drugflow-molstar 0.3.77 → 0.4.1

package/lib/labels.d.ts

@@ -1,2 +1,2 @@
 import { PluginBehavior } from 'Molstar/mol-plugin/behavior';
-export declare const PDBeLociLabelProvider: import("molstar/lib/mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, unknown>;
+export declare const PDBeLociLabelProvider: import("molstar/lib/mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;

package/lib/labels.js

@@ -1,42 +1,39 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PDBeLociLabelProvider = void 0;
-var behavior_1 = require("Molstar/mol-plugin/behavior");
-var structure_1 = require("Molstar/mol-model/structure");
-var label_1 = require("Molstar/mol-theme/label");
+const behavior_1 = require("Molstar/mol-plugin/behavior");
+const structure_1 = require("Molstar/mol-model/structure");
+const label_1 = require("Molstar/mol-theme/label");
 exports.PDBeLociLabelProvider = behavior_1.PluginBehavior.create({
     name: 'pdbe-loci-label-provider',
     category: 'interaction',
-    ctor: /** @class */ (function () {
-        function class_1(ctx) {
-            var _this = this;
+    ctor: class {
+        register() { this.ctx.managers.lociLabels.addProvider(this.f); }
+        unregister() { this.ctx.managers.lociLabels.removeProvider(this.f); }
+        constructor(ctx) {
             this.ctx = ctx;
             this.f = {
-                label: function (loci) {
-                    var customState = (_this.ctx.customState);
-                    var superpositionView = (customState && customState.initParams.superposition) ? true : false;
-                    var label = [];
+                label: (loci) => {
+                    const customState = (this.ctx.customState);
+                    const superpositionView = (customState && customState.initParams.superposition) ? true : false;
+                    const label = [];
                     if (!superpositionView && structure_1.StructureElement.Loci.is(loci) && loci.elements.length === 1) {
-                        var entityNames = new Set();
-                        for (var _i = 0, _a = loci.elements; _i < _a.length; _i++) {
-                            var u = _a[_i].unit;
-                            var l = structure_1.StructureElement.Location.create(loci.structure, u, u.elements[0]);
-                            var name_1 = structure_1.StructureProperties.entity.pdbx_description(l).join(', ');
-                            entityNames.add(name_1);
+                        const entityNames = new Set();
+                        for (const { unit: u } of loci.elements) {
+                            const l = structure_1.StructureElement.Location.create(loci.structure, u, u.elements[0]);
+                            const name = structure_1.StructureProperties.entity.pdbx_description(l).join(', ');
+                            entityNames.add(name);
                         }
                         if (entityNames.size === 1)
-                            entityNames.forEach(function (name) { return label.push(name); });
+                            entityNames.forEach(name => label.push(name));
                     }
                     label.push((0, label_1.lociLabel)(loci));
-                    return label.filter(function (l) { return !!l; }).join('</br>');
+                    return label.filter(l => !!l).join('</br>');
                 },
-                group: function (label) { return label.toString().replace(/Model [0-9]+/g, 'Models'); },
+                group: (label) => label.toString().replace(/Model [0-9]+/g, 'Models'),
                 priority: 100
             };
         }
-        class_1.prototype.register = function () { this.ctx.managers.lociLabels.addProvider(this.f); };
-        class_1.prototype.unregister = function () { this.ctx.managers.lociLabels.removeProvider(this.f); };
-        return class_1;
-    }()),
+    },
     display: { name: 'Provide PDBe Loci Label' }
 });

package/lib/loci-details.d.ts

@@ -1,6 +1,6 @@
 import { Bond } from 'Molstar/mol-model/structure';
 import { Loci } from 'Molstar/mol-model/loci';
-export declare type EventDetail = {
+export type EventDetail = {
     models?: string[];
     entity_id?: string;
     label_asym_id?: string;
@@ -20,7 +20,7 @@ export declare type EventDetail = {
     button?: number;
     modifiers?: any;
 };
-declare type LabelGranularity = 'element' | 'conformation' | 'residue' | 'chain' | 'structure';
+type LabelGranularity = 'element' | 'conformation' | 'residue' | 'chain' | 'structure';
 export declare function lociDetails(loci: Loci): EventDetail | undefined;
 export declare function bondLabel(bond: Bond.Location, granularity: LabelGranularity): any;
 export declare function _bundleLabel(bundle: Loci.Bundle<any>, granularity: LabelGranularity): EventDetail | (EventDetail | undefined)[];

package/lib/loci-details.js

@@ -1,18 +1,17 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports._bundleLabel = exports.bondLabel = exports.lociDetails = void 0;
-var tslib_1 = require("tslib");
-var structure_1 = require("Molstar/mol-model/structure");
-var int_1 = require("Molstar/mol-data/int");
-var sifts_mapping_1 = require("Molstar/mol-model-props/sequence/sifts-mapping");
+const structure_1 = require("Molstar/mol-model/structure");
+const int_1 = require("Molstar/mol-data/int");
+const sifts_mapping_1 = require("Molstar/mol-model-props/sequence/sifts-mapping");
 function lociDetails(loci) {
     switch (loci.kind) {
         case 'structure-loci':
-            return { models: loci.structure.models.map(function (m) { return m.entry; }).filter(function (l) { return !!l; }) };
+            return { models: loci.structure.models.map(m => m.entry).filter(l => !!l) };
         case 'element-loci':
             return structureElementStatsDetail(structure_1.StructureElement.Stats.ofLoci(loci));
         case 'bond-loci':
-            var bond = loci.bonds[0];
+            const bond = loci.bonds[0];
             return bond ? bondLabel(bond, 'element') : '';
         default:
             return void 0;
@@ -20,7 +19,7 @@ function lociDetails(loci) {
 }
 exports.lociDetails = lociDetails;
 function structureElementStatsDetail(stats) {
-    var chainCount = stats.chainCount, residueCount = stats.residueCount, elementCount = stats.elementCount;
+    const { chainCount, residueCount, elementCount } = stats;
     if (elementCount === 1 && residueCount === 0 && chainCount === 0) {
         return getElementDetails(stats.firstElementLoc, 'element');
     }
@@ -31,10 +30,9 @@ function structureElementStatsDetail(stats) {
         return void 0;
     }
 }
-function getElementDetails(location, granularity) {
-    if (granularity === void 0) { granularity = 'element'; }
-    var basicDetails = {};
-    var entry = location.unit.model.entry;
+function getElementDetails(location, granularity = 'element') {
+    const basicDetails = {};
+    let entry = location.unit.model.entry;
     if (entry.length > 30)
         entry = entry.substr(0, 27) + '\u2026'; // ellipsis
     basicDetails['entry_id'] = entry; // entry
@@ -42,17 +40,17 @@ function getElementDetails(location, granularity) {
         basicDetails['model'] = location.unit.model.modelNum; // model
         basicDetails['instance'] = location.unit.conformation.operator.name; // instance
     }
-    var elementDetails;
+    let elementDetails;
     if (structure_1.Unit.isAtomic(location.unit)) {
         elementDetails = atomicElementDetails(location, granularity);
     }
     else if (structure_1.Unit.isCoarse(location.unit)) {
         elementDetails = coarseElementDetails(location, granularity);
     }
-    return tslib_1.__assign(tslib_1.__assign({}, basicDetails), elementDetails);
+    return { ...basicDetails, ...elementDetails };
 }
 function atomicElementDetails(location, granularity) {
-    var elementDetails = {
+    const elementDetails = {
         entity_id: structure_1.StructureProperties.chain.label_entity_id(location),
         label_asym_id: structure_1.StructureProperties.chain.label_asym_id(location),
         auth_asym_id: structure_1.StructureProperties.chain.auth_asym_id(location),
@@ -65,29 +63,29 @@ function atomicElementDetails(location, granularity) {
         atom_id: [structure_1.StructureProperties.atom.label_atom_id(location)],
         alt_id: structure_1.StructureProperties.atom.label_alt_id(location)
     };
-    var unpLabel = sifts_mapping_1.SIFTSMapping.getLabel(location);
+    const unpLabel = sifts_mapping_1.SIFTSMapping.getLabel(location);
     if (unpLabel) {
-        var unpLabelDetails = unpLabel.split(' ');
+        const unpLabelDetails = unpLabel.split(' ');
         if (unpLabelDetails[0] === 'UNP') {
             elementDetails.unp_accession = unpLabelDetails[1];
             elementDetails.unp_seq_id = +unpLabelDetails[2];
         }
     }
-    var microHetCompIds = structure_1.StructureProperties.residue.microheterogeneityCompIds(location);
+    const microHetCompIds = structure_1.StructureProperties.residue.microheterogeneityCompIds(location);
     elementDetails['micro_het_comp_ids'] = granularity === 'residue' && microHetCompIds.length > 1 ?
         microHetCompIds : [elementDetails['comp_id']];
     return elementDetails;
 }
 function coarseElementDetails(location, granularity) {
-    var elementDetails = {
+    const elementDetails = {
         asym_id: structure_1.StructureProperties.coarse.asym_id(location),
         seq_id_begin: structure_1.StructureProperties.coarse.seq_id_begin(location),
         seq_id_end: structure_1.StructureProperties.coarse.seq_id_end(location)
     };
     if (granularity === 'residue') {
         if (elementDetails.seq_id_begin === elementDetails.seq_id_end) {
-            var entityIndex = structure_1.StructureProperties.coarse.entityKey(location);
-            var seq = location.unit.model.sequence.byEntityKey[entityIndex];
+            const entityIndex = structure_1.StructureProperties.coarse.entityKey(location);
+            const seq = location.unit.model.sequence.byEntityKey[entityIndex];
             elementDetails['comp_id'] = seq.sequence.compId.value(elementDetails.seq_id_begin - 1); // 1-indexed
         }
     }
@@ -101,27 +99,26 @@ function bondLabel(bond, granularity) {
 }
 exports.bondLabel = bondLabel;
 function _bundleLabel(bundle, granularity) {
-    var isSingleElements = true;
-    for (var _i = 0, _a = bundle.loci; _i < _a.length; _i++) {
-        var l = _a[_i];
+    let isSingleElements = true;
+    for (const l of bundle.loci) {
         if (!structure_1.StructureElement.Loci.is(l) || structure_1.StructureElement.Loci.size(l) !== 1) {
             isSingleElements = false;
             break;
         }
     }
     if (isSingleElements) {
-        var locations = bundle.loci.map(function (l) {
-            var _a = l.elements[0], unit = _a.unit, indices = _a.indices;
+        const locations = bundle.loci.map(l => {
+            const { unit, indices } = l.elements[0];
             return structure_1.StructureElement.Location.create(l.structure, unit, unit.elements[int_1.OrderedSet.start(indices)]);
         });
-        var elementDetailsArr = locations.map(function (l) { return getElementDetails(l, granularity); });
-        var atomIds = [elementDetailsArr[0].atom_id[0], elementDetailsArr[1].atom_id[0]];
-        var elementDetails = elementDetailsArr[0];
+        const elementDetailsArr = locations.map(l => getElementDetails(l, granularity));
+        const atomIds = [elementDetailsArr[0].atom_id[0], elementDetailsArr[1].atom_id[0]];
+        const elementDetails = elementDetailsArr[0];
         elementDetails['atom_id'] = atomIds;
         return elementDetails;
     }
     else {
-        var elementDetails = bundle.loci.map(function (l) { return lociDetails(l); });
+        const elementDetails = bundle.loci.map(l => lociDetails(l));
         return elementDetails;
     }
 }

package/lib/sifts-mapping.js

@@ -1,13 +1,12 @@
 "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");
+const db_1 = require("Molstar/mol-data/db");
+const mmcif_1 = require("Molstar/mol-model-formats/structure/mmcif");
+const custom_property_1 = require("Molstar/mol-model/custom-property");
+const 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)({
@@ -15,57 +14,55 @@ var SIFTSMapping;
         }),
         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) }];
-            });
-        }); }
+        getParams: () => ({}),
+        isApplicable: (data) => isAvailable(data),
+        obtain: async (ctx, data) => {
+            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;
+        const { pdbx_sifts_xref_db_name: db_name, pdbx_sifts_xref_db_acc: db_acc, pdbx_sifts_xref_db_num: db_num, pdbx_sifts_xref_db_res: db_res } = model.sourceData.data.db.atom_site;
         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;
+        const model = loc.unit.model;
+        const data = SIFTSMapping.Provider.get(model).value;
         if (!data)
             return '';
-        var rI = model.atomicHierarchy.residueAtomSegments.index[loc.element];
+        const 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;
+        const model = loc.unit.model;
+        const data = SIFTSMapping.Provider.get(model).value;
         if (!data)
             return;
-        var rI = model.atomicHierarchy.residueAtomSegments.index[loc.element];
-        var dbName = data.dbName[rI];
+        const rI = model.atomicHierarchy.residueAtomSegments.index[loc.element];
+        const dbName = data.dbName[rI];
         if (!dbName)
             return;
-        return "".concat(dbName, " ").concat(data.accession[rI], " ").concat(data.num[rI], " ").concat(data.residue[rI]);
+        return `${dbName} ${data.accession[rI]} ${data.num[rI]} ${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;
+        const { pdbx_sifts_xref_db_name: db_name, pdbx_sifts_xref_db_acc: db_acc, pdbx_sifts_xref_db_num: db_num, pdbx_sifts_xref_db_res: db_res } = model.sourceData.data.db.atom_site;
         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 */) {
+        const { atomSourceIndex } = model.atomicHierarchy;
+        const { count, offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
+        const dbName = new Array(count);
+        const accession = new Array(count);
+        const num = new Array(count);
+        const residue = new Array(count);
+        for (let i = 0; i < count; i++) {
+            const row = atomSourceIndex.value(residueOffsets[i]);
+            if (db_name.valueKind(row) !== db_1.Column.ValueKind.Present) {
                 dbName[i] = '';
                 accession[i] = '';
                 num[i] = '';
@@ -77,7 +74,6 @@ var SIFTSMapping;
             num[i] = db_num.value(row);
             residue[i] = db_res.value(row);
         }
-        return { dbName: dbName, accession: accession, num: num, residue: residue };
+        return { dbName, accession, num, residue };
     }
-})(SIFTSMapping || (SIFTSMapping = {}));
-exports.SIFTSMapping = SIFTSMapping;
+})(SIFTSMapping || (exports.SIFTSMapping = SIFTSMapping = {}));

package/lib/sifts-mappings-behaviour.js

@@ -1,64 +1,60 @@
 "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");
+const int_1 = require("Molstar/mol-data/int");
+const sifts_mapping_1 = require("./sifts-mapping");
+const sifts_mapping_2 = require("Molstar/mol-model-props/sequence/themes/sifts-mapping");
+const structure_1 = require("Molstar/mol-model/structure");
+const param_definition_1 = require("Molstar/mol-util/param-definition");
+const 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)
+    ctor: class extends behavior_1.PluginBehavior.Handler {
+        constructor() {
+            super(...arguments);
+            this.provider = sifts_mapping_1.SIFTSMapping.Provider;
+            this.labelProvider = {
+                label: (loci) => {
+                    if (!this.params.showTooltip)
                         return;
                     return PDBeBestDatabaseSequenceMappingLabel(loci);
                 }
             };
-            return _this;
         }
-        class_1.prototype.update = function (p) {
-            var updated = (this.params.autoAttach !== p.autoAttach ||
+        update(p) {
+            const 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 () {
+        }
+        register() {
             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 () {
+        }
+        unregister() {
             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 ({
+        }
+    },
+    params: () => ({
         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)]);
+        const e = loci.elements[0];
+        const u = e.unit;
+        const 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

@@ -8,7 +8,7 @@ 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 = {
+export type InitParams = {
     moleculeId?: string;
     superposition?: boolean;
     pdbeUrl?: string;

package/lib/spec.js

@@ -1,20 +1,42 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DefaultParams = exports.createPluginUI = exports.DefaultPluginUISpec = exports.DefaultPluginSpec = void 0;
-var tslib_1 = require("tslib");
-var React = tslib_1.__importStar(require("react"));
-var ReactDOM = tslib_1.__importStar(require("react-dom"));
-var volume_1 = require("Molstar/mol-plugin-ui/custom/volume");
-var plugin_1 = require("Molstar/mol-plugin-ui/plugin");
-var behavior_1 = require("Molstar/mol-plugin/behavior");
-var transformers_1 = require("Molstar/mol-plugin/behavior/dynamic/volume-streaming/transformers");
-var context_1 = require("Molstar/mol-plugin-ui/context");
-var spec_1 = require("Molstar/mol-plugin/spec");
-var config_1 = require("Molstar/mol-plugin/config");
-var actions_1 = require("Molstar/mol-plugin-state/actions");
-var labels_1 = require("./labels");
-var sifts_mappings_behaviour_1 = require("./sifts-mappings-behaviour");
-var DefaultPluginSpec = function () { return ({
+const React = __importStar(require("react"));
+const ReactDOM = __importStar(require("react-dom"));
+const volume_1 = require("Molstar/mol-plugin-ui/custom/volume");
+const plugin_1 = require("Molstar/mol-plugin-ui/plugin");
+const behavior_1 = require("Molstar/mol-plugin/behavior");
+const transformers_1 = require("Molstar/mol-plugin/behavior/dynamic/volume-streaming/transformers");
+const context_1 = require("Molstar/mol-plugin-ui/context");
+const spec_1 = require("Molstar/mol-plugin/spec");
+const config_1 = require("Molstar/mol-plugin/config");
+const actions_1 = require("Molstar/mol-plugin-state/actions");
+const labels_1 = require("./labels");
+const sifts_mappings_behaviour_1 = require("./sifts-mappings-behaviour");
+const DefaultPluginSpec = () => ({
     actions: [
         spec_1.PluginSpec.Action(actions_1.StateActions.Structure.EnableStructureCustomProps)
     ],
@@ -37,33 +59,23 @@ var DefaultPluginSpec = function () { return ({
     config: [
         [config_1.PluginConfig.VolumeStreaming.DefaultServer, 'https://www.ebi.ac.uk/pdbe/volume-server']
     ]
-}); };
+});
 exports.DefaultPluginSpec = DefaultPluginSpec;
-var DefaultPluginUISpec = function () { return (tslib_1.__assign(tslib_1.__assign({}, (0, exports.DefaultPluginSpec)()), { customParamEditors: [
+const DefaultPluginUISpec = () => ({
+    ...(0, exports.DefaultPluginSpec)(),
+    customParamEditors: [
         [transformers_1.CreateVolumeStreamingBehavior, volume_1.VolumeStreamingCustomControls]
-    ] })); };
+    ],
+});
 exports.DefaultPluginUISpec = DefaultPluginUISpec;
-function createPluginUI(target, spec, options) {
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var ctx;
-        return tslib_1.__generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    ctx = new context_1.PluginUIContext(spec || (0, exports.DefaultPluginUISpec)());
-                    return [4 /*yield*/, ctx.init()];
-                case 1:
-                    _a.sent();
-                    if (!(options === null || options === void 0 ? void 0 : options.onBeforeUIRender)) return [3 /*break*/, 3];
-                    return [4 /*yield*/, options.onBeforeUIRender(ctx)];
-                case 2:
-                    _a.sent();
-                    _a.label = 3;
-                case 3:
-                    ReactDOM.render(React.createElement(plugin_1.Plugin, { plugin: ctx }), target);
-                    return [2 /*return*/, ctx];
-            }
-        });
-    });
+async function createPluginUI(target, spec, options) {
+    const ctx = new context_1.PluginUIContext(spec || (0, exports.DefaultPluginUISpec)());
+    await ctx.init();
+    if (options?.onBeforeUIRender) {
+        await options.onBeforeUIRender(ctx);
+    }
+    ReactDOM.render(React.createElement(plugin_1.Plugin, { plugin: ctx }), target);
+    return ctx;
 }
 exports.createPluginUI = createPluginUI;
 exports.DefaultParams = {

package/lib/structure_contact3d.d.ts

@@ -1,7 +1,7 @@
 import { StateTransformer } from 'molstar/lib/mol-state';
 import { PluginStateObject as SO } from 'molstar/lib/mol-plugin-state/objects';
 export { StructureSelectionsContact3D };
-declare type StructureSelectionsContact3D = typeof StructureSelectionsContact3D;
+type StructureSelectionsContact3D = typeof StructureSelectionsContact3D;
 declare const StructureSelectionsContact3D: StateTransformer<SO.Molecule.Structure.Selections, SO.Shape.Representation3D, import("molstar/lib/mol-util/param-definition").ParamDefinition.Normalize<{
     visuals: ("text" | "cylinder")[];
     unitLabel: string;
@@ -21,7 +21,7 @@ declare const StructureSelectionsContact3D: StateTransformer<SO.Molecule.Structu
     tether: boolean;
     tetherLength: number;
     tetherBaseWidth: number;
-    attachment: "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right";
+    attachment: "middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right";
     fontFamily: import("molstar/lib/mol-geo/geometry/text/font-atlas").FontFamily;
     fontQuality: number;
     fontStyle: import("molstar/lib/mol-geo/geometry/text/font-atlas").FontStyle;
@@ -42,9 +42,15 @@ declare const StructureSelectionsContact3D: StateTransformer<SO.Molecule.Structu
             position: any;
             rotation: any;
             scale: any;
+            transform: any;
         }>[];
     }>;
+    emissive: number;
+    density: number;
     instanceGranularity: boolean;
+    lod: import("molstar/lib/mol-math/linear-algebra").Vec3;
+    cellSize: number;
+    batchSize: number;
     lineSizeAttenuation: boolean;
     linesSize: number;
     dashLength: number;
@@ -53,8 +59,11 @@ declare const StructureSelectionsContact3D: StateTransformer<SO.Molecule.Structu
     sizeAspectRatio: number;
     doubleSided: boolean;
     ignoreLight: boolean;
-    xrayShaded: boolean;
-    transparentBackfaces: string;
+    celShaded: boolean;
+    xrayShaded: boolean | "inverted";
+    transparentBackfaces: "off" | "on" | "opaque";
+    solidInterior: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
+    colorMode: "default" | "interpolate";
 }>>;