pdbe-molstar 3.4.0 → 3.5.0

package/lib/viewer.js

@@ -8,6 +8,8 @@ const behavior_2 = require("molstar/lib/extensions/model-archive/quality-assessm
 const mp4_export_1 = require("molstar/lib/extensions/mp4-export");
 const behavior_3 = require("molstar/lib/extensions/mvs/behavior");
 const custom_tooltips_prop_1 = require("molstar/lib/extensions/mvs/components/custom-tooltips-prop");
+const load_1 = require("molstar/lib/extensions/mvs/load");
+const mvs_data_1 = require("molstar/lib/extensions/mvs/mvs-data");
 const pdbe_1 = require("molstar/lib/extensions/pdbe");
 const loci_1 = require("molstar/lib/mol-model/loci");
 const structure_1 = require("molstar/lib/mol-model/structure");
@@ -42,6 +44,7 @@ const rx_event_helper_1 = require("molstar/lib/mol-util/rx-event-helper");
 const custom_events_1 = require("./custom-events");
 const behavior_4 = require("./domain-annotations/behavior");
 const Foldseek = tslib_1.__importStar(require("./extensions/foldseek"));
+const Interactions = tslib_1.__importStar(require("./extensions/interactions"));
 const behavior_5 = require("./extensions/state-gallery/behavior");
 const manager_1 = require("./extensions/state-gallery/manager");
 const ui_1 = require("./extensions/state-gallery/ui");
@@ -177,8 +180,8 @@ class PDBeMolstarPlugin {
              * If `structureId` or `structureNumber` is provided, use the specified structure (numbered from 1!);
              * otherwise use the last added structure. */
             interactivityFocus: (params) => tslib_1.__awaiter(this, void 0, void 0, function* () {
-                var _b;
-                const structureNumberOrId = (_b = params.structureId) !== null && _b !== void 0 ? _b : params.structureNumber;
+                var _a;
+                const structureNumberOrId = (_a = params.structureId) !== null && _a !== void 0 ? _a : params.structureNumber;
                 const loci = this.getLociForParams(params.data, structureNumberOrId);
                 this.plugin.managers.structure.focus.setFromLoci(loci);
             }),
@@ -187,8 +190,8 @@ class PDBeMolstarPlugin {
              * If `focus`, also zoom on the highlighted part.
              * If `structureId` or `structureNumber` is provided, use the specified structure (numbered from 1!); otherwise use the last added structure. */
             highlight: (params) => tslib_1.__awaiter(this, void 0, void 0, function* () {
-                var _c;
-                const loci = this.getLociForParams(params.data, (_c = params.structureId) !== null && _c !== void 0 ? _c : params.structureNumber);
+                var _a;
+                const loci = this.getLociForParams(params.data, (_a = params.structureId) !== null && _a !== void 0 ? _a : params.structureNumber);
                 if (loci_1.Loci.isEmpty(loci))
                     return;
                 if (params.color) {
@@ -211,17 +214,17 @@ class PDBeMolstarPlugin {
              * If `structureNumber` is provided, apply to the specified structure (numbered from 1!); otherwise apply to all loaded structures.
              * Remove any previously added coloring and extra representations, unless `keepColors` and/or `keepRepresentations` is set. */
             select: (params) => tslib_1.__awaiter(this, void 0, void 0, function* () {
-                var _d, _e, _f, _g;
-                const structureNumberOrId = (_d = params.structureId) !== null && _d !== void 0 ? _d : params.structureNumber;
+                var _a, _b, _c, _d;
+                const structureNumberOrId = (_a = params.structureId) !== null && _a !== void 0 ? _a : params.structureNumber;
                 yield this.visual.clearSelection(structureNumberOrId, { keepColors: params.keepColors, keepRepresentations: params.keepRepresentations });
                 // Structure list to apply selection
                 const structures = this.getStructures(structureNumberOrId);
                 // Filter selection items that apply added representations
                 const addedReprParams = {};
                 for (const param of params.data) {
-                    const repr = (_e = param.representation) !== null && _e !== void 0 ? _e : (param.sideChain ? 'ball-and-stick' : undefined);
+                    const repr = (_b = param.representation) !== null && _b !== void 0 ? _b : (param.sideChain ? 'ball-and-stick' : undefined);
                     if (repr) {
-                        ((_f = addedReprParams[repr]) !== null && _f !== void 0 ? _f : (addedReprParams[repr] = [])).push(param);
+                        ((_c = addedReprParams[repr]) !== null && _c !== void 0 ? _c : (addedReprParams[repr] = [])).push(param);
                     }
                 }
                 const DefaultSelectColor = color_1.Color.fromRgb(255, 112, 3);
@@ -265,7 +268,7 @@ class PDBeMolstarPlugin {
                         yield this.plugin.build()
                             .to(struct.structureRef.cell)
                             .apply(model_1.StructureComponent, { type: { name: 'bundle', params: bundle }, label: repr }, { tags: helpers_1.Tags.AddedComponent })
-                            .apply(representation_1.StructureRepresentation3D, (0, structure_representation_params_1.createStructureRepresentationParams)(this.plugin, (_g = struct.structureRef.cell.obj) === null || _g === void 0 ? void 0 : _g.data, { type: repr }))
+                            .apply(representation_1.StructureRepresentation3D, (0, structure_representation_params_1.createStructureRepresentationParams)(this.plugin, (_d = struct.structureRef.cell.obj) === null || _d === void 0 ? void 0 : _d.data, { type: repr }))
                             .apply(transforms_1.StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, { layers: overpaintLayers }, { tags: helpers_1.Tags.Overpaint })
                             .commit();
                         // Track that reprs have been added (for later clearSelection)
@@ -309,9 +312,9 @@ class PDBeMolstarPlugin {
              * `structureNumber` counts from 1; if not provided, tooltips will be applied to all loaded structures.
              * Example: `await this.visual.tooltips({ data: [{ struct_asym_id: 'A', tooltip: 'Chain A' }, { struct_asym_id: 'B', tooltip: 'Chain B' }] });`. */
             tooltips: (params) => tslib_1.__awaiter(this, void 0, void 0, function* () {
-                var _h;
+                var _a;
                 // Structure list to apply tooltips
-                const structures = this.getStructures((_h = params.structureId) !== null && _h !== void 0 ? _h : params.structureNumber);
+                const structures = this.getStructures((_a = params.structureId) !== null && _a !== void 0 ? _a : params.structureNumber);
                 for (const struct of structures) {
                     const selections = this.getSelections(params.data, struct.number);
                     const customTooltipProps = {
@@ -436,8 +439,8 @@ class PDBeMolstarPlugin {
         return (0, spec_from_html_1.initParamsFromHtmlAttributes)(element);
     }
     render(target, options) {
-        var _a, _b;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             console.debug('Rendering PDBeMolstarPlugin instance with options:', options);
             // Validate options
             if (!options) {
@@ -604,7 +607,7 @@ class PDBeMolstarPlugin {
                         assemblyId: this.initParams.assemblyId,
                         isBinary: dataSource.isBinary,
                         progressMessage: `Loading ${(_b = this.initParams.moleculeId) !== null && _b !== void 0 ? _b : ''} ...`,
-                        id: 'main',
+                        id: PDBeMolstarPlugin.MAIN_STRUCTURE_ID,
                     });
                 }
                 // Subscribe to events from other PDB Component
@@ -658,22 +661,17 @@ class PDBeMolstarPlugin {
         return this.plugin.state.data;
     }
     createLigandStructure(isBranched) {
-        var _a, e_1, _b, _c;
-        var _d, _e;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, e_1, _b, _c;
+            var _d, _e;
             if (this.assemblyRef === '')
                 return;
             try {
-                for (var _f = true, _g = tslib_1.__asyncValues(this.plugin.managers.structure.hierarchy.currentComponentGroups), _h; _h = yield _g.next(), _a = _h.done, !_a;) {
+                for (var _f = true, _g = tslib_1.__asyncValues(this.plugin.managers.structure.hierarchy.currentComponentGroups), _h; _h = yield _g.next(), _a = _h.done, !_a; _f = true) {
                     _c = _h.value;
                     _f = false;
-                    try {
-                        const comp = _c;
-                        yield commands_1.PluginCommands.State.RemoveObject(this.plugin, { state: comp[0].cell.parent, ref: comp[0].cell.transform.ref, removeParentGhosts: true });
-                    }
-                    finally {
-                        _f = true;
-                    }
+                    const comp = _c;
+                    yield commands_1.PluginCommands.State.RemoveObject(this.plugin, { state: comp[0].cell.parent, ref: comp[0].cell.transform.ref, removeParentGhosts: true });
                 }
             }
             catch (e_1_1) { e_1 = { error: e_1_1 }; }
@@ -713,8 +711,8 @@ class PDBeMolstarPlugin {
             }
         });
     }
-    load({ url, format = 'mmcif', isBinary = false, assemblyId = '', progressMessage, id }, fullLoad = true) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+    load(_a) {
+        return tslib_1.__awaiter(this, arguments, void 0, function* ({ url, format = 'mmcif', isBinary = false, assemblyId = '', progressMessage, id }, fullLoad = true) {
             yield (0, helpers_1.runWithProgressMessage)(this.plugin, progressMessage, () => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 var _a, _b;
                 let success = false;
@@ -810,8 +808,8 @@ class PDBeMolstarPlugin {
      * E.g. `styles={polymer:'putty',nonStandard:'ball-and-stick'}` - apply only putty to polymer, only ball-and-stick to non-standard residues, leave other components untouched.
      * E.g. `styles='ball-and-stick'` - apply only ball-and-stick to all components. */
     applyVisualStyles(structureRef, styles) {
-        var _a, _b;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             if (styles === undefined)
                 return;
             const components = this.plugin.state.data.selectQ(q => q.byRef(structureRef).subtree().withTransformer(model_1.StructureComponent));
@@ -850,8 +848,8 @@ class PDBeMolstarPlugin {
     }
     /** Remove all structure components of the given structure which correspond to any component type listed in `deleteComponents`. */
     deleteStructureComponents(structureRef, deleteComponents) {
-        var _a, _b;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             if (deleteComponents.length === 0)
                 return;
             const comps = this.plugin.state.data.selectQ(q => q.byRef(structureRef).subtree().withTransformer(model_1.StructureComponent));
@@ -963,7 +961,10 @@ exports.PDBeMolstarPlugin = PDBeMolstarPlugin;
 /** Helper functions related to specific views or use cases */
 PDBeMolstarPlugin.extensions = {
     Foldseek: Foldseek,
+    Interactions: Interactions,
+    MVS: { MVSData: mvs_data_1.MVSData, loadMVS: load_1.loadMVS },
     StateGallery: behavior_5.StateGalleryExtensionFunctions,
 };
 /** Components for building custom UI layouts */
 PDBeMolstarPlugin.UIComponents = components_1.UIComponents;
+PDBeMolstarPlugin.MAIN_STRUCTURE_ID = 'main';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "pdbe-molstar",
-  "version": "3.4.0",
+  "version": "3.5.0",
   "description": "Molstar implementation for PDBe",
   "main": "index.js",
   "scripts": {
@@ -65,7 +65,7 @@
     "sass": "^1.80.4",
     "sass-loader": "^16.0.2",
     "style-loader": "^4.0.0",
-    "typescript": "^4.6.4",
+    "typescript": "^5.7.3",
     "typescript-eslint": "^8.2.0",
     "webpack": "^5.95.0",
     "webpack-cli": "^5.1.4"
@@ -78,7 +78,7 @@
     "d3-scale": "^4.0.2",
     "d3-selection": "^3.0.0",
     "lit": "^3.1.1",
-    "molstar": "4.8.0",
+    "molstar": "4.17.0",
     "path-browserify": "^1.0.1",
     "stream-browserify": "^3.0.0",
     "vm-browserify": "^1.1.2"