drugflow-molstar 0.3.77 → 0.4.1

package/lib/domain-annotations/behavior.js

@@ -1,11 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PDBeDomainAnnotations = void 0;
-var tslib_1 = require("tslib");
-var prop_1 = require("./prop");
-var color_1 = require("./color");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
-var behavior_1 = require("Molstar/mol-plugin/behavior");
+const prop_1 = require("./prop");
+const color_1 = require("./color");
+const param_definition_1 = require("Molstar/mol-util/param-definition");
+const behavior_1 = require("Molstar/mol-plugin/behavior");
 exports.PDBeDomainAnnotations = behavior_1.PluginBehavior.create({
     name: 'pdbe-domain-annotations-prop',
     category: 'custom-props',
@@ -13,37 +12,34 @@ exports.PDBeDomainAnnotations = behavior_1.PluginBehavior.create({
         name: 'Domain annotations',
         description: 'Data for domain annotations, obtained via PDBe.'
     },
-    ctor: /** @class */ (function (_super) {
-        tslib_1.__extends(class_1, _super);
-        function class_1() {
-            var _this = _super !== null && _super.apply(this, arguments) || this;
-            _this.provider = prop_1.DomainAnnotationsProvider;
-            _this.labelDomainAnnotations = {
-                label: function (loci) { return void 0; }
+    ctor: class extends behavior_1.PluginBehavior.Handler {
+        constructor() {
+            super(...arguments);
+            this.provider = prop_1.DomainAnnotationsProvider;
+            this.labelDomainAnnotations = {
+                label: (loci) => void 0
             };
-            return _this;
         }
-        class_1.prototype.register = function () {
+        register() {
             this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
             this.ctx.managers.lociLabels.addProvider(this.labelDomainAnnotations);
             this.ctx.representation.structure.themes.colorThemeRegistry.add(color_1.DomainAnnotationsColorThemeProvider);
-        };
-        class_1.prototype.update = function (p) {
-            var updated = this.params.autoAttach !== p.autoAttach;
+        }
+        update(p) {
+            let 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;
-        };
-        class_1.prototype.unregister = function () {
+        }
+        unregister() {
             this.ctx.customModelProperties.unregister(prop_1.DomainAnnotationsProvider.descriptor.name);
             this.ctx.managers.lociLabels.removeProvider(this.labelDomainAnnotations);
             this.ctx.representation.structure.themes.colorThemeRegistry.remove(color_1.DomainAnnotationsColorThemeProvider);
-        };
-        return class_1;
-    }(behavior_1.PluginBehavior.Handler)),
-    params: function () { return ({
+        }
+    },
+    params: () => ({
         autoAttach: param_definition_1.ParamDefinition.Boolean(false),
         showTooltip: param_definition_1.ParamDefinition.Boolean(true)
-    }); }
+    })
 });

package/lib/domain-annotations/color.d.ts

@@ -4,7 +4,7 @@ import { ParamDefinition as PD } from 'Molstar/mol-util/param-definition';
 export declare const DomainAnnotationsColorThemeParams: {
     type: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "">>;
 };
-declare type Params = any;
+type Params = any;
 export declare function DomainAnnotationsColorTheme(ctx: ThemeDataContext, props: PD.Values<Params>): ColorTheme<Params>;
 export declare const DomainAnnotationsColorThemeProvider: ColorTheme.Provider<Params, 'pdbe-domain-annotations'>;
 export {};

package/lib/domain-annotations/color.js

@@ -1,13 +1,14 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DomainAnnotationsColorThemeProvider = exports.DomainAnnotationsColorTheme = exports.DomainAnnotationsColorThemeParams = void 0;
-var prop_1 = require("./prop");
-var structure_1 = require("Molstar/mol-model/structure");
-var color_1 = require("Molstar/mol-util/color");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
-var DomainColors = [
-    color_1.Color.fromRgb(170, 170, 170),
-    color_1.Color.fromRgb(255, 112, 3)
+const prop_1 = require("./prop");
+const structure_1 = require("Molstar/mol-model/structure");
+const color_1 = require("Molstar/mol-theme/color");
+const color_2 = require("Molstar/mol-util/color");
+const param_definition_1 = require("Molstar/mol-util/param-definition");
+const DomainColors = [
+    color_2.Color.fromRgb(170, 170, 170), // not applicable
+    color_2.Color.fromRgb(255, 112, 3)
 ];
 exports.DomainAnnotationsColorThemeParams = {
     type: param_definition_1.ParamDefinition.MappedStatic('', {
@@ -15,19 +16,19 @@ exports.DomainAnnotationsColorThemeParams = {
     })
 };
 function DomainAnnotationsColorTheme(ctx, props) {
-    var color;
+    let color;
     if (ctx.structure && !ctx.structure.isEmpty && ctx.structure.models[0].customProperties.has(prop_1.DomainAnnotationsProvider.descriptor)) {
-        var getDomains_1 = prop_1.DomainAnnotations.getDomains;
-        var issue_1 = props.type.params.kind;
-        color = function (location) {
-            if (structure_1.StructureElement.Location.is(location) && getDomains_1(location).indexOf(issue_1) >= 0) {
+        const getDomains = prop_1.DomainAnnotations.getDomains;
+        const issue = props.type.params.kind;
+        color = (location) => {
+            if (structure_1.StructureElement.Location.is(location) && getDomains(location).indexOf(issue) >= 0) {
                 return DomainColors[1];
             }
             return DomainColors[0];
         };
     }
     else {
-        color = function () { return DomainColors[0]; };
+        color = () => DomainColors[0];
     }
     return {
         factory: DomainAnnotationsColorTheme,
@@ -41,13 +42,13 @@ exports.DomainAnnotationsColorTheme = DomainAnnotationsColorTheme;
 exports.DomainAnnotationsColorThemeProvider = {
     name: 'pdbe-domain-annotations',
     label: 'Domain annotations',
-    category: "Miscellaneous" /* Misc */,
+    category: color_1.ColorTheme.Category.Misc,
     factory: DomainAnnotationsColorTheme,
-    getParams: function (ctx) {
-        var domainNames = prop_1.DomainAnnotations.getDomainNames(ctx.structure);
-        var domainTypes = prop_1.DomainAnnotations.getDomainTypes(ctx.structure);
-        var optionObj = {};
-        domainTypes.forEach(function (tp, index) {
+    getParams: ctx => {
+        const domainNames = prop_1.DomainAnnotations.getDomainNames(ctx.structure);
+        const domainTypes = prop_1.DomainAnnotations.getDomainTypes(ctx.structure);
+        const optionObj = {};
+        domainTypes.forEach((tp, index) => {
             if (domainNames[index].length > 0) {
                 optionObj[tp] = param_definition_1.ParamDefinition.Group({
                     kind: param_definition_1.ParamDefinition.Select(domainNames[index][0], param_definition_1.ParamDefinition.arrayToOptions(domainNames[index]))
@@ -68,11 +69,11 @@ exports.DomainAnnotationsColorThemeProvider = {
         }
     },
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.DomainAnnotationsColorThemeParams),
-    isApplicable: function (ctx) { var _a; return prop_1.DomainAnnotations.isApplicable((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models[0]); },
+    isApplicable: (ctx) => prop_1.DomainAnnotations.isApplicable(ctx.structure?.models[0]),
     ensureCustomProperties: {
-        attach: function (ctx, data) {
+        attach: (ctx, data) => {
             return data.structure ? prop_1.DomainAnnotationsProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve();
         },
-        detach: function (data) { return data.structure && data.structure.models[0].customProperties.reference(prop_1.DomainAnnotationsProvider.descriptor, false); }
+        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(prop_1.DomainAnnotationsProvider.descriptor, false)
     }
 };

package/lib/domain-annotations/prop.d.ts

@@ -5,7 +5,7 @@ import { CustomModelProperty } from 'Molstar/mol-model-props/common/custom-model
 import { ParamDefinition as PD } from 'Molstar/mol-util/param-definition';
 import { CustomProperty } from 'Molstar/mol-model-props/common/custom-property';
 export { DomainAnnotations };
-declare type DomainAnnotations = PropertyWrapper<{
+type DomainAnnotations = PropertyWrapper<{
     domains: IndexedCustomProperty.Residue<string[]>;
     domainNames: string[][];
     domainTypes: string[];
@@ -30,6 +30,6 @@ declare namespace DomainAnnotations {
 export declare const DomainAnnotationsParams: {
     serverUrl: PD.Text<string>;
 };
-export declare type DomainAnnotationsParams = typeof DomainAnnotationsParams;
-export declare type DomainAnnotationsProps = PD.Values<DomainAnnotationsParams>;
+export type DomainAnnotationsParams = typeof DomainAnnotationsParams;
+export type DomainAnnotationsProps = PD.Values<DomainAnnotationsParams>;
 export declare const DomainAnnotationsProvider: CustomModelProperty.Provider<DomainAnnotationsParams, DomainAnnotations>;

package/lib/domain-annotations/prop.js

@@ -1,19 +1,18 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DomainAnnotationsProvider = exports.DomainAnnotationsParams = exports.DomainAnnotations = void 0;
-var tslib_1 = require("tslib");
-var structure_1 = require("Molstar/mol-model/structure");
-var wrapper_1 = require("Molstar/mol-model-props/common/wrapper");
-var custom_model_property_1 = require("Molstar/mol-model-props/common/custom-model-property");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
-var array_1 = require("Molstar/mol-util/array");
-var assets_1 = require("Molstar/mol-util/assets");
-var custom_property_1 = require("Molstar/mol-model/custom-property");
+const structure_1 = require("Molstar/mol-model/structure");
+const wrapper_1 = require("Molstar/mol-model-props/common/wrapper");
+const custom_model_property_1 = require("Molstar/mol-model-props/common/custom-model-property");
+const param_definition_1 = require("Molstar/mol-util/param-definition");
+const array_1 = require("Molstar/mol-util/array");
+const assets_1 = require("Molstar/mol-util/assets");
+const custom_property_1 = require("Molstar/mol-model/custom-property");
 var DomainAnnotations;
 (function (DomainAnnotations) {
     DomainAnnotations.DefaultServerUrl = 'https://www.ebi.ac.uk/pdbe/api/mappings';
     function getEntryUrl(pdbId, serverUrl) {
-        return "".concat(serverUrl, "/").concat(pdbId.toLowerCase());
+        return `${serverUrl}/${pdbId.toLowerCase()}`;
     }
     DomainAnnotations.getEntryUrl = getEntryUrl;
     function isApplicable(model) {
@@ -21,45 +20,35 @@ var DomainAnnotations;
     }
     DomainAnnotations.isApplicable = isApplicable;
     function fromJson(model, data) {
-        var info = wrapper_1.PropertyWrapper.createInfo();
-        var domainMap = createdomainMapFromJson(model, data);
-        return { info: info, data: domainMap };
+        const info = wrapper_1.PropertyWrapper.createInfo();
+        const domainMap = createdomainMapFromJson(model, data);
+        return { info, data: domainMap };
     }
     DomainAnnotations.fromJson = fromJson;
-    function fromServer(ctx, model, props) {
-        return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var url, json, data;
-            return tslib_1.__generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        url = assets_1.Asset.getUrlAsset(ctx.assetManager, getEntryUrl(model.entryId, props.serverUrl));
-                        return [4 /*yield*/, ctx.assetManager.resolve(url, 'json').runInContext(ctx.runtime)];
-                    case 1:
-                        json = _a.sent();
-                        data = json.data[model.entryId.toLowerCase()];
-                        if (!data)
-                            throw new Error('missing data');
-                        return [2 /*return*/, { value: fromJson(model, data), assets: [json] }];
-                }
-            });
-        });
+    async function fromServer(ctx, model, props) {
+        const url = assets_1.Asset.getUrlAsset(ctx.assetManager, getEntryUrl(model.entryId, props.serverUrl));
+        const json = await ctx.assetManager.resolve(url, 'json').runInContext(ctx.runtime);
+        const data = json.data[model.entryId.toLowerCase()];
+        if (!data)
+            throw new Error('missing data');
+        return { value: fromJson(model, data), assets: [json] };
     }
     DomainAnnotations.fromServer = fromServer;
-    var _emptyArray = [];
+    const _emptyArray = [];
     function getDomains(e) {
         if (!structure_1.Unit.isAtomic(e.unit))
             return _emptyArray;
-        var prop = exports.DomainAnnotationsProvider.get(e.unit.model).value;
+        const prop = exports.DomainAnnotationsProvider.get(e.unit.model).value;
         if (!prop || !prop.data)
             return _emptyArray;
-        var rI = e.unit.residueIndex[e.element];
+        const rI = e.unit.residueIndex[e.element];
         return prop.data.domains.has(rI) ? prop.data.domains.get(rI) : _emptyArray;
     }
     DomainAnnotations.getDomains = getDomains;
     function getDomainTypes(structure) {
         if (!structure)
             return _emptyArray;
-        var prop = exports.DomainAnnotationsProvider.get(structure.models[0]).value;
+        const prop = exports.DomainAnnotationsProvider.get(structure.models[0]).value;
         if (!prop || !prop.data)
             return _emptyArray;
         return prop.data.domainTypes;
@@ -68,14 +57,13 @@ var DomainAnnotations;
     function getDomainNames(structure) {
         if (!structure)
             return _emptyArray;
-        var prop = exports.DomainAnnotationsProvider.get(structure.models[0]).value;
+        const prop = exports.DomainAnnotationsProvider.get(structure.models[0]).value;
         if (!prop || !prop.data)
             return _emptyArray;
         return prop.data.domainNames;
     }
     DomainAnnotations.getDomainNames = getDomainNames;
-})(DomainAnnotations || (DomainAnnotations = {}));
-exports.DomainAnnotations = DomainAnnotations;
+})(DomainAnnotations || (exports.DomainAnnotations = DomainAnnotations = {}));
 exports.DomainAnnotationsParams = {
     serverUrl: param_definition_1.ParamDefinition.Text(DomainAnnotations.DefaultServerUrl, { description: 'JSON API Server URL' })
 };
@@ -86,62 +74,52 @@ exports.DomainAnnotationsProvider = custom_model_property_1.CustomModelProperty.
     }),
     type: 'static',
     defaultParams: exports.DomainAnnotationsParams,
-    getParams: function (data) { return exports.DomainAnnotationsParams; },
-    isApplicable: function (data) { return DomainAnnotations.isApplicable(data); },
-    obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
-        var p;
-        return tslib_1.__generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.DomainAnnotationsParams)), props);
-                    return [4 /*yield*/, DomainAnnotations.fromServer(ctx, data, p)];
-                case 1: return [2 /*return*/, _a.sent()];
-            }
-        });
-    }); }
+    getParams: (data) => exports.DomainAnnotationsParams,
+    isApplicable: (data) => DomainAnnotations.isApplicable(data),
+    obtain: async (ctx, data, props) => {
+        const p = { ...param_definition_1.ParamDefinition.getDefaultValues(exports.DomainAnnotationsParams), ...props };
+        return await DomainAnnotations.fromServer(ctx, data, p);
+    }
 });
 function findChainLabel(map, label_entity_id, label_asym_id) {
-    var entityIndex = map.entities.getEntityIndex;
-    var eI = entityIndex(label_entity_id);
+    const entityIndex = map.entities.getEntityIndex;
+    const eI = entityIndex(label_entity_id);
     if (eI < 0 || !map.entity_index_label_asym_id.has(eI))
         return -1;
-    var cm = map.entity_index_label_asym_id.get(eI);
+    const cm = map.entity_index_label_asym_id.get(eI);
     if (!cm)
         return -1;
     return cm.has(label_asym_id) ? cm.get(label_asym_id) : -1;
 }
 function findResidue(modelData, map, label_entity_id, label_asym_id, label_seq_id) {
-    var cI = findChainLabel(map, label_entity_id, label_asym_id);
+    const cI = findChainLabel(map, label_entity_id, label_asym_id);
     if (cI < 0)
         return -1;
-    var rm = map.chain_index_auth_seq_id.get(cI);
+    const rm = map.chain_index_auth_seq_id.get(cI);
     return rm.has(label_seq_id) ? rm.get(label_seq_id) : -1;
 }
 function createdomainMapFromJson(modelData, data) {
-    var domainTypes = [];
-    var domainNames = [];
-    var ret = new Map();
-    var defaultDomains = ['Pfam', 'InterPro', 'CATH', 'SCOP'];
-    for (var _i = 0, _a = Object.keys(data); _i < _a.length; _i++) {
-        var db_name = _a[_i];
+    const domainTypes = [];
+    const domainNames = [];
+    const ret = new Map();
+    const defaultDomains = ['Pfam', 'InterPro', 'CATH', 'SCOP'];
+    for (const db_name of Object.keys(data)) {
         if (defaultDomains.indexOf(db_name) === -1)
             continue;
-        var tempDomains = [];
+        const tempDomains = [];
         domainTypes.push(db_name);
-        var db = data[db_name];
-        for (var _b = 0, _c = Object.keys(db); _b < _c.length; _b++) {
-            var db_code = _c[_b];
-            var domain = db[db_code];
-            for (var _d = 0, _e = domain.mappings; _d < _e.length; _d++) {
-                var map = _e[_d];
+        const db = data[db_name];
+        for (const db_code of Object.keys(db)) {
+            const domain = db[db_code];
+            for (const map of domain.mappings) {
                 (0, array_1.arraySetAdd)(tempDomains, domain.identifier);
-                var indexData = modelData.atomicHierarchy.index;
-                var indexMap = indexData.map;
-                for (var i = map.start.residue_number; i <= map.end.residue_number; i++) {
-                    var seq_id = i;
-                    var idx = findResidue(modelData, indexMap, map.entity_id + '', map.chain_id, seq_id);
-                    var addVal = [domain.identifier];
-                    var prevVal = ret.get(idx);
+                const indexData = modelData.atomicHierarchy.index;
+                const indexMap = indexData.map;
+                for (let i = map.start.residue_number; i <= map.end.residue_number; i++) {
+                    const seq_id = i;
+                    const idx = findResidue(modelData, indexMap, map.entity_id + '', map.chain_id, seq_id);
+                    let addVal = [domain.identifier];
+                    const prevVal = ret.get(idx);
                     if (prevVal) {
                         prevVal.push(domain.identifier);
                         addVal = prevVal;
@@ -154,7 +132,7 @@ function createdomainMapFromJson(modelData, data) {
     }
     return {
         domains: structure_1.IndexedCustomProperty.fromResidueMap(ret),
-        domainNames: domainNames,
-        domainTypes: domainTypes
+        domainNames,
+        domainTypes
     };
 }

package/lib/drugflow-molstar-component-build-0.3.78.js

@@ -0,0 +1,2 @@
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package/lib/drugflow-molstar-component-build-0.4.1.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.4.1.js.LICENSE.txt */
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package/lib/helpers.d.ts

@@ -2,8 +2,8 @@ import { PluginContext } from 'Molstar/mol-plugin/context';
 import Expression from 'Molstar/mol-script/language/expression';
 import { BuiltInTrajectoryFormat } from 'Molstar/mol-plugin-state/formats/trajectory';
 import { Model } from 'Molstar/mol-model/structure';
-export declare type SupportedFormats = 'mmcif' | 'bcif' | 'cif' | 'pdb' | 'sdf';
-export declare type LoadParams = {
+export type SupportedFormats = 'mmcif' | 'bcif' | 'cif' | 'pdb' | 'sdf';
+export type LoadParams = {
     url: string;
     format?: BuiltInTrajectoryFormat;
     assemblyId?: string;
@@ -25,7 +25,7 @@ export declare namespace PDBeVolumes {
 export declare namespace AlphafoldView {
     function getLociByPLDDT(score: number, contextData: any): import("molstar/lib/mol-model/structure/structure/element/loci").Loci;
 }
-export declare type LigandQueryParam = {
+export type LigandQueryParam = {
     label_comp_id_list?: any;
     auth_asym_id?: string;
     struct_asym_id?: string;
@@ -43,7 +43,7 @@ export declare namespace LigandView {
         surroundings: Expression.Expression;
     };
 }
-export declare type QueryParam = {
+export type QueryParam = {
     auth_seq_id?: number;
     entity_id?: string;
     auth_asym_id?: string;