drugflow-molstar 0.4.7 → 0.4.8

package/lib/structure_contact3d.d.ts

@@ -2,64 +2,57 @@ import { StateTransformer } from 'molstar/lib/mol-state';
 import { PluginStateObject as SO } from 'molstar/lib/mol-plugin-state/objects';
 export { 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<{
+declare const StructureSelectionsContact3D: StateTransformer<SO.Molecule.Structure.Selections, SO.Shape.Representation3D, import("Molstar/mol-util/param-definition").ParamDefinition.Normalize<{
     visuals: ("text" | "cylinder")[];
     unitLabel: string;
     borderWidth: number;
     customText: string;
-    textColor: import("molstar/lib/mol-util/color").Color;
+    textColor: import("Molstar/mol-util/color").Color;
     textSize: number;
     sizeFactor: number;
-    borderColor: import("molstar/lib/mol-util/color").Color;
+    borderColor: import("Molstar/mol-util/color").Color;
     offsetX: number;
     offsetY: number;
     offsetZ: number;
     background: boolean;
     backgroundMargin: number;
-    backgroundColor: import("molstar/lib/mol-util/color").Color;
+    backgroundColor: import("Molstar/mol-util/color").Color;
     backgroundOpacity: number;
     tether: boolean;
     tetherLength: number;
     tetherBaseWidth: number;
-    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;
+    attachment: "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right";
+    fontFamily: import("Molstar/mol-geo/geometry/text/font-atlas").FontFamily;
     fontQuality: number;
-    fontStyle: import("molstar/lib/mol-geo/geometry/text/font-atlas").FontStyle;
-    fontVariant: import("molstar/lib/mol-geo/geometry/text/font-atlas").FontVariant;
-    fontWeight: import("molstar/lib/mol-geo/geometry/text/font-atlas").FontWeight;
+    fontStyle: import("Molstar/mol-geo/geometry/text/font-atlas").FontStyle;
+    fontVariant: import("Molstar/mol-geo/geometry/text/font-atlas").FontVariant;
+    fontWeight: import("Molstar/mol-geo/geometry/text/font-atlas").FontWeight;
     alpha: number;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
-    material: import("molstar/lib/mol-util/param-definition").ParamDefinition.Normalize<{
+    material: import("Molstar/mol-util/param-definition").ParamDefinition.Normalize<{
         metalness: number;
         roughness: number;
         bumpiness: number;
     }>;
-    clip: import("molstar/lib/mol-util/param-definition").ParamDefinition.Normalize<{
-        variant: import("molstar/lib/mol-util/clip").Clip.Variant;
-        objects: import("molstar/lib/mol-util/param-definition").ParamDefinition.Normalize<{
+    clip: import("Molstar/mol-util/param-definition").ParamDefinition.Normalize<{
+        variant: import("Molstar/mol-util/clip").Clip.Variant;
+        objects: import("Molstar/mol-util/param-definition").ParamDefinition.Normalize<{
             type: any;
             invert: any;
             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;
     interactionType: string;
-    cylinderColor: import("molstar/lib/mol-util/color").Color;
+    cylinderColor: import("Molstar/mol-util/color").Color;
     sizeAspectRatio: number;
     doubleSided: boolean;
     ignoreLight: boolean;
-    celShaded: boolean;
     xrayShaded: boolean | "inverted";
     transparentBackfaces: "off" | "on" | "opaque";
     solidInterior: boolean;

package/lib/structure_contact3d.js

@@ -1,39 +1,60 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.StructureSelectionsContact3D = void 0;
-const mol_state_1 = require("molstar/lib/mol-state");
-const mol_task_1 = require("molstar/lib/mol-task");
-const objects_1 = require("molstar/lib/mol-plugin-state/objects");
-const helpers_1 = require("molstar/lib/mol-plugin-state/transforms/helpers");
-const contact_1 = require("./contact");
-const StructureSelectionsContact3D = objects_1.PluginStateTransform.BuiltIn({
+var tslib_1 = require("tslib");
+var mol_state_1 = require("molstar/lib/mol-state");
+var mol_task_1 = require("molstar/lib/mol-task");
+var objects_1 = require("molstar/lib/mol-plugin-state/objects");
+var helpers_1 = require("molstar/lib/mol-plugin-state/transforms/helpers");
+var contact_1 = require("./contact");
+var StructureSelectionsContact3D = objects_1.PluginStateTransform.BuiltIn({
     name: 'structure-selections-contact-3d',
     display: '3D Contact',
     from: objects_1.PluginStateObject.Molecule.Structure.Selections,
     to: objects_1.PluginStateObject.Shape.Representation3D,
-    params: () => ({
-        ...contact_1.ContactParams,
-    })
+    params: function () { return (tslib_1.__assign({}, contact_1.ContactParams)); }
 })({
-    canAutoUpdate({ oldParams, newParams }) {
+    canAutoUpdate: function (_a) {
+        var oldParams = _a.oldParams, newParams = _a.newParams;
         return true;
     },
-    apply({ a, params }, plugin) {
-        return mol_task_1.Task.create('Structure Contact', async (ctx) => {
-            const data = (0, helpers_1.getDistanceDataFromStructureSelections)(a.data);
-            const repr = (0, contact_1.ContactRepresentation)({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => contact_1.ContactParams);
-            await repr.createOrUpdate(params, data).runInContext(ctx);
-            return new objects_1.PluginStateObject.Shape.Representation3D({ repr, sourceData: data }, { label: `Contact` });
-        });
+    apply: function (_a, plugin) {
+        var _this = this;
+        var a = _a.a, params = _a.params;
+        return mol_task_1.Task.create('Structure Contact', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            var data, repr;
+            var _a;
+            return tslib_1.__generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        data = (0, helpers_1.getDistanceDataFromStructureSelections)(a.data);
+                        repr = (0, contact_1.ContactRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return contact_1.ContactParams; });
+                        return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
+                    case 1:
+                        _b.sent();
+                        return [2 /*return*/, new objects_1.PluginStateObject.Shape.Representation3D({ repr: repr, sourceData: data }, { label: "Contact" })];
+                }
+            });
+        }); });
     },
-    update({ a, b, oldParams, newParams }, plugin) {
-        return mol_task_1.Task.create('Structure Contact', async (ctx) => {
-            const props = { ...b.data.repr.props, ...newParams };
-            const data = (0, helpers_1.getDistanceDataFromStructureSelections)(a.data);
-            await b.data.repr.createOrUpdate(props, data).runInContext(ctx);
-            b.data.sourceData = data;
-            return mol_state_1.StateTransformer.UpdateResult.Updated;
-        });
+    update: function (_a, plugin) {
+        var _this = this;
+        var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
+        return mol_task_1.Task.create('Structure Contact', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            var props, data;
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
+                        data = (0, helpers_1.getDistanceDataFromStructureSelections)(a.data);
+                        return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
+                    case 1:
+                        _a.sent();
+                        b.data.sourceData = data;
+                        return [2 /*return*/, mol_state_1.StateTransformer.UpdateResult.Updated];
+                }
+            });
+        }); });
     },
 });
 exports.StructureSelectionsContact3D = StructureSelectionsContact3D;

package/lib/subscribe-events.js

@@ -1,17 +1,17 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.subscribeToComponentEvents = void 0;
+exports.subscribeToComponentEvents = subscribeToComponentEvents;
 function subscribeToComponentEvents(wrapperCtx) {
     document.addEventListener('PDB.interactions.click', function (e) {
         if (typeof e.detail !== 'undefined') {
-            const data = e.detail.interacting_nodes ? { data: e.detail.interacting_nodes } : { data: [e.detail.selected_node] };
+            var data = e.detail.interacting_nodes ? { data: e.detail.interacting_nodes } : { data: [e.detail.selected_node] };
             data.data[0]['focus'] = true;
             wrapperCtx.visual.select(data);
         }
     });
     document.addEventListener('PDB.interactions.mouseover', function (e) {
         if (typeof e.detail !== 'undefined') {
-            const data = e.detail.interacting_nodes ? { data: e.detail.interacting_nodes } : { data: [e.detail.selected_node] };
+            var data = e.detail.interacting_nodes ? { data: e.detail.interacting_nodes } : { data: [e.detail.selected_node] };
             wrapperCtx.visual.highlight(data);
         }
     });
@@ -21,7 +21,7 @@ function subscribeToComponentEvents(wrapperCtx) {
     document.addEventListener('PDB.topologyViewer.click', function (e) {
         if (typeof e.eventData !== 'undefined') {
             // Create query object from event data
-            let highlightQuery = {
+            var highlightQuery = {
                 entity_id: e.eventData.entityId,
                 struct_asym_id: e.eventData.structAsymId,
                 start_residue_number: e.eventData.residueNumber,
@@ -38,7 +38,7 @@ function subscribeToComponentEvents(wrapperCtx) {
             // Abort if entryid do not match or viewer type is unipdb
             // if(e.eventData.entryId != scope.pdbId) return;
             // Create query object from event data
-            let highlightQuery = {
+            var highlightQuery = {
                 entity_id: e.eventData.entityId,
                 struct_asym_id: e.eventData.structAsymId,
                 start_residue_number: e.eventData.residueNumber,
@@ -53,7 +53,7 @@ function subscribeToComponentEvents(wrapperCtx) {
     });
     document.addEventListener('protvista-mouseover', function (e) {
         if (typeof e.detail !== 'undefined') {
-            let highlightQuery = undefined;
+            var highlightQuery = undefined;
             // Create query object from event data
             if (e.detail.start && e.detail.end) {
                 highlightQuery = {
@@ -76,8 +76,8 @@ function subscribeToComponentEvents(wrapperCtx) {
     });
     document.addEventListener('protvista-click', function (e) {
         if (typeof e.detail !== 'undefined') {
-            let showInteraction = false;
-            let highlightQuery = undefined;
+            var showInteraction = false;
+            var highlightQuery = undefined;
             // Create query object from event data
             if (e.detail.start && e.detail.end) {
                 highlightQuery = {
@@ -101,7 +101,7 @@ function subscribeToComponentEvents(wrapperCtx) {
                     highlightQuery['sideChain'] = true;
                 }
                 else {
-                    let selColor = undefined;
+                    var selColor = undefined;
                     if (e.detail.trackIndex > -1 && e.detail.feature.locations && e.detail.feature.locations[0].fragments[e.detail.trackIndex].color)
                         selColor = e.detail.feature.locations[0].fragments[e.detail.trackIndex].color;
                     if (typeof selColor == 'undefined' && e.detail.feature.color)
@@ -112,9 +112,9 @@ function subscribeToComponentEvents(wrapperCtx) {
                         selColor = { r: 65, g: 96, b: 91 };
                     }
                     else {
-                        let isRgb = /rgb/g;
+                        var isRgb = /rgb/g;
                         if (isRgb.test(selColor)) {
-                            let rgbArr = selColor.substring(4, selColor.length - 1).split(',');
+                            var rgbArr = selColor.substring(4, selColor.length - 1).split(',');
                             selColor = { r: rgbArr[0], g: rgbArr[1], b: rgbArr[2] };
                         }
                     }
@@ -125,15 +125,15 @@ function subscribeToComponentEvents(wrapperCtx) {
             }
         }
     });
-    const elementTypeArrForRange = ['uniprot', 'pfam', 'cath', 'scop', 'strand', 'helice'];
-    const elementTypeArrForSingle = ['chain', 'quality', 'quality_outlier', 'binding site', 'alternate conformer'];
+    var elementTypeArrForRange = ['uniprot', 'pfam', 'cath', 'scop', 'strand', 'helice'];
+    var elementTypeArrForSingle = ['chain', 'quality', 'quality_outlier', 'binding site', 'alternate conformer'];
     document.addEventListener('PDB.seqViewer.click', function (e) {
         if (typeof e.eventData !== 'undefined') {
             // Abort if entryid and entityid do not match or viewer type is unipdb
             // if(e.eventData.entryId != scope.pdbId) return;
             if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForSingle.indexOf(e.eventData.elementData.elementType) > -1) {
                 // Create query object from event data
-                const highlightQuery = {
+                var highlightQuery = {
                     entity_id: e.eventData.entityId,
                     struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
                     start_residue_number: e.eventData.residueNumber,
@@ -145,9 +145,9 @@ function subscribeToComponentEvents(wrapperCtx) {
                 wrapperCtx.visual.select({ data: [highlightQuery] });
             }
             else if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForRange.indexOf(e.eventData.elementData.elementType) > -1) {
-                const seqColorArray = e.eventData.elementData.color;
+                var seqColorArray = e.eventData.elementData.color;
                 // Create query object from event data
-                const highlightQuery = {
+                var highlightQuery = {
                     entity_id: e.eventData.entityId,
                     struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
                     start_residue_number: e.eventData.elementData.pathData.start.residue_number,
@@ -165,7 +165,7 @@ function subscribeToComponentEvents(wrapperCtx) {
             // if(e.eventData.entryId != scope.pdbId) return;
             if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForSingle.indexOf(e.eventData.elementData.elementType) > -1) {
                 // Create query object from event data
-                let highlightQuery = {
+                var highlightQuery = {
                     entity_id: e.eventData.entityId,
                     struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
                     start_residue_number: e.eventData.residueNumber,
@@ -176,7 +176,7 @@ function subscribeToComponentEvents(wrapperCtx) {
             }
             else if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForRange.indexOf(e.eventData.elementData.elementType) > -1) {
                 // Create query object from event data
-                let highlightQuery = {
+                var highlightQuery = {
                     entity_id: e.eventData.entityId,
                     struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
                     start_residue_number: e.eventData.elementData.pathData.start.residue_number,
@@ -191,4 +191,3 @@ function subscribeToComponentEvents(wrapperCtx) {
         wrapperCtx.visual.clearHighlight();
     });
 }
-exports.subscribeToComponentEvents = subscribeToComponentEvents;

package/lib/superposition-export.js

@@ -1,108 +1,184 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.superpositionExportHierarchy = void 0;
-const utf8_1 = require("Molstar/mol-io/common/utf8");
-const structure_1 = require("Molstar/mol-model/structure");
-const mol_task_1 = require("Molstar/mol-task");
-const date_1 = require("Molstar/mol-util/date");
-const download_1 = require("Molstar/mol-util/download");
-const zip_1 = require("Molstar/mol-util/zip/zip");
-const commands_1 = require("Molstar/mol-plugin/commands");
-async function superpositionExportHierarchy(plugin, options) {
-    try {
-        await plugin.runTask(_superpositionExportHierarchy(plugin, options), { useOverlay: true });
-    }
-    catch (e) {
-        console.error(e);
-        plugin.log.error(`Model export failed. See console for details.`);
-    }
-}
 exports.superpositionExportHierarchy = superpositionExportHierarchy;
-function _superpositionExportHierarchy(plugin, options) {
-    return mol_task_1.Task.create('Export', async (ctx) => {
-        await ctx.update({ message: 'Exporting...', isIndeterminate: true, canAbort: false });
-        const format = options?.format ?? 'cif';
-        //  const { structures } = plugin.managers.structure.hierarchy.current;
-        const customState = plugin.customState;
-        const superpositionState = customState.superpositionState;
-        const segmentIndex = superpositionState.activeSegment - 1;
-        const files = [];
-        const entryMap = new Map();
-        const structures = superpositionState.loadedStructs[segmentIndex].slice();
-        if (superpositionState.alphafold.ref)
-            structures.push(`AF-${customState.initParams.moleculeId}`);
-        for (const molId of structures) {
-            const modelRef = superpositionState.models[molId];
-            if (!modelRef)
-                continue;
-            let isStrHidden = false;
-            const _s = plugin.managers.structure.hierarchy.current.refs.get(modelRef);
-            if (_s.cell.state.isHidden)
-                isStrHidden = true;
-            for (const strComp of _s.components) {
-                if (strComp.cell.state.isHidden)
-                    isStrHidden = true;
-            }
-            if (isStrHidden)
-                continue;
-            const s = _s.transform?.cell.obj?.data ?? _s.cell.obj?.data;
-            if (!s)
-                continue;
-            if (s.models.length > 1) {
-                plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Multimodel exports not supported.`);
-                continue;
-            }
-            if (s.units.some((u) => !structure_1.Unit.isAtomic(u))) {
-                plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Non-atomic model exports not supported.`);
-                continue;
-            }
-            const name = entryMap.has(s.model.entryId)
-                ? `${s.model.entryId}_${entryMap.get(s.model.entryId) + 1}.${format}`
-                : `${s.model.entryId}.${format}`;
-            entryMap.set(s.model.entryId, (entryMap.get(s.model.entryId) ?? 0) + 1);
-            await ctx.update({ message: `Exporting ${s.model.entryId}...`, isIndeterminate: true, canAbort: false });
-            if (s.elementCount > 100000) {
-                // Give UI chance to update, only needed for larger structures.
-                await new Promise(res => setTimeout(res, 50));
-            }
-            try {
-                files.push([name, (0, structure_1.to_mmCIF)(s.model.entryId, s, format === 'bcif', { copyAllCategories: true })]);
+var tslib_1 = require("tslib");
+var utf8_1 = require("Molstar/mol-io/common/utf8");
+var structure_1 = require("Molstar/mol-model/structure");
+var mol_task_1 = require("Molstar/mol-task");
+var date_1 = require("Molstar/mol-util/date");
+var download_1 = require("Molstar/mol-util/download");
+var zip_1 = require("Molstar/mol-util/zip/zip");
+var commands_1 = require("Molstar/mol-plugin/commands");
+function superpositionExportHierarchy(plugin, options) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var e_1;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    _a.trys.push([0, 2, , 3]);
+                    return [4 /*yield*/, plugin.runTask(_superpositionExportHierarchy(plugin, options), { useOverlay: true })];
+                case 1:
+                    _a.sent();
+                    return [3 /*break*/, 3];
+                case 2:
+                    e_1 = _a.sent();
+                    console.error(e_1);
+                    plugin.log.error("Model export failed. See console for details.");
+                    return [3 /*break*/, 3];
+                case 3: return [2 /*return*/];
             }
-            catch (e) {
-                if (format === 'cif' && s.elementCount > 2000000) {
-                    plugin.log.warn(`[Export] The structure might be too big to be exported as Text CIF, consider using the BinaryCIF format instead.`);
-                }
-                throw e;
-            }
-        }
-        if (files.length === 0) {
-            commands_1.PluginCommands.Toast.Show(plugin, {
-                title: 'Export Models',
-                message: 'No visible structure in the 3D view to export!',
-                key: 'superposition-toast-1',
-                timeoutMs: 7000
-            });
-            return;
-        }
-        if (files.length === 1) {
-            (0, download_1.download)(new Blob([files[0][1]]), files[0][0]);
-        }
-        else if (files.length > 1) {
-            const zipData = {};
-            for (const [fn, data] of files) {
-                if (data instanceof Uint8Array) {
-                    zipData[fn] = data;
-                }
-                else {
-                    const bytes = new Uint8Array((0, utf8_1.utf8ByteCount)(data));
-                    (0, utf8_1.utf8Write)(bytes, 0, data);
-                    zipData[fn] = bytes;
-                }
-            }
-            await ctx.update({ message: `Compressing Data...`, isIndeterminate: true, canAbort: false });
-            const buffer = await (0, zip_1.zip)(ctx, zipData);
-            (0, download_1.download)(new Blob([new Uint8Array(buffer, 0, buffer.byteLength)]), `structures_${(0, date_1.getFormattedTime)()}.zip`);
-        }
-        plugin.log.info(`[Export] Done.`);
+        });
     });
 }
+function _superpositionExportHierarchy(plugin, options) {
+    var _this = this;
+    return mol_task_1.Task.create('Export', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var format, customState, superpositionState, segmentIndex, files, entryMap, structures, structures_1, structures_1_1, molId, modelRef, isStrHidden, _s, _a, _b, strComp, s, name_1, e_2_1, zipData, files_1, files_1_1, _c, fn, data, bytes, buffer;
+        var e_2, _d, e_3, _e, e_4, _f;
+        var _g, _h, _j, _k, _l, _m, _o, _p;
+        return tslib_1.__generator(this, function (_q) {
+            switch (_q.label) {
+                case 0: return [4 /*yield*/, ctx.update({ message: 'Exporting...', isIndeterminate: true, canAbort: false })];
+                case 1:
+                    _q.sent();
+                    format = (_g = options === null || options === void 0 ? void 0 : options.format) !== null && _g !== void 0 ? _g : 'cif';
+                    customState = plugin.customState;
+                    superpositionState = customState.superpositionState;
+                    segmentIndex = superpositionState.activeSegment - 1;
+                    files = [];
+                    entryMap = new Map();
+                    structures = superpositionState.loadedStructs[segmentIndex].slice();
+                    if (superpositionState.alphafold.ref)
+                        structures.push("AF-".concat(customState.initParams.moleculeId));
+                    _q.label = 2;
+                case 2:
+                    _q.trys.push([2, 9, 10, 11]);
+                    structures_1 = tslib_1.__values(structures), structures_1_1 = structures_1.next();
+                    _q.label = 3;
+                case 3:
+                    if (!!structures_1_1.done) return [3 /*break*/, 8];
+                    molId = structures_1_1.value;
+                    modelRef = superpositionState.models[molId];
+                    if (!modelRef)
+                        return [3 /*break*/, 7];
+                    isStrHidden = false;
+                    _s = plugin.managers.structure.hierarchy.current.refs.get(modelRef);
+                    if (_s.cell.state.isHidden)
+                        isStrHidden = true;
+                    try {
+                        for (_a = (e_3 = void 0, tslib_1.__values(_s.components)), _b = _a.next(); !_b.done; _b = _a.next()) {
+                            strComp = _b.value;
+                            if (strComp.cell.state.isHidden)
+                                isStrHidden = true;
+                        }
+                    }
+                    catch (e_3_1) { e_3 = { error: e_3_1 }; }
+                    finally {
+                        try {
+                            if (_b && !_b.done && (_e = _a.return)) _e.call(_a);
+                        }
+                        finally { if (e_3) throw e_3.error; }
+                    }
+                    if (isStrHidden)
+                        return [3 /*break*/, 7];
+                    s = (_k = (_j = (_h = _s.transform) === null || _h === void 0 ? void 0 : _h.cell.obj) === null || _j === void 0 ? void 0 : _j.data) !== null && _k !== void 0 ? _k : (_l = _s.cell.obj) === null || _l === void 0 ? void 0 : _l.data;
+                    if (!s)
+                        return [3 /*break*/, 7];
+                    if (s.models.length > 1) {
+                        plugin.log.warn("[Export] Skipping ".concat((_m = _s.cell.obj) === null || _m === void 0 ? void 0 : _m.label, ": Multimodel exports not supported."));
+                        return [3 /*break*/, 7];
+                    }
+                    if (s.units.some(function (u) { return !structure_1.Unit.isAtomic(u); })) {
+                        plugin.log.warn("[Export] Skipping ".concat((_o = _s.cell.obj) === null || _o === void 0 ? void 0 : _o.label, ": Non-atomic model exports not supported."));
+                        return [3 /*break*/, 7];
+                    }
+                    name_1 = entryMap.has(s.model.entryId)
+                        ? "".concat(s.model.entryId, "_").concat(entryMap.get(s.model.entryId) + 1, ".").concat(format)
+                        : "".concat(s.model.entryId, ".").concat(format);
+                    entryMap.set(s.model.entryId, ((_p = entryMap.get(s.model.entryId)) !== null && _p !== void 0 ? _p : 0) + 1);
+                    return [4 /*yield*/, ctx.update({ message: "Exporting ".concat(s.model.entryId, "..."), isIndeterminate: true, canAbort: false })];
+                case 4:
+                    _q.sent();
+                    if (!(s.elementCount > 100000)) return [3 /*break*/, 6];
+                    // Give UI chance to update, only needed for larger structures.
+                    return [4 /*yield*/, new Promise(function (res) { return setTimeout(res, 50); })];
+                case 5:
+                    // Give UI chance to update, only needed for larger structures.
+                    _q.sent();
+                    _q.label = 6;
+                case 6:
+                    try {
+                        files.push([name_1, (0, structure_1.to_mmCIF)(s.model.entryId, s, format === 'bcif', { copyAllCategories: true })]);
+                    }
+                    catch (e) {
+                        if (format === 'cif' && s.elementCount > 2000000) {
+                            plugin.log.warn("[Export] The structure might be too big to be exported as Text CIF, consider using the BinaryCIF format instead.");
+                        }
+                        throw e;
+                    }
+                    _q.label = 7;
+                case 7:
+                    structures_1_1 = structures_1.next();
+                    return [3 /*break*/, 3];
+                case 8: return [3 /*break*/, 11];
+                case 9:
+                    e_2_1 = _q.sent();
+                    e_2 = { error: e_2_1 };
+                    return [3 /*break*/, 11];
+                case 10:
+                    try {
+                        if (structures_1_1 && !structures_1_1.done && (_d = structures_1.return)) _d.call(structures_1);
+                    }
+                    finally { if (e_2) throw e_2.error; }
+                    return [7 /*endfinally*/];
+                case 11:
+                    if (files.length === 0) {
+                        commands_1.PluginCommands.Toast.Show(plugin, {
+                            title: 'Export Models',
+                            message: 'No visible structure in the 3D view to export!',
+                            key: 'superposition-toast-1',
+                            timeoutMs: 7000
+                        });
+                        return [2 /*return*/];
+                    }
+                    if (!(files.length === 1)) return [3 /*break*/, 12];
+                    (0, download_1.download)(new Blob([files[0][1]]), files[0][0]);
+                    return [3 /*break*/, 15];
+                case 12:
+                    if (!(files.length > 1)) return [3 /*break*/, 15];
+                    zipData = {};
+                    try {
+                        for (files_1 = tslib_1.__values(files), files_1_1 = files_1.next(); !files_1_1.done; files_1_1 = files_1.next()) {
+                            _c = tslib_1.__read(files_1_1.value, 2), fn = _c[0], data = _c[1];
+                            if (data instanceof Uint8Array) {
+                                zipData[fn] = data;
+                            }
+                            else {
+                                bytes = new Uint8Array((0, utf8_1.utf8ByteCount)(data));
+                                (0, utf8_1.utf8Write)(bytes, 0, data);
+                                zipData[fn] = bytes;
+                            }
+                        }
+                    }
+                    catch (e_4_1) { e_4 = { error: e_4_1 }; }
+                    finally {
+                        try {
+                            if (files_1_1 && !files_1_1.done && (_f = files_1.return)) _f.call(files_1);
+                        }
+                        finally { if (e_4) throw e_4.error; }
+                    }
+                    return [4 /*yield*/, ctx.update({ message: "Compressing Data...", isIndeterminate: true, canAbort: false })];
+                case 13:
+                    _q.sent();
+                    return [4 /*yield*/, (0, zip_1.zip)(ctx, zipData)];
+                case 14:
+                    buffer = _q.sent();
+                    (0, download_1.download)(new Blob([new Uint8Array(buffer, 0, buffer.byteLength)]), "structures_".concat((0, date_1.getFormattedTime)(), ".zip"));
+                    _q.label = 15;
+                case 15:
+                    plugin.log.info("[Export] Done.");
+                    return [2 /*return*/];
+            }
+        });
+    }); });
+}

package/lib/superposition-focus-representation.d.ts

@@ -4,7 +4,7 @@ import { PluginContext } from 'Molstar/mol-plugin/context';
 declare const SuperpositionFocusRepresentationParams: (plugin: PluginContext) => {
     expandRadius: PD.Numeric;
     surroundingsParams: PD.Group<PD.Normalize<{
-        [x: string]: any;
+        [x: string]: /*elided*/ any;
     }>>;
 };
 type SuperpositionFocusRepresentationProps = PD.ValuesFor<ReturnType<typeof SuperpositionFocusRepresentationParams>>;
@@ -12,5 +12,5 @@ export declare enum SuperpositionFocusRepresentationTags {
     SurrSel = "superposition-focus-surr-sel",
     SurrRepr = "superposition-focus-surr-repr"
 }
-export declare const SuperpositionFocusRepresentation: import("molstar/lib/mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, SuperpositionFocusRepresentationProps>;
+export declare const SuperpositionFocusRepresentation: import("Molstar/mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, SuperpositionFocusRepresentationProps>;
 export {};