drugflow-molstar 0.3.77 → 0.4.1

package/lib/structure_contact3d.js

@@ -1,60 +1,39 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.StructureSelectionsContact3D = void 0;
-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({
+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({
     name: 'structure-selections-contact-3d',
     display: '3D Contact',
     from: objects_1.PluginStateObject.Molecule.Structure.Selections,
     to: objects_1.PluginStateObject.Shape.Representation3D,
-    params: function () { return (tslib_1.__assign({}, contact_1.ContactParams)); }
+    params: () => ({
+        ...contact_1.ContactParams,
+    })
 })({
-    canAutoUpdate: function (_a) {
-        var oldParams = _a.oldParams, newParams = _a.newParams;
+    canAutoUpdate({ oldParams, newParams }) {
         return true;
     },
-    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" })];
-                }
-            });
-        }); });
+    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` });
+        });
     },
-    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];
-                }
-            });
-        }); });
+    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;
+        });
     },
 });
 exports.StructureSelectionsContact3D = StructureSelectionsContact3D;

package/lib/subscribe-events.js

@@ -4,14 +4,14 @@ exports.subscribeToComponentEvents = void 0;
 function subscribeToComponentEvents(wrapperCtx) {
     document.addEventListener('PDB.interactions.click', function (e) {
         if (typeof e.detail !== 'undefined') {
-            var data = e.detail.interacting_nodes ? { data: e.detail.interacting_nodes } : { data: [e.detail.selected_node] };
+            const 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') {
-            var data = e.detail.interacting_nodes ? { data: e.detail.interacting_nodes } : { data: [e.detail.selected_node] };
+            const 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
-            var highlightQuery = {
+            let 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
-            var highlightQuery = {
+            let 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') {
-            var highlightQuery = undefined;
+            let 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') {
-            var showInteraction = false;
-            var highlightQuery = undefined;
+            let showInteraction = false;
+            let 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 {
-                    var selColor = undefined;
+                    let 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 {
-                        var isRgb = /rgb/g;
+                        let isRgb = /rgb/g;
                         if (isRgb.test(selColor)) {
-                            var rgbArr = selColor.substring(4, selColor.length - 1).split(',');
+                            let 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) {
             }
         }
     });
-    var elementTypeArrForRange = ['uniprot', 'pfam', 'cath', 'scop', 'strand', 'helice'];
-    var elementTypeArrForSingle = ['chain', 'quality', 'quality_outlier', 'binding site', 'alternate conformer'];
+    const elementTypeArrForRange = ['uniprot', 'pfam', 'cath', 'scop', 'strand', 'helice'];
+    const 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
-                var highlightQuery = {
+                const 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) {
-                var seqColorArray = e.eventData.elementData.color;
+                const seqColorArray = e.eventData.elementData.color;
                 // Create query object from event data
-                var highlightQuery = {
+                const 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
-                var highlightQuery = {
+                let 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
-                var highlightQuery = {
+                let 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,

package/lib/superposition-export.js

@@ -1,152 +1,108 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.superpositionExportHierarchy = void 0;
-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*/];
-            }
-        });
-    });
+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) {
-    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, _i, structures_1, molId, modelRef, isStrHidden, _s, _a, _b, strComp, s, name_1, zipData, _c, files_1, _d, fn, data, bytes, buffer;
-        var _e, _f, _g, _h, _j, _k, _l, _m;
-        return tslib_1.__generator(this, function (_o) {
-            switch (_o.label) {
-                case 0: return [4 /*yield*/, ctx.update({ message: 'Exporting...', isIndeterminate: true, canAbort: false })];
-                case 1:
-                    _o.sent();
-                    format = (_e = options === null || options === void 0 ? void 0 : options.format) !== null && _e !== void 0 ? _e : '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));
-                    _i = 0, structures_1 = structures;
-                    _o.label = 2;
-                case 2:
-                    if (!(_i < structures_1.length)) return [3 /*break*/, 7];
-                    molId = structures_1[_i];
-                    modelRef = superpositionState.models[molId];
-                    if (!modelRef)
-                        return [3 /*break*/, 6];
-                    isStrHidden = false;
-                    _s = plugin.managers.structure.hierarchy.current.refs.get(modelRef);
-                    if (_s.cell.state.isHidden)
-                        isStrHidden = true;
-                    for (_a = 0, _b = _s.components; _a < _b.length; _a++) {
-                        strComp = _b[_a];
-                        if (strComp.cell.state.isHidden)
-                            isStrHidden = true;
-                    }
-                    if (isStrHidden)
-                        return [3 /*break*/, 6];
-                    s = (_h = (_g = (_f = _s.transform) === null || _f === void 0 ? void 0 : _f.cell.obj) === null || _g === void 0 ? void 0 : _g.data) !== null && _h !== void 0 ? _h : (_j = _s.cell.obj) === null || _j === void 0 ? void 0 : _j.data;
-                    if (!s)
-                        return [3 /*break*/, 6];
-                    if (s.models.length > 1) {
-                        plugin.log.warn("[Export] Skipping ".concat((_k = _s.cell.obj) === null || _k === void 0 ? void 0 : _k.label, ": Multimodel exports not supported."));
-                        return [3 /*break*/, 6];
-                    }
-                    if (s.units.some(function (u) { return !structure_1.Unit.isAtomic(u); })) {
-                        plugin.log.warn("[Export] Skipping ".concat((_l = _s.cell.obj) === null || _l === void 0 ? void 0 : _l.label, ": Non-atomic model exports not supported."));
-                        return [3 /*break*/, 6];
-                    }
-                    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, ((_m = entryMap.get(s.model.entryId)) !== null && _m !== void 0 ? _m : 0) + 1);
-                    return [4 /*yield*/, ctx.update({ message: "Exporting ".concat(s.model.entryId, "..."), isIndeterminate: true, canAbort: false })];
-                case 3:
-                    _o.sent();
-                    if (!(s.elementCount > 100000)) return [3 /*break*/, 5];
-                    // Give UI chance to update, only needed for larger structures.
-                    return [4 /*yield*/, new Promise(function (res) { return setTimeout(res, 50); })];
-                case 4:
-                    // Give UI chance to update, only needed for larger structures.
-                    _o.sent();
-                    _o.label = 5;
-                case 5:
-                    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;
-                    }
-                    _o.label = 6;
-                case 6:
-                    _i++;
-                    return [3 /*break*/, 2];
-                case 7:
-                    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*/, 8];
-                    (0, download_1.download)(new Blob([files[0][1]]), files[0][0]);
-                    return [3 /*break*/, 11];
-                case 8:
-                    if (!(files.length > 1)) return [3 /*break*/, 11];
-                    zipData = {};
-                    for (_c = 0, files_1 = files; _c < files_1.length; _c++) {
-                        _d = files_1[_c], fn = _d[0], data = _d[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;
-                        }
-                    }
-                    return [4 /*yield*/, ctx.update({ message: "Compressing Data...", isIndeterminate: true, canAbort: false })];
-                case 9:
-                    _o.sent();
-                    return [4 /*yield*/, (0, zip_1.zip)(ctx, zipData)];
-                case 10:
-                    buffer = _o.sent();
-                    (0, download_1.download)(new Blob([new Uint8Array(buffer, 0, buffer.byteLength)]), "structures_".concat((0, date_1.getFormattedTime)(), ".zip"));
-                    _o.label = 11;
-                case 11:
-                    plugin.log.info("[Export] Done.");
-                    return [2 /*return*/];
+    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 ${s.model.entryId}...`, isIndeterminate: true, canAbort: false });
+            if (s.elementCount > 100000) {
+                // Give UI chance to update, only needed for larger structures.
+                await new Promise(res => setTimeout(res, 50));
             }
-        });
-    }); });
+            try {
+                files.push([name, (0, structure_1.to_mmCIF)(s.model.entryId, s, format === 'bcif', { copyAllCategories: true })]);
+            }
+            catch (e) {
+                if (format === 'cif' && s.elementCount > 2000000) {
+                    plugin.log.warn(`[Export] The structure might be too big to be exported as Text CIF, consider using the BinaryCIF format instead.`);
+                }
+                throw e;
+            }
+        }
+        if (files.length === 0) {
+            commands_1.PluginCommands.Toast.Show(plugin, {
+                title: 'Export Models',
+                message: 'No visible structure in the 3D view to export!',
+                key: 'superposition-toast-1',
+                timeoutMs: 7000
+            });
+            return;
+        }
+        if (files.length === 1) {
+            (0, download_1.download)(new Blob([files[0][1]]), files[0][0]);
+        }
+        else if (files.length > 1) {
+            const zipData = {};
+            for (const [fn, data] of files) {
+                if (data instanceof Uint8Array) {
+                    zipData[fn] = data;
+                }
+                else {
+                    const bytes = new Uint8Array((0, utf8_1.utf8ByteCount)(data));
+                    (0, utf8_1.utf8Write)(bytes, 0, data);
+                    zipData[fn] = bytes;
+                }
+            }
+            await ctx.update({ message: `Compressing Data...`, isIndeterminate: true, canAbort: false });
+            const buffer = await (0, zip_1.zip)(ctx, zipData);
+            (0, download_1.download)(new Blob([new Uint8Array(buffer, 0, buffer.byteLength)]), `structures_${(0, date_1.getFormattedTime)()}.zip`);
+        }
+        plugin.log.info(`[Export] Done.`);
+    });
 }

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

@@ -7,7 +7,7 @@ declare const SuperpositionFocusRepresentationParams: (plugin: PluginContext) =>
         [x: string]: any;
     }>>;
 };
-declare type SuperpositionFocusRepresentationProps = PD.ValuesFor<ReturnType<typeof SuperpositionFocusRepresentationParams>>;
+type SuperpositionFocusRepresentationProps = PD.ValuesFor<ReturnType<typeof SuperpositionFocusRepresentationParams>>;
 export declare enum SuperpositionFocusRepresentationTags {
     SurrSel = "superposition-focus-surr-sel",
     SurrRepr = "superposition-focus-surr-repr"