.unit.model;
-        var data = SIFTSMapping.Provider.get(model).value;
-        if (!data)
-            return '';
-        var rI = model.atomicHierarchy.residueAtomSegments.index[loc.element];
-        return data.accession[rI];
-    }
-    SIFTSMapping.getKey = getKey;
-    function getLabel(loc) {
-        var model = loc.unit.model;
-        var data = SIFTSMapping.Provider.get(model).value;
-        if (!data)
-            return;
-        var rI = model.atomicHierarchy.residueAtomSegments.index[loc.element];
-        var dbName = data.dbName[rI];
-        if (!dbName)
-            return;
-        return "".concat(dbName, " ").concat(data.accession[rI], " ").concat(data.num[rI], " ").concat(data.residue[rI]);
-    }
-    SIFTSMapping.getLabel = getLabel;
-    function fromCif(model) {
-        if (!mmcif_1.MmcifFormat.is(model.sourceData))
-            return;
-        var _a = model.sourceData.data.db.atom_site, db_name = _a.pdbx_sifts_xref_db_name, db_acc = _a.pdbx_sifts_xref_db_acc, db_num = _a.pdbx_sifts_xref_db_num, db_res = _a.pdbx_sifts_xref_db_res;
-        if (!db_name.isDefined || !db_acc.isDefined || !db_num.isDefined || !db_res.isDefined)
-            return;
-        var atomSourceIndex = model.atomicHierarchy.atomSourceIndex;
-        var _b = model.atomicHierarchy.residueAtomSegments, count = _b.count, residueOffsets = _b.offsets;
-        var dbName = new Array(count);
-        var accession = new Array(count);
-        var num = new Array(count);
-        var residue = new Array(count);
-        for (var i = 0; i < count; i++) {
-            var row = atomSourceIndex.value(residueOffsets[i]);
-            if (db_name.valueKind(row) !== 0 /* Present */) {
-                dbName[i] = '';
-                accession[i] = '';
-                num[i] = '';
-                residue[i] = '';
-                continue;
-            }
-            dbName[i] = db_name.value(row);
-            accession[i] = db_acc.value(row);
-            num[i] = db_num.value(row);
-            residue[i] = db_res.value(row);
-        }
-        return { dbName: dbName, accession: accession, num: num, residue: residue };
-    }
-})(SIFTSMapping || (SIFTSMapping = {}));
-exports.SIFTSMapping = SIFTSMapping;
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.SIFTSMapping = void 0;
+var tslib_1 = require("tslib");
+var mmcif_1 = require("Molstar/mol-model-formats/structure/mmcif");
+var custom_property_1 = require("Molstar/mol-model/custom-property");
+var custom_model_property_1 = require("Molstar/mol-model-props/common/custom-model-property");
+var SIFTSMapping;
+(function (SIFTSMapping) {
+    var _this = this;
+    SIFTSMapping.Provider = custom_model_property_1.CustomModelProperty.createProvider({
+        label: 'SIFTS Mapping',
+        descriptor: (0, custom_property_1.CustomPropertyDescriptor)({
+            name: 'sifts_sequence_mapping'
+        }),
+        type: 'static',
+        defaultParams: {},
+        getParams: function () { return ({}); },
+        isApplicable: function (data) { return isAvailable(data); },
+        obtain: function (ctx, data) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
+                return [2 /*return*/, { value: fromCif(data) }];
+            });
+        }); }
+    });
+    function isAvailable(model) {
+        if (!mmcif_1.MmcifFormat.is(model.sourceData))
+            return false;
+        var _a = model.sourceData.data.db.atom_site, db_name = _a.pdbx_sifts_xref_db_name, db_acc = _a.pdbx_sifts_xref_db_acc, db_num = _a.pdbx_sifts_xref_db_num, db_res = _a.pdbx_sifts_xref_db_res;
+        return db_name.isDefined && db_acc.isDefined && db_num.isDefined && db_res.isDefined;
+    }
+    SIFTSMapping.isAvailable = isAvailable;
+    function getKey(loc) {
+        var model = loc.unit.model;
+        var data = SIFTSMapping.Provider.get(model).value;
+        if (!data)
+            return '';
+        var rI = model.atomicHierarchy.residueAtomSegments.index[loc.element];
+        return data.accession[rI];
+    }
+    SIFTSMapping.getKey = getKey;
+    function getLabel(loc) {
+        var model = loc.unit.model;
+        var data = SIFTSMapping.Provider.get(model).value;
+        if (!data)
+            return;
+        var rI = model.atomicHierarchy.residueAtomSegments.index[loc.element];
+        var dbName = data.dbName[rI];
+        if (!dbName)
+            return;
+        return "".concat(dbName, " ").concat(data.accession[rI], " ").concat(data.num[rI], " ").concat(data.residue[rI]);
+    }
+    SIFTSMapping.getLabel = getLabel;
+    function fromCif(model) {
+        if (!mmcif_1.MmcifFormat.is(model.sourceData))
+            return;
+        var _a = model.sourceData.data.db.atom_site, db_name = _a.pdbx_sifts_xref_db_name, db_acc = _a.pdbx_sifts_xref_db_acc, db_num = _a.pdbx_sifts_xref_db_num, db_res = _a.pdbx_sifts_xref_db_res;
+        if (!db_name.isDefined || !db_acc.isDefined || !db_num.isDefined || !db_res.isDefined)
+            return;
+        var atomSourceIndex = model.atomicHierarchy.atomSourceIndex;
+        var _b = model.atomicHierarchy.residueAtomSegments, count = _b.count, residueOffsets = _b.offsets;
+        var dbName = new Array(count);
+        var accession = new Array(count);
+        var num = new Array(count);
+        var residue = new Array(count);
+        for (var i = 0; i < count; i++) {
+            var row = atomSourceIndex.value(residueOffsets[i]);
+            if (db_name.valueKind(row) !== 0 /* Present */) {
+                dbName[i] = '';
+                accession[i] = '';
+                num[i] = '';
+                residue[i] = '';
+                continue;
+            }
+            dbName[i] = db_name.value(row);
+            accession[i] = db_acc.value(row);
+            num[i] = db_num.value(row);
+            residue[i] = db_res.value(row);
+        }
+        return { dbName: dbName, accession: accession, num: num, residue: residue };
+    }
+})(SIFTSMapping || (SIFTSMapping = {}));
+exports.SIFTSMapping = SIFTSMapping;

package/lib/sifts-mappings-behaviour.d.ts

@@ -1,5 +1,5 @@
-import { PluginBehavior } from 'Molstar/mol-plugin/behavior';
-export declare const PDBeSIFTSMapping: import("molstar/lib/mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
-    autoAttach: boolean;
-    showTooltip: boolean;
-}>;
+import { PluginBehavior } from 'Molstar/mol-plugin/behavior';
+export declare const PDBeSIFTSMapping: import("molstar/lib/mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
+    autoAttach: boolean;
+    showTooltip: boolean;
+}>;

package/lib/sifts-mappings-behaviour.js

@@ -1,64 +1,64 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.PDBeSIFTSMapping = void 0;
-var tslib_1 = require("tslib");
-var int_1 = require("Molstar/mol-data/int");
-var sifts_mapping_1 = require("./sifts-mapping");
-var sifts_mapping_2 = require("Molstar/mol-model-props/sequence/themes/sifts-mapping");
-var structure_1 = require("Molstar/mol-model/structure");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
-var behavior_1 = require("Molstar/mol-plugin/behavior");
-exports.PDBeSIFTSMapping = behavior_1.PluginBehavior.create({
-    name: 'pdbe-sifts-mapping-prop',
-    category: 'custom-props',
-    display: { name: 'PDBe SIFTS Mapping' },
-    ctor: /** @class */ (function (_super) {
-        tslib_1.__extends(class_1, _super);
-        function class_1() {
-            var _this = _super !== null && _super.apply(this, arguments) || this;
-            _this.provider = sifts_mapping_1.SIFTSMapping.Provider;
-            _this.labelProvider = {
-                label: function (loci) {
-                    if (!_this.params.showTooltip)
-                        return;
-                    return PDBeBestDatabaseSequenceMappingLabel(loci);
-                }
-            };
-            return _this;
-        }
-        class_1.prototype.update = function (p) {
-            var updated = (this.params.autoAttach !== p.autoAttach ||
-                this.params.showTooltip !== p.showTooltip);
-            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.register = function () {
-            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
-            this.ctx.representation.structure.themes.colorThemeRegistry.add(sifts_mapping_2.SIFTSMappingColorThemeProvider);
-            this.ctx.managers.lociLabels.addProvider(this.labelProvider);
-        };
-        class_1.prototype.unregister = function () {
-            this.ctx.customModelProperties.unregister(this.provider.descriptor.name);
-            this.ctx.representation.structure.themes.colorThemeRegistry.remove(sifts_mapping_2.SIFTSMappingColorThemeProvider);
-            this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
-        };
-        return class_1;
-    }(behavior_1.PluginBehavior.Handler)),
-    params: function () { return ({
-        autoAttach: param_definition_1.ParamDefinition.Boolean(true),
-        showTooltip: param_definition_1.ParamDefinition.Boolean(true)
-    }); }
-});
-//
-function PDBeBestDatabaseSequenceMappingLabel(loci) {
-    if (loci.kind === 'element-loci') {
-        if (loci.elements.length === 0)
-            return;
-        var e = loci.elements[0];
-        var u = e.unit;
-        var se = structure_1.StructureElement.Location.create(loci.structure, u, u.elements[int_1.OrderedSet.getAt(e.indices, 0)]);
-        return sifts_mapping_1.SIFTSMapping.getLabel(se);
-    }
-}
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.PDBeSIFTSMapping = void 0;
+var tslib_1 = require("tslib");
+var int_1 = require("Molstar/mol-data/int");
+var sifts_mapping_1 = require("./sifts-mapping");
+var sifts_mapping_2 = require("Molstar/mol-model-props/sequence/themes/sifts-mapping");
+var structure_1 = require("Molstar/mol-model/structure");
+var param_definition_1 = require("Molstar/mol-util/param-definition");
+var behavior_1 = require("Molstar/mol-plugin/behavior");
+exports.PDBeSIFTSMapping = behavior_1.PluginBehavior.create({
+    name: 'pdbe-sifts-mapping-prop',
+    category: 'custom-props',
+    display: { name: 'PDBe SIFTS Mapping' },
+    ctor: /** @class */ (function (_super) {
+        tslib_1.__extends(class_1, _super);
+        function class_1() {
+            var _this = _super !== null && _super.apply(this, arguments) || this;
+            _this.provider = sifts_mapping_1.SIFTSMapping.Provider;
+            _this.labelProvider = {
+                label: function (loci) {
+                    if (!_this.params.showTooltip)
+                        return;
+                    return PDBeBestDatabaseSequenceMappingLabel(loci);
+                }
+            };
+            return _this;
+        }
+        class_1.prototype.update = function (p) {
+            var updated = (this.params.autoAttach !== p.autoAttach ||
+                this.params.showTooltip !== p.showTooltip);
+            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.register = function () {
+            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(sifts_mapping_2.SIFTSMappingColorThemeProvider);
+            this.ctx.managers.lociLabels.addProvider(this.labelProvider);
+        };
+        class_1.prototype.unregister = function () {
+            this.ctx.customModelProperties.unregister(this.provider.descriptor.name);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(sifts_mapping_2.SIFTSMappingColorThemeProvider);
+            this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
+        };
+        return class_1;
+    }(behavior_1.PluginBehavior.Handler)),
+    params: function () { return ({
+        autoAttach: param_definition_1.ParamDefinition.Boolean(true),
+        showTooltip: param_definition_1.ParamDefinition.Boolean(true)
+    }); }
+});
+//
+function PDBeBestDatabaseSequenceMappingLabel(loci) {
+    if (loci.kind === 'element-loci') {
+        if (loci.elements.length === 0)
+            return;
+        var e = loci.elements[0];
+        var u = e.unit;
+        var se = structure_1.StructureElement.Location.create(loci.structure, u, u.elements[int_1.OrderedSet.getAt(e.indices, 0)]);
+        return sifts_mapping_1.SIFTSMapping.getLabel(se);
+    }
+}

package/lib/spec.d.ts

@@ -1,76 +1,76 @@
-import { PluginUIContext } from 'Molstar/mol-plugin-ui/context';
-import { PluginSpec } from 'Molstar/mol-plugin/spec';
-import { PluginUISpec } from 'Molstar/mol-plugin-ui/spec';
-import { Loci } from 'Molstar/mol-model/loci';
-import { QueryParam, LigandQueryParam } from './helpers';
-export declare const DefaultPluginSpec: () => PluginSpec;
-export declare const DefaultPluginUISpec: () => PluginUISpec;
-export declare function createPluginUI(target: HTMLElement, spec?: PluginUISpec, options?: {
-    onBeforeUIRender?: (ctx: PluginUIContext) => (Promise<void> | void);
-}): Promise<PluginUIContext>;
-export declare type InitParams = {
-    moleculeId?: string;
-    superposition?: boolean;
-    pdbeUrl?: string;
-    loadMaps?: boolean;
-    validationAnnotation?: boolean;
-    domainAnnotation?: boolean;
-    lowPrecisionCoords?: boolean;
-    landscape?: boolean;
-    reactive?: boolean;
-    expanded?: boolean;
-    hideControls?: boolean;
-    hideCanvasControls?: ['expand', 'selection', 'animation', 'controlToggle', 'controlInfo'];
-    subscribeEvents?: boolean;
-    pdbeLink?: boolean;
-    assemblyId?: string;
-    selectInteraction?: boolean;
-    sequencePanel?: boolean;
-    ligandView?: LigandQueryParam;
-    defaultPreset?: 'default' | "unitcell" | "all-models" | "supercell";
-    bgColor?: {
-        r: number;
-        g: number;
-        b: number;
-    };
-    customData?: {
-        url: string;
-        format: string;
-        binary: boolean;
-        pdb_string: string;
-    };
-    loadCartoonsOnly?: boolean;
-    alphafoldView?: boolean;
-    selectBindings?: any;
-    focusBindings?: any;
-    lighting?: 'flat' | 'matte' | 'glossy' | 'metallic' | 'plastic' | undefined;
-    selectColor?: {
-        r: number;
-        g: number;
-        b: number;
-    };
-    highlightColor?: {
-        r: number;
-        g: number;
-        b: number;
-    };
-    superpositionParams?: {
-        matrixAccession?: string;
-        segment?: number;
-        cluster?: number[];
-        superposeCompleteCluster?: boolean;
-        ligandView?: boolean;
-    };
-    hideStructure?: ['polymer', 'het', 'water', 'carbs', 'nonStandard', 'coarse'];
-    visualStyle?: 'cartoon' | 'ball-and-stick';
-    encoding: 'cif' | 'bcif';
-    granularity?: Loci.Granularity;
-    selection?: {
-        data: QueryParam[];
-        nonSelectedColor?: any;
-        clearPrevious?: boolean;
-    };
-    mapSettings: any;
-    [key: string]: any;
-};
-export declare const DefaultParams: InitParams;
+import { PluginUIContext } from 'Molstar/mol-plugin-ui/context';
+import { PluginSpec } from 'Molstar/mol-plugin/spec';
+import { PluginUISpec } from 'Molstar/mol-plugin-ui/spec';
+import { Loci } from 'Molstar/mol-model/loci';
+import { QueryParam, LigandQueryParam } from './helpers';
+export declare const DefaultPluginSpec: () => PluginSpec;
+export declare const DefaultPluginUISpec: () => PluginUISpec;
+export declare function createPluginUI(target: HTMLElement, spec?: PluginUISpec, options?: {
+    onBeforeUIRender?: (ctx: PluginUIContext) => (Promise<void> | void);
+}): Promise<PluginUIContext>;
+export declare type InitParams = {
+    moleculeId?: string;
+    superposition?: boolean;
+    pdbeUrl?: string;
+    loadMaps?: boolean;
+    validationAnnotation?: boolean;
+    domainAnnotation?: boolean;
+    lowPrecisionCoords?: boolean;
+    landscape?: boolean;
+    reactive?: boolean;
+    expanded?: boolean;
+    hideControls?: boolean;
+    hideCanvasControls?: ['expand', 'selection', 'animation', 'controlToggle', 'controlInfo'];
+    subscribeEvents?: boolean;
+    pdbeLink?: boolean;
+    assemblyId?: string;
+    selectInteraction?: boolean;
+    sequencePanel?: boolean;
+    ligandView?: LigandQueryParam;
+    defaultPreset?: 'default' | "unitcell" | "all-models" | "supercell";
+    bgColor?: {
+        r: number;
+        g: number;
+        b: number;
+    };
+    customData?: {
+        url: string;
+        format: string;
+        binary: boolean;
+        pdb_string: string;
+    };
+    loadCartoonsOnly?: boolean;
+    alphafoldView?: boolean;
+    selectBindings?: any;
+    focusBindings?: any;
+    lighting?: 'flat' | 'matte' | 'glossy' | 'metallic' | 'plastic' | undefined;
+    selectColor?: {
+        r: number;
+        g: number;
+        b: number;
+    };
+    highlightColor?: {
+        r: number;
+        g: number;
+        b: number;
+    };
+    superpositionParams?: {
+        matrixAccession?: string;
+        segment?: number;
+        cluster?: number[];
+        superposeCompleteCluster?: boolean;
+        ligandView?: boolean;
+    };
+    hideStructure?: ['polymer', 'het', 'water', 'carbs', 'nonStandard', 'coarse'];
+    visualStyle?: 'cartoon' | 'ball-and-stick';
+    encoding: 'cif' | 'bcif';
+    granularity?: Loci.Granularity;
+    selection?: {
+        data: QueryParam[];
+        nonSelectedColor?: any;
+        clearPrevious?: boolean;
+    };
+    mapSettings: any;
+    [key: string]: any;
+};
+export declare const DefaultParams: InitParams;