drugflow-molstar 0.3.77 → 0.4.1

package/lib/superposition.js

@@ -1,25 +1,24 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderSuperposition = exports.superposeAf = exports.loadAfStructure = exports.initSuperposition = void 0;
-var tslib_1 = require("tslib");
-var linear_algebra_1 = require("Molstar/mol-math/linear-algebra");
-var builder_1 = require("Molstar/mol-script/language/builder");
-var mol_state_1 = require("Molstar/mol-state");
-var transforms_1 = require("Molstar/mol-plugin-state/transforms");
-var assets_1 = require("Molstar/mol-util/assets");
-var helpers_1 = require("./helpers");
-var lists_1 = require("Molstar/mol-util/color/lists");
-var color_1 = require("Molstar/mol-util/color/color");
-var script_1 = require("Molstar/mol-script/script");
-var mol_task_1 = require("Molstar/mol-task");
-var superposition_sifts_mapping_1 = require("./superposition-sifts-mapping");
-var alphafold_transparency_1 = require("./alphafold-transparency");
-var structure_1 = require("Molstar/mol-model/structure");
+const linear_algebra_1 = require("Molstar/mol-math/linear-algebra");
+const builder_1 = require("Molstar/mol-script/language/builder");
+const mol_state_1 = require("Molstar/mol-state");
+const transforms_1 = require("Molstar/mol-plugin-state/transforms");
+const assets_1 = require("Molstar/mol-util/assets");
+const helpers_1 = require("./helpers");
+const lists_1 = require("Molstar/mol-util/color/lists");
+const color_1 = require("Molstar/mol-util/color/color");
+const script_1 = require("Molstar/mol-script/script");
+const mol_task_1 = require("Molstar/mol-task");
+const superposition_sifts_mapping_1 = require("./superposition-sifts-mapping");
+const alphafold_transparency_1 = require("./alphafold-transparency");
+const structure_1 = require("Molstar/mol-model/structure");
 function getRandomColor(plugin, segmentIndex) {
-    var clList = lists_1.ColorLists;
-    var spState = plugin.customState.superpositionState;
-    var palleteIndex = spState.colorState[segmentIndex].palleteIndex;
-    var colorIndex = spState.colorState[segmentIndex].colorIndex;
+    const clList = lists_1.ColorLists;
+    const spState = plugin.customState.superpositionState;
+    let palleteIndex = spState.colorState[segmentIndex].palleteIndex;
+    let colorIndex = spState.colorState[segmentIndex].colorIndex;
     if (clList[spState.colorPalette[palleteIndex]].list[colorIndex + 1]) {
         colorIndex += 1;
     }
@@ -27,598 +26,418 @@ function getRandomColor(plugin, segmentIndex) {
         colorIndex = 0;
         palleteIndex = spState.colorPalette[palleteIndex + 1] ? palleteIndex + 1 : 0;
     }
-    var palleteName = spState.colorPalette[palleteIndex];
+    const palleteName = spState.colorPalette[palleteIndex];
     plugin.customState.superpositionState.colorState[segmentIndex].palleteIndex = palleteIndex;
     plugin.customState.superpositionState.colorState[segmentIndex].colorIndex = colorIndex;
     return clList[palleteName].list[colorIndex];
 }
-function initSuperposition(plugin) {
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var customState, superpositionParams, segmentData, afStrUrls, segmentIndex, clusterIndexs, entryList, clusters;
-        return tslib_1.__generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, plugin.clear()];
-                case 1:
-                    _a.sent();
-                    customState = plugin.customState;
-                    superpositionParams = customState.initParams.superpositionParams;
-                    plugin.customState.superpositionState = {
-                        models: {},
-                        entries: {},
-                        refMaps: {},
-                        segmentData: void 0,
-                        matrixData: {},
-                        activeSegment: 0,
-                        loadedStructs: [],
-                        visibleRefs: [],
-                        invalidStruct: [],
-                        noMatrixStruct: [],
-                        hets: {},
-                        colorPalette: ['dark-2', 'red-yellow-green', 'paired', 'set-1', 'accent', 'set-2', 'rainbow'],
-                        colorState: [],
-                        alphafold: {
-                            apiData: {
-                                cif: '',
-                                pae: '',
-                                length: 0
-                            },
-                            length: 0,
-                            ref: '',
-                            traceOnly: true,
-                            visibility: [],
-                            transforms: [],
-                            rmsds: [],
-                            coordinateSystems: []
-                        }
-                    };
-                    // Get segment and cluster information for the given uniprot accession
-                    return [4 /*yield*/, getSegmentData(plugin)];
-                case 2:
-                    // Get segment and cluster information for the given uniprot accession
-                    _a.sent();
-                    segmentData = plugin.customState.superpositionState.segmentData;
-                    if (!segmentData)
-                        return [2 /*return*/];
-                    // Load Matrix Data
-                    return [4 /*yield*/, getMatrixData(plugin)];
-                case 3:
-                    // Load Matrix Data
-                    _a.sent();
-                    if (!plugin.customState.superpositionState.segmentData)
-                        return [2 /*return*/];
-                    return [4 /*yield*/, getAfUrl(plugin, customState.initParams.moleculeId)];
-                case 4:
-                    afStrUrls = _a.sent();
-                    if (afStrUrls)
-                        customState.superpositionState.alphafold.apiData = afStrUrls;
-                    segmentData.forEach(function () {
-                        plugin.customState.superpositionState.loadedStructs.push([]);
-                        plugin.customState.superpositionState.visibleRefs.push([]);
-                        plugin.customState.superpositionState.colorState.push({ palleteIndex: 0, colorIndex: -1 });
-                    });
-                    segmentIndex = (superpositionParams && superpositionParams.segment) ? superpositionParams.segment - 1 : 0;
-                    plugin.customState.superpositionState.activeSegment = segmentIndex + 1;
-                    clusterIndexs = (superpositionParams && superpositionParams.cluster) ? superpositionParams.cluster : void 0;
-                    // Emit segment API data load event
-                    plugin.customState.events.superpositionInit.next(true);
-                    entryList = [];
-                    clusters = segmentData[segmentIndex].clusters;
-                    clusters.forEach(function (cluster, clusterIndex) {
-                        // Validate for cluster index if provided in superPositionParams
-                        if (clusterIndexs && clusterIndexs.indexOf(clusterIndex) === -1)
-                            return;
-                        // Add respresentative structure to the list
-                        if (superpositionParams && superpositionParams.superposeAll) {
-                            entryList = entryList.concat(cluster);
-                        }
-                        else {
-                            entryList.push(cluster[0]);
-                        }
-                    });
-                    return [4 /*yield*/, renderSuperposition(plugin, segmentIndex, entryList)];
-                case 5:
-                    _a.sent();
-                    return [2 /*return*/];
-            }
-        });
+async function initSuperposition(plugin) {
+    await plugin.clear();
+    const customState = plugin.customState;
+    const superpositionParams = customState.initParams.superpositionParams;
+    plugin.customState.superpositionState = {
+        models: {},
+        entries: {},
+        refMaps: {},
+        segmentData: void 0,
+        matrixData: {},
+        activeSegment: 0,
+        loadedStructs: [],
+        visibleRefs: [],
+        invalidStruct: [],
+        noMatrixStruct: [],
+        hets: {},
+        colorPalette: ['dark-2', 'red-yellow-green', 'paired', 'set-1', 'accent', 'set-2', 'rainbow'],
+        colorState: [],
+        alphafold: {
+            apiData: {
+                cif: '',
+                pae: '',
+                length: 0
+            },
+            length: 0,
+            ref: '',
+            traceOnly: true,
+            visibility: [],
+            transforms: [],
+            rmsds: [],
+            coordinateSystems: []
+        }
+    };
+    // Get segment and cluster information for the given uniprot accession
+    await getSegmentData(plugin);
+    const segmentData = plugin.customState.superpositionState.segmentData;
+    if (!segmentData)
+        return;
+    // Load Matrix Data
+    await getMatrixData(plugin);
+    if (!plugin.customState.superpositionState.segmentData)
+        return;
+    const afStrUrls = await getAfUrl(plugin, customState.initParams.moleculeId);
+    if (afStrUrls)
+        customState.superpositionState.alphafold.apiData = afStrUrls;
+    segmentData.forEach(() => {
+        plugin.customState.superpositionState.loadedStructs.push([]);
+        plugin.customState.superpositionState.visibleRefs.push([]);
+        plugin.customState.superpositionState.colorState.push({ palleteIndex: 0, colorIndex: -1 });
+    });
+    // Set segment and cluster details from superPositionParams
+    const segmentIndex = (superpositionParams && superpositionParams.segment) ? superpositionParams.segment - 1 : 0;
+    plugin.customState.superpositionState.activeSegment = segmentIndex + 1;
+    const clusterIndexs = (superpositionParams && superpositionParams.cluster) ? superpositionParams.cluster : void 0;
+    // Emit segment API data load event
+    plugin.customState.events.superpositionInit.next(true);
+    // Get entry list to load matrix data
+    let entryList = [];
+    const clusters = segmentData[segmentIndex].clusters;
+    clusters.forEach((cluster, clusterIndex) => {
+        // Validate for cluster index if provided in superPositionParams
+        if (clusterIndexs && clusterIndexs.indexOf(clusterIndex) === -1)
+            return;
+        // Add respresentative structure to the list
+        if (superpositionParams && superpositionParams.superposeAll) {
+            entryList = entryList.concat(cluster);
+        }
+        else {
+            entryList.push(cluster[0]);
+        }
     });
+    await renderSuperposition(plugin, segmentIndex, entryList);
 }
 exports.initSuperposition = initSuperposition;
 function createCarbVisLabel(carbLigNamesAndCount) {
-    var compList = [];
-    for (var carbCompId in carbLigNamesAndCount) {
-        compList.push("".concat(carbCompId, " (").concat(carbLigNamesAndCount[carbCompId], ")"));
+    const compList = [];
+    for (const carbCompId in carbLigNamesAndCount) {
+        compList.push(`${carbCompId} (${carbLigNamesAndCount[carbCompId]})`);
     }
     return compList.join(', ');
 }
-function getAfUrl(plugin, accession) {
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var apiResponse, apiData;
-        var _this = this;
-        return tslib_1.__generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Get AlphaFold URL', function (ctx) { 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.fetch({ url: "https://alphafold.ebi.ac.uk/api/prediction/".concat(accession), type: 'json' }).runInContext(ctx)];
-                                case 1:
-                                    apiResponse = _a.sent();
-                                    if (apiResponse && (apiResponse === null || apiResponse === void 0 ? void 0 : apiResponse[0].bcifUrl)) {
-                                        apiData = {
-                                            cif: apiResponse === null || apiResponse === void 0 ? void 0 : apiResponse[0].cifUrl,
-                                            pae: apiResponse === null || apiResponse === void 0 ? void 0 : apiResponse[0].paeImageUrl,
-                                            length: apiResponse === null || apiResponse === void 0 ? void 0 : apiResponse[0].uniprotEnd
-                                        };
-                                    }
-                                    return [3 /*break*/, 3];
-                                case 2:
-                                    e_1 = _a.sent();
-                                    return [3 /*break*/, 3];
-                                case 3: return [2 /*return*/];
-                            }
-                        });
-                    }); }))];
-                case 1:
-                    _a.sent();
-                    return [2 /*return*/, apiData];
+async function getAfUrl(plugin, accession) {
+    let apiResponse;
+    let apiData;
+    await plugin.runTask(mol_task_1.Task.create('Get AlphaFold URL', async (ctx) => {
+        try {
+            apiResponse = await plugin.fetch({ url: `https://alphafold.ebi.ac.uk/api/prediction/${accession}`, type: 'json' }).runInContext(ctx);
+            if (apiResponse && apiResponse?.[0].bcifUrl) {
+                apiData = {
+                    cif: apiResponse?.[0].cifUrl,
+                    pae: apiResponse?.[0].paeImageUrl,
+                    length: apiResponse?.[0].uniprotEnd
+                };
             }
-        });
-    });
+        }
+        catch (e) {
+            // console.warn(e);
+        }
+    }));
+    return apiData;
 }
-function loadAfStructure(plugin) {
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var customState, structure, strInstance, spState, chainSel;
-        return tslib_1.__generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    customState = plugin.customState;
-                    return [4 /*yield*/, loadStructure(plugin, customState.superpositionState.alphafold.apiData.cif, 'mmcif', false)];
-                case 1:
-                    structure = (_a.sent()).structure;
-                    strInstance = structure;
-                    if (!strInstance)
-                        return [2 /*return*/, false];
-                    spState = plugin.customState.superpositionState;
-                    spState.alphafold.ref = strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref;
-                    spState.models["AF-".concat(customState.initParams.moleculeId)] = strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref;
-                    return [4 /*yield*/, plugin.builders.structure.tryCreateComponentStatic(strInstance, 'polymer', { label: "AlphaFold Structure", tags: ["alphafold-chain", "superposition-sel"] })];
-                case 2:
-                    chainSel = _a.sent();
-                    if (!chainSel) return [3 /*break*/, 4];
-                    return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'plddt-confidence', size: 'uniform', sizeParams: { value: 1.5 } }, { tag: "af-superposition-visual" })];
-                case 3:
-                    _a.sent();
-                    return [2 /*return*/, strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref];
-                case 4: return [2 /*return*/, false];
-            }
-        });
-    });
+async function loadAfStructure(plugin) {
+    const customState = plugin.customState;
+    const { structure } = await loadStructure(plugin, customState.superpositionState.alphafold.apiData.cif, 'mmcif', false);
+    const strInstance = structure;
+    if (!strInstance)
+        return false;
+    // Store Refs in state
+    const spState = plugin.customState.superpositionState;
+    spState.alphafold.ref = strInstance?.ref;
+    spState.models[`AF-${customState.initParams.moleculeId}`] = strInstance?.ref;
+    const chainSel = await plugin.builders.structure.tryCreateComponentStatic(strInstance, 'polymer', { label: `AlphaFold Structure`, tags: [`alphafold-chain`, `superposition-sel`] });
+    if (chainSel) {
+        await plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'plddt-confidence', size: 'uniform', sizeParams: { value: 1.5 } }, { tag: `af-superposition-visual` });
+        return strInstance?.ref;
+    }
+    return false;
 }
 exports.loadAfStructure = loadAfStructure;
-function superposeAf(plugin, traceOnly, segmentIndex) {
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var customState, spState, afStrRef, _a, afStr, segmentNum, mappingResult_1, coordinateSystems_1, failedPairsResult_1, zeroOverlapPairsResult_1, minRmsd_1, minIndex_1, rmsdList_1, segmentClusters;
-        return tslib_1.__generator(this, function (_b) {
-            switch (_b.label) {
-                case 0:
-                    customState = plugin.customState;
-                    if (!customState.superpositionState || !customState.superpositionState.segmentData)
-                        return [2 /*return*/];
-                    spState = customState.superpositionState;
-                    _a = spState.alphafold.ref;
-                    if (_a) return [3 /*break*/, 2];
-                    return [4 /*yield*/, loadAfStructure(plugin)];
-                case 1:
-                    _a = (_b.sent());
-                    _b.label = 2;
-                case 2:
-                    afStrRef = _a;
-                    if (!afStrRef)
-                        return [2 /*return*/];
-                    afStr = plugin.managers.structure.hierarchy.current.refs.get(afStrRef);
-                    segmentNum = segmentIndex ? segmentIndex : spState.activeSegment - 1;
-                    if (!spState.alphafold.transforms[segmentNum]) {
-                        mappingResult_1 = [];
-                        coordinateSystems_1 = [];
-                        failedPairsResult_1 = [];
-                        zeroOverlapPairsResult_1 = [];
-                        minRmsd_1 = 0;
-                        minIndex_1 = 0;
-                        rmsdList_1 = [];
-                        segmentClusters = spState.segmentData[segmentNum].clusters;
-                        segmentClusters.forEach(function (cluster) {
-                            var _a, _b, _c;
-                            var modelRef = spState.models["".concat(cluster[0].pdb_id, "_").concat(cluster[0].struct_asym_id)];
-                            if (modelRef) {
-                                var structHierarchy = plugin.managers.structure.hierarchy.current.refs.get(modelRef);
-                                if (structHierarchy) {
-                                    var input = [structHierarchy.components[0], afStr];
-                                    var structures = input.map(function (s) { var _a; return (_a = s.cell.obj) === null || _a === void 0 ? void 0 : _a.data; });
-                                    var _d = (0, superposition_sifts_mapping_1.alignAndSuperposeWithSIFTSMapping)(structures, { traceOnly: traceOnly, includeResidueTest: function (loc) { return structure_1.StructureProperties.atom.B_iso_or_equiv(loc) > 70; },
-                                        applyTestIndex: [1] }), entries = _d.entries, failedPairs = _d.failedPairs, zeroOverlapPairs = _d.zeroOverlapPairs;
-                                    if (entries.length === 0 || (entries && entries[0] && entries[0].transform.rmsd.toFixed(1) === '0.0')) {
-                                        var alignWithoutPlddt = (0, superposition_sifts_mapping_1.alignAndSuperposeWithSIFTSMapping)(structures, { traceOnly: traceOnly });
-                                        entries = alignWithoutPlddt.entries;
-                                    }
-                                    if (entries && entries[0]) {
-                                        mappingResult_1.push(entries[0]);
-                                        coordinateSystems_1.push((_c = (_b = (_a = input[0]) === null || _a === void 0 ? void 0 : _a.transform) === null || _b === void 0 ? void 0 : _b.cell.obj) === null || _c === void 0 ? void 0 : _c.data.coordinateSystem);
-                                        var totalMappings = mappingResult_1.length;
-                                        if (totalMappings === 1 || entries[0].transform.rmsd < minRmsd_1) {
-                                            minRmsd_1 = entries[0].transform.rmsd;
-                                            minIndex_1 = totalMappings === 1 ? 0 : mappingResult_1.length - 1;
-                                        }
-                                        rmsdList_1.push("".concat(cluster[0].pdb_id, " chain ").concat(cluster[0].struct_asym_id, ":").concat(entries[0].transform.rmsd.toFixed(2)));
-                                    }
-                                    else {
-                                        if (failedPairs.length > 0)
-                                            failedPairsResult_1.push(failedPairs);
-                                        if (zeroOverlapPairs.length > 0)
-                                            zeroOverlapPairsResult_1.push(zeroOverlapPairs);
-                                        // rmsdList.push(`${cluster[0].pdb_id} ${cluster[0].struct_asym_id}:-`)
-                                    }
-                                }
-                            }
-                        });
-                        // console.log(failedPairsResult);
-                        // console.log(zeroOverlapPairsResult);
-                        if (mappingResult_1.length > 0) {
-                            spState.alphafold.visibility[segmentNum] = true;
-                            spState.alphafold.transforms[segmentNum] = mappingResult_1[minIndex_1].transform.bTransform;
-                            spState.alphafold.coordinateSystems[segmentNum] = coordinateSystems_1[minIndex_1];
-                            spState.alphafold.rmsds[segmentNum] = rmsdList_1.sort(function (a, b) { return parseFloat(a.split(':')[1]) - parseFloat(b.split(':')[1]); });
+async function superposeAf(plugin, traceOnly, segmentIndex) {
+    const customState = plugin.customState;
+    if (!customState.superpositionState || !customState.superpositionState.segmentData)
+        return;
+    const spState = customState.superpositionState;
+    // Load AF structure
+    const afStrRef = spState.alphafold.ref || await loadAfStructure(plugin);
+    if (!afStrRef)
+        return;
+    const afStr = plugin.managers.structure.hierarchy.current.refs.get(afStrRef);
+    const segmentNum = segmentIndex ? segmentIndex : spState.activeSegment - 1;
+    if (!spState.alphafold.transforms[segmentNum]) {
+        // Create representative list
+        const mappingResult = [];
+        const coordinateSystems = [];
+        const failedPairsResult = [];
+        const zeroOverlapPairsResult = [];
+        let minRmsd = 0;
+        let minIndex = 0;
+        let rmsdList = [];
+        const segmentClusters = spState.segmentData[segmentNum].clusters;
+        segmentClusters.forEach((cluster) => {
+            const modelRef = spState.models[`${cluster[0].pdb_id}_${cluster[0].struct_asym_id}`];
+            if (modelRef) {
+                const structHierarchy = plugin.managers.structure.hierarchy.current.refs.get(modelRef);
+                if (structHierarchy) {
+                    const input = [structHierarchy.components[0], afStr];
+                    const structures = input.map(s => s.cell.obj?.data);
+                    let { entries, failedPairs, zeroOverlapPairs } = (0, superposition_sifts_mapping_1.alignAndSuperposeWithSIFTSMapping)(structures, { traceOnly,
+                        includeResidueTest: loc => structure_1.StructureProperties.atom.B_iso_or_equiv(loc) > 70,
+                        applyTestIndex: [1]
+                    });
+                    if (entries.length === 0 || (entries && entries[0] && entries[0].transform.rmsd.toFixed(1) === '0.0')) {
+                        const alignWithoutPlddt = (0, superposition_sifts_mapping_1.alignAndSuperposeWithSIFTSMapping)(structures, { traceOnly });
+                        entries = alignWithoutPlddt.entries;
+                    }
+                    if (entries && entries[0]) {
+                        mappingResult.push(entries[0]);
+                        coordinateSystems.push(input[0]?.transform?.cell.obj?.data.coordinateSystem);
+                        const totalMappings = mappingResult.length;
+                        if (totalMappings === 1 || entries[0].transform.rmsd < minRmsd) {
+                            minRmsd = entries[0].transform.rmsd;
+                            minIndex = totalMappings === 1 ? 0 : mappingResult.length - 1;
                         }
+                        rmsdList.push(`${cluster[0].pdb_id} chain ${cluster[0].struct_asym_id}:${entries[0].transform.rmsd.toFixed(2)}`);
                     }
-                    return [4 /*yield*/, afTransform(plugin, afStr.cell, spState.alphafold.transforms[segmentNum], spState.alphafold.coordinateSystems[segmentNum])];
-                case 3:
-                    _b.sent();
-                    (0, alphafold_transparency_1.applyAFTransparency)(plugin, afStr, 0.8, 70);
-                    return [2 /*return*/, true];
+                    else {
+                        if (failedPairs.length > 0)
+                            failedPairsResult.push(failedPairs);
+                        if (zeroOverlapPairs.length > 0)
+                            zeroOverlapPairsResult.push(zeroOverlapPairs);
+                        // rmsdList.push(`${cluster[0].pdb_id} ${cluster[0].struct_asym_id}:-`)
+                    }
+                }
             }
         });
-    });
+        // console.log(failedPairsResult);
+        // console.log(zeroOverlapPairsResult);
+        if (mappingResult.length > 0) {
+            spState.alphafold.visibility[segmentNum] = true;
+            spState.alphafold.transforms[segmentNum] = mappingResult[minIndex].transform.bTransform;
+            spState.alphafold.coordinateSystems[segmentNum] = coordinateSystems[minIndex];
+            spState.alphafold.rmsds[segmentNum] = rmsdList.sort((a, b) => parseFloat(a.split(':')[1]) - parseFloat(b.split(':')[1]));
+        }
+    }
+    await afTransform(plugin, afStr.cell, spState.alphafold.transforms[segmentNum], spState.alphafold.coordinateSystems[segmentNum]);
+    (0, alphafold_transparency_1.applyAFTransparency)(plugin, afStr, 0.8, 70);
+    return true;
 }
 exports.superposeAf = superposeAf;
-function renderSuperposition(plugin, segmentIndex, entryList) {
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var customState, superpositionParams, busyFlagOn;
-        var _this = this;
-        return tslib_1.__generator(this, function (_a) {
-            customState = plugin.customState;
-            superpositionParams = customState.initParams.superpositionParams;
-            busyFlagOn = false;
-            if (entryList.length > 1) {
-                busyFlagOn = true;
-                customState.events.isBusy.next(true);
+async function renderSuperposition(plugin, segmentIndex, entryList) {
+    const customState = plugin.customState;
+    const superpositionParams = customState.initParams.superpositionParams;
+    let busyFlagOn = false;
+    if (entryList.length > 1) {
+        busyFlagOn = true;
+        customState.events.isBusy.next(true);
+    }
+    // Load Coordinates and render respresentations
+    return plugin.dataTransaction(async () => {
+        const spState = plugin.customState.superpositionState;
+        for await (const s of entryList) {
+            // validate matrix availability
+            if (!spState.matrixData[`${s.pdb_id}_${s.auth_asym_id}`]) {
+                spState.noMatrixStruct.push(`${s.pdb_id}_${s.struct_asym_id}`);
+                spState.invalidStruct.push(`${s.pdb_id}_${s.struct_asym_id}`);
+                continue;
             }
-            // Load Coordinates and render respresentations
-            return [2 /*return*/, plugin.dataTransaction(function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-                    var spState, entryList_1, entryList_1_1, s, strUrl, strInstance, modelRef, clearOnFail, polymerInstance, modelInstance, isBinary, _a, model, structure, matrix, chainSel, uniformColor1, uniformColor2, invalidStruct, state, hetInfo, hets, hets_1, hets_1_1, het, ligand, labelTagParams, hetColor, _b, r, g, b, ligandExp, e_2_1, carbEntityCount, allCarbPolymers, polymerChainWithSurroundings, i, _i, _c, carbEntityChainId, carbEntityChain, carbEntityChainInVicinity, data, carbChainSel, carbLigands, carbLigNamesAndCount, carbLigList, _d, _e, carbLigs, ligResDetails, carbVisLabel, branchedEntity, labelTagParams, ligandExp, loadedStructIndex, e_3_1;
-                    var e_3, _f, e_2, _g;
-                    return tslib_1.__generator(this, function (_h) {
-                        switch (_h.label) {
-                            case 0:
-                                spState = plugin.customState.superpositionState;
-                                _h.label = 1;
-                            case 1:
-                                _h.trys.push([1, 41, 42, 47]);
-                                entryList_1 = tslib_1.__asyncValues(entryList);
-                                _h.label = 2;
-                            case 2: return [4 /*yield*/, entryList_1.next()];
-                            case 3:
-                                if (!(entryList_1_1 = _h.sent(), !entryList_1_1.done)) return [3 /*break*/, 40];
-                                s = entryList_1_1.value;
-                                // validate matrix availability
-                                if (!spState.matrixData["".concat(s.pdb_id, "_").concat(s.auth_asym_id)]) {
-                                    spState.noMatrixStruct.push("".concat(s.pdb_id, "_").concat(s.struct_asym_id));
-                                    spState.invalidStruct.push("".concat(s.pdb_id, "_").concat(s.struct_asym_id));
-                                    return [3 /*break*/, 39];
-                                }
-                                spState.loadedStructs[segmentIndex].push("".concat(s.pdb_id, "_").concat(s.struct_asym_id));
-                                strUrl = "".concat(customState.initParams.pdbeUrl, "model-server/v1/").concat(s.pdb_id, "/atoms?auth_asym_id=").concat(s.auth_asym_id, "&encoding=").concat(customState.initParams.encoding);
-                                if (superpositionParams && superpositionParams.ligandView)
-                                    strUrl = "https://www.ebi.ac.uk/pdbe/entry-files/download/".concat(s.pdb_id, ".bcif");
-                                strInstance = void 0;
-                                modelRef = void 0;
-                                clearOnFail = true;
-                                if (!(superpositionParams && superpositionParams.ligandView && spState.entries[s.pdb_id])) return [3 /*break*/, 5];
-                                polymerInstance = plugin.state.data.select(spState.entries[s.pdb_id])[0];
-                                modelRef = polymerInstance.transform.parent;
-                                modelInstance = plugin.state.data.select(modelRef)[0];
-                                return [4 /*yield*/, plugin.builders.structure.createStructure(modelInstance, { name: 'model', params: {} })];
-                            case 4:
-                                strInstance = _h.sent();
-                                clearOnFail = false;
-                                return [3 /*break*/, 7];
-                            case 5:
-                                isBinary = customState.initParams.encoding === 'bcif' ? true : false;
-                                return [4 /*yield*/, loadStructure(plugin, strUrl, 'mmcif', isBinary)];
-                            case 6:
-                                _a = _h.sent(), model = _a.model, structure = _a.structure;
-                                strInstance = structure;
-                                modelRef = model.ref;
-                                _h.label = 7;
-                            case 7:
-                                if (!strInstance)
-                                    return [3 /*break*/, 39];
-                                // Store Refs in state
-                                if (!spState.models["".concat(s.pdb_id, "_").concat(s.struct_asym_id)])
-                                    spState.models["".concat(s.pdb_id, "_").concat(s.struct_asym_id)] = strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref;
-                                if (superpositionParams && superpositionParams.ligandView && !spState.entries[s.pdb_id])
-                                    spState.entries[s.pdb_id] = strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref;
-                                matrix = linear_algebra_1.Mat4.ofRows(plugin.customState.superpositionState.matrixData["".concat(s.pdb_id, "_").concat(s.auth_asym_id)].matrix);
-                                return [4 /*yield*/, transform(plugin, strInstance, matrix)];
-                            case 8:
-                                _h.sent();
-                                chainSel = void 0;
-                                if (!((superpositionParams && superpositionParams.ligandView) && s.is_representative)) return [3 /*break*/, 12];
-                                uniformColor1 = getRandomColor(plugin, segmentIndex);
-                                return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(strInstance, chainSelection(s.struct_asym_id), "Chain-".concat(segmentIndex), { label: "Chain", tags: ["superposition-sel"] })];
-                            case 9:
-                                chainSel = _h.sent();
-                                if (!chainSel) return [3 /*break*/, 11];
-                                return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'uniform', colorParams: { value: uniformColor1 }, size: 'uniform' }, { tag: "superposition-visual" })];
-                            case 10:
-                                _h.sent();
-                                spState.refMaps[chainSel.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
-                                _h.label = 11;
-                            case 11: return [3 /*break*/, 16];
-                            case 12:
-                                if (!((superpositionParams && superpositionParams.ligandView) && !s.is_representative)) return [3 /*break*/, 13];
-                                return [3 /*break*/, 16];
-                            case 13:
-                                uniformColor2 = getRandomColor(plugin, segmentIndex);
-                                return [4 /*yield*/, plugin.builders.structure.tryCreateComponentStatic(strInstance, 'polymer', { label: "Chain", tags: ["Chain-".concat(segmentIndex), "superposition-sel"] })];
-                            case 14:
-                                chainSel = _h.sent();
-                                if (!chainSel) return [3 /*break*/, 16];
-                                return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'uniform', colorParams: { value: uniformColor2 }, size: 'uniform' }, { tag: "superposition-visual" })];
-                            case 15:
-                                _h.sent();
-                                spState.refMaps[chainSel.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
-                                _h.label = 16;
-                            case 16:
-                                invalidStruct = chainSel ? false : true;
-                                if (!(superpositionParams && superpositionParams.ligandView)) return [3 /*break*/, 39];
-                                state = plugin.state.data;
-                                return [4 /*yield*/, getLigandNamesFromModelData(plugin, state, modelRef)];
-                            case 17:
-                                hetInfo = _h.sent();
-                                hets = hetInfo ? hetInfo.hetNames : [];
-                                if (!(hets && hets.length > 0)) return [3 /*break*/, 31];
-                                _h.label = 18;
-                            case 18:
-                                _h.trys.push([18, 25, 26, 31]);
-                                hets_1 = (e_2 = void 0, tslib_1.__asyncValues(hets));
-                                _h.label = 19;
-                            case 19: return [4 /*yield*/, hets_1.next()];
-                            case 20:
-                                if (!(hets_1_1 = _h.sent(), !hets_1_1.done)) return [3 /*break*/, 24];
-                                het = hets_1_1.value;
-                                ligand = builder_1.MolScriptBuilder.struct.generator.atomGroups({
-                                    'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), s.auth_asym_id]),
-                                    'residue-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.label_comp_id(), het]),
-                                    'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()])
-                                });
-                                labelTagParams = { label: "".concat(het), tags: ["superposition-ligand-sel"] };
-                                hetColor = color_1.Color.fromRgb(253, 3, 253);
-                                if (superpositionParams && superpositionParams.ligandColor) {
-                                    _b = superpositionParams.ligandColor, r = _b.r, g = _b.g, b = _b.b;
-                                    hetColor = color_1.Color.fromRgb(r, g, b);
-                                }
-                                return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(strInstance, ligand, "".concat(het, "-").concat(segmentIndex), labelTagParams)];
-                            case 21:
-                                ligandExp = _h.sent();
-                                if (!ligandExp) return [3 /*break*/, 23];
-                                return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(ligandExp, { type: 'ball-and-stick', color: 'uniform', colorParams: { value: hetColor } }, { tag: "superposition-ligand-visual" })];
-                            case 22:
-                                _h.sent();
-                                spState.refMaps[ligandExp.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
-                                invalidStruct = false;
-                                _h.label = 23;
-                            case 23: return [3 /*break*/, 19];
-                            case 24: return [3 /*break*/, 31];
-                            case 25:
-                                e_2_1 = _h.sent();
-                                e_2 = { error: e_2_1 };
-                                return [3 /*break*/, 31];
-                            case 26:
-                                _h.trys.push([26, , 29, 30]);
-                                if (!(hets_1_1 && !hets_1_1.done && (_g = hets_1.return))) return [3 /*break*/, 28];
-                                return [4 /*yield*/, _g.call(hets_1)];
-                            case 27:
-                                _h.sent();
-                                _h.label = 28;
-                            case 28: return [3 /*break*/, 30];
-                            case 29:
-                                if (e_2) throw e_2.error;
-                                return [7 /*endfinally*/];
-                            case 30: return [7 /*endfinally*/];
-                            case 31:
-                                carbEntityCount = hetInfo ? hetInfo.carbEntityCount : 0;
-                                if (!(carbEntityCount > 0)) return [3 /*break*/, 38];
-                                return [4 /*yield*/, getCarbPolymerDetailsFromApi(plugin, s.pdb_id)];
-                            case 32:
-                                allCarbPolymers = _h.sent();
-                                polymerChainWithSurroundings = builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
-                                    0: builder_1.MolScriptBuilder.struct.generator.atomGroups({
-                                        'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
-                                        'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), s.auth_asym_id]),
-                                        'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()])
-                                    }),
-                                    radius: 5,
-                                    'as-whole-residues': true
-                                });
-                                i = 0;
-                                _i = 0, _c = allCarbPolymers.branchedChains;
-                                _h.label = 33;
-                            case 33:
-                                if (!(_i < _c.length)) return [3 /*break*/, 38];
-                                carbEntityChainId = _c[_i];
-                                carbEntityChain = builder_1.MolScriptBuilder.struct.generator.atomGroups({
-                                    'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'branched']),
-                                    'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), carbEntityChainId]),
-                                    'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()])
-                                });
-                                carbEntityChainInVicinity = builder_1.MolScriptBuilder.struct.filter.intersectedBy({
-                                    0: polymerChainWithSurroundings,
-                                    by: carbEntityChain
-                                });
-                                data = (plugin.state.data.select(strInstance.ref)[0].obj).data;
-                                carbChainSel = script_1.Script.getStructureSelection(carbEntityChainInVicinity, data);
-                                if (!(carbChainSel && carbChainSel.kind === 'sequence')) return [3 /*break*/, 36];
-                                carbLigands = [];
-                                carbLigNamesAndCount = {};
-                                carbLigList = [];
-                                for (_d = 0, _e = allCarbPolymers.branchedLigands[i]; _d < _e.length; _d++) {
-                                    carbLigs = _e[_d];
-                                    ligResDetails = carbLigs.split('-');
-                                    carbLigands.push(builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_seq_id(), +ligResDetails[1]]));
-                                    if (carbLigNamesAndCount[ligResDetails[0]]) {
-                                        carbLigNamesAndCount[ligResDetails[0]]++;
-                                    }
-                                    else {
-                                        carbLigNamesAndCount[ligResDetails[0]] = 1;
-                                    }
-                                    carbLigList.push(ligResDetails[0]);
-                                }
-                                carbVisLabel = createCarbVisLabel(carbLigNamesAndCount);
-                                branchedEntity = builder_1.MolScriptBuilder.struct.generator.atomGroups({
-                                    'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'branched']),
-                                    'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()]),
-                                    'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), carbEntityChainId]),
-                                    'residue-test': builder_1.MolScriptBuilder.core.logic.or(carbLigands)
-                                });
-                                labelTagParams = { label: "".concat(carbVisLabel), tags: ["superposition-carb-sel"] };
-                                return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(strInstance, branchedEntity, "".concat(carbLigList.join('-'), "-").concat(segmentIndex), labelTagParams)];
-                            case 34:
-                                ligandExp = _h.sent();
-                                if (!ligandExp) return [3 /*break*/, 36];
-                                return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(ligandExp, { type: 'carbohydrate' }, { tag: "superposition-carb-visual" })];
-                            case 35:
-                                _h.sent();
-                                spState.refMaps[ligandExp.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
-                                invalidStruct = false;
-                                _h.label = 36;
-                            case 36:
-                                i++;
-                                _h.label = 37;
-                            case 37:
-                                _i++;
-                                return [3 /*break*/, 33];
-                            case 38:
-                                if (invalidStruct) {
-                                    spState.invalidStruct.push("".concat(s.pdb_id, "_").concat(s.struct_asym_id));
-                                    loadedStructIndex = spState.loadedStructs[segmentIndex].indexOf("".concat(s.pdb_id, "_").concat(s.struct_asym_id));
-                                    if (loadedStructIndex > -1)
-                                        spState.loadedStructs[segmentIndex].splice(loadedStructIndex, 1);
-                                    // remove downloaded data
-                                    if (clearOnFail) {
-                                        // const m = plugin.state.data.select(modelRef)[0];
-                                        // const t = plugin.state.data.select(m.transform.parent)[0];
-                                        // const d = plugin.state.data.select(t.transform.parent)[0];
-                                        // PluginCommands.State.RemoveObject(plugin, { state: d.parent!, ref: d.transform.parent, removeParentGhosts: true });
-                                    }
+            spState.loadedStructs[segmentIndex].push(`${s.pdb_id}_${s.struct_asym_id}`);
+            // Set Coordinate server url
+            let strUrl = `${customState.initParams.pdbeUrl}model-server/v1/${s.pdb_id}/atoms?auth_asym_id=${s.auth_asym_id}&encoding=${customState.initParams.encoding}`;
+            if (superpositionParams && superpositionParams.ligandView)
+                strUrl = `https://www.ebi.ac.uk/pdbe/entry-files/download/${s.pdb_id}.bcif`;
+            // Load Data
+            let strInstance;
+            let modelRef;
+            let clearOnFail = true;
+            if (superpositionParams && superpositionParams.ligandView && spState.entries[s.pdb_id]) {
+                const polymerInstance = plugin.state.data.select(spState.entries[s.pdb_id])[0];
+                modelRef = polymerInstance.transform.parent;
+                const modelInstance = plugin.state.data.select(modelRef)[0];
+                strInstance = await plugin.builders.structure.createStructure(modelInstance, { name: 'model', params: {} });
+                clearOnFail = false;
+            }
+            else {
+                const isBinary = customState.initParams.encoding === 'bcif' ? true : false;
+                const { model, structure } = await loadStructure(plugin, strUrl, 'mmcif', isBinary);
+                strInstance = structure;
+                modelRef = model.ref;
+            }
+            if (!strInstance)
+                continue;
+            // Store Refs in state
+            if (!spState.models[`${s.pdb_id}_${s.struct_asym_id}`])
+                spState.models[`${s.pdb_id}_${s.struct_asym_id}`] = strInstance?.ref;
+            if (superpositionParams && superpositionParams.ligandView && !spState.entries[s.pdb_id])
+                spState.entries[s.pdb_id] = strInstance?.ref;
+            // Apply tranform matrix
+            const matrix = linear_algebra_1.Mat4.ofRows(plugin.customState.superpositionState.matrixData[`${s.pdb_id}_${s.auth_asym_id}`].matrix);
+            await transform(plugin, strInstance, matrix);
+            // Create representations
+            let chainSel;
+            if ((superpositionParams && superpositionParams.ligandView) && s.is_representative) {
+                const uniformColor1 = getRandomColor(plugin, segmentIndex); // random color
+                chainSel = await plugin.builders.structure.tryCreateComponentFromExpression(strInstance, chainSelection(s.struct_asym_id), `Chain-${segmentIndex}`, { label: `Chain`, tags: [`superposition-sel`] });
+                if (chainSel) {
+                    await plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'uniform', colorParams: { value: uniformColor1 }, size: 'uniform' }, { tag: `superposition-visual` });
+                    spState.refMaps[chainSel.ref] = `${s.pdb_id}_${s.struct_asym_id}`;
+                }
+            }
+            else if ((superpositionParams && superpositionParams.ligandView) && !s.is_representative) {
+                // Do nothing
+            }
+            else {
+                const uniformColor2 = getRandomColor(plugin, segmentIndex); // random color
+                chainSel = await plugin.builders.structure.tryCreateComponentStatic(strInstance, 'polymer', { label: `Chain`, tags: [`Chain-${segmentIndex}`, `superposition-sel`] });
+                if (chainSel) {
+                    await plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'uniform', colorParams: { value: uniformColor2 }, size: 'uniform' }, { tag: `superposition-visual` });
+                    spState.refMaps[chainSel.ref] = `${s.pdb_id}_${s.struct_asym_id}`;
+                }
+                // // const addTooltipUpdate = plugin.state.behaviors.build().to(BestDatabaseSequenceMapping.id).update(BestDatabaseSequenceMapping, (old: any) => { old.showTooltip = true; });
+                // // await plugin.runTask(plugin.state.behaviors.updateTree(addTooltipUpdate));
+                // BestDatabaseSequenceMapping
+                // console.log(plugin.state.data.select(modelRef)[0])
+            }
+            let invalidStruct = chainSel ? false : true;
+            if (superpositionParams && superpositionParams.ligandView) {
+                const state = plugin.state.data;
+                const hetInfo = await getLigandNamesFromModelData(plugin, state, modelRef);
+                const hets = hetInfo ? hetInfo.hetNames : [];
+                // const interactingHets = [];
+                if (hets && hets.length > 0) {
+                    for await (const het of hets) {
+                        const ligand = builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                            'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), s.auth_asym_id]),
+                            'residue-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.label_comp_id(), het]),
+                            'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()])
+                        });
+                        let labelTagParams = { label: `${het}`, tags: [`superposition-ligand-sel`] };
+                        let hetColor = color_1.Color.fromRgb(253, 3, 253);
+                        if (superpositionParams && superpositionParams.ligandColor) {
+                            const { r, g, b } = superpositionParams.ligandColor;
+                            hetColor = color_1.Color.fromRgb(r, g, b);
+                        }
+                        const ligandExp = await plugin.builders.structure.tryCreateComponentFromExpression(strInstance, ligand, `${het}-${segmentIndex}`, labelTagParams);
+                        if (ligandExp) {
+                            await plugin.builders.structure.representation.addRepresentation(ligandExp, { type: 'ball-and-stick', color: 'uniform', colorParams: { value: hetColor } }, { tag: `superposition-ligand-visual` });
+                            spState.refMaps[ligandExp.ref] = `${s.pdb_id}_${s.struct_asym_id}`;
+                            invalidStruct = false;
+                            // interactingHets.push(het);
+                        }
+                    }
+                }
+                const carbEntityCount = hetInfo ? hetInfo.carbEntityCount : 0;
+                if (carbEntityCount > 0) {
+                    // Get Carbohydrate Polymers details from PDBe API
+                    const allCarbPolymers = await getCarbPolymerDetailsFromApi(plugin, s.pdb_id);
+                    // Polymer chain + surroundings query
+                    const polymerChainWithSurroundings = builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
+                        0: builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                            'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
+                            'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), s.auth_asym_id]),
+                            'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()])
+                        }),
+                        radius: 5,
+                        'as-whole-residues': true
+                    });
+                    let i = 0;
+                    for (const carbEntityChainId of allCarbPolymers.branchedChains) {
+                        const carbEntityChain = builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                            'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'branched']),
+                            'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), carbEntityChainId]),
+                            'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()])
+                        });
+                        const carbEntityChainInVicinity = builder_1.MolScriptBuilder.struct.filter.intersectedBy({
+                            0: polymerChainWithSurroundings,
+                            by: carbEntityChain
+                        });
+                        const data = (plugin.state.data.select(strInstance.ref)[0].obj).data;
+                        const carbChainSel = script_1.Script.getStructureSelection(carbEntityChainInVicinity, data);
+                        if (carbChainSel && carbChainSel.kind === 'sequence') {
+                            // console.log(carbEntityChainId + ' chain present in 5 A radius');
+                            const carbLigands = [];
+                            const carbLigNamesAndCount = {};
+                            const carbLigList = [];
+                            for (const carbLigs of allCarbPolymers.branchedLigands[i]) {
+                                const ligResDetails = carbLigs.split('-');
+                                carbLigands.push(builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_seq_id(), +ligResDetails[1]]));
+                                if (carbLigNamesAndCount[ligResDetails[0]]) {
+                                    carbLigNamesAndCount[ligResDetails[0]]++;
                                 }
                                 else {
-                                    // if(interactingHets.length > 0) spState.hets[`${s.pdb_id}_${s.struct_asym_id}`] = interactingHets;
+                                    carbLigNamesAndCount[ligResDetails[0]] = 1;
                                 }
-                                _h.label = 39;
-                            case 39: return [3 /*break*/, 2];
-                            case 40: return [3 /*break*/, 47];
-                            case 41:
-                                e_3_1 = _h.sent();
-                                e_3 = { error: e_3_1 };
-                                return [3 /*break*/, 47];
-                            case 42:
-                                _h.trys.push([42, , 45, 46]);
-                                if (!(entryList_1_1 && !entryList_1_1.done && (_f = entryList_1.return))) return [3 /*break*/, 44];
-                                return [4 /*yield*/, _f.call(entryList_1)];
-                            case 43:
-                                _h.sent();
-                                _h.label = 44;
-                            case 44: return [3 /*break*/, 46];
-                            case 45:
-                                if (e_3) throw e_3.error;
-                                return [7 /*endfinally*/];
-                            case 46: return [7 /*endfinally*/];
-                            case 47:
-                                if (busyFlagOn) {
-                                    busyFlagOn = false;
-                                    customState.events.isBusy.next(false);
-                                }
-                                return [2 /*return*/];
+                                carbLigList.push(ligResDetails[0]);
+                            }
+                            const carbVisLabel = createCarbVisLabel(carbLigNamesAndCount);
+                            const branchedEntity = builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                                'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'branched']),
+                                'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()]),
+                                'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), carbEntityChainId]),
+                                'residue-test': builder_1.MolScriptBuilder.core.logic.or(carbLigands)
+                            });
+                            let labelTagParams = { label: `${carbVisLabel}`, tags: [`superposition-carb-sel`] };
+                            const ligandExp = await plugin.builders.structure.tryCreateComponentFromExpression(strInstance, branchedEntity, `${carbLigList.join('-')}-${segmentIndex}`, labelTagParams);
+                            if (ligandExp) {
+                                await plugin.builders.structure.representation.addRepresentation(ligandExp, { type: 'carbohydrate' }, { tag: `superposition-carb-visual` });
+                                spState.refMaps[ligandExp.ref] = `${s.pdb_id}_${s.struct_asym_id}`;
+                                invalidStruct = false;
+                            }
                         }
-                    });
-                }); })];
-        });
-    });
-}
-exports.renderSuperposition = renderSuperposition;
-function getLigandNamesFromModelData(plugin, state, modelRef) {
-    var _a;
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var cell, model, structures, _i, _b, s, structure, info;
-        return tslib_1.__generator(this, function (_c) {
-            switch (_c.label) {
-                case 0:
-                    cell = state.select(modelRef)[0];
-                    if (!cell || !cell.obj)
-                        return [2 /*return*/, void 0];
-                    model = cell.obj.data;
-                    if (!model)
-                        return [2 /*return*/];
-                    structures = [];
-                    for (_i = 0, _b = plugin.managers.structure.hierarchy.selection.structures; _i < _b.length; _i++) {
-                        s = _b[_i];
-                        structure = (_a = s.cell.obj) === null || _a === void 0 ? void 0 : _a.data;
-                        if (structure)
-                            structures.push(structure);
+                        i++;
+                    }
+                }
+                if (invalidStruct) {
+                    spState.invalidStruct.push(`${s.pdb_id}_${s.struct_asym_id}`);
+                    const loadedStructIndex = spState.loadedStructs[segmentIndex].indexOf(`${s.pdb_id}_${s.struct_asym_id}`);
+                    if (loadedStructIndex > -1)
+                        spState.loadedStructs[segmentIndex].splice(loadedStructIndex, 1);
+                    // remove downloaded data
+                    if (clearOnFail) {
+                        // const m = plugin.state.data.select(modelRef)[0];
+                        // const t = plugin.state.data.select(m.transform.parent)[0];
+                        // const d = plugin.state.data.select(t.transform.parent)[0];
+                        // PluginCommands.State.RemoveObject(plugin, { state: d.parent!, ref: d.transform.parent, removeParentGhosts: true });
                     }
-                    return [4 /*yield*/, helpers_1.ModelInfo.get(model, structures)];
-                case 1:
-                    info = _c.sent();
-                    return [2 /*return*/, info];
+                }
+                else {
+                    // if(interactingHets.length > 0) spState.hets[`${s.pdb_id}_${s.struct_asym_id}`] = interactingHets;
+                }
             }
-        });
+        }
+        if (busyFlagOn) {
+            busyFlagOn = false;
+            customState.events.isBusy.next(false);
+        }
     });
 }
-function loadStructure(plugin, url, format, isBinary) {
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var data, trajectory, model, modelProperties, structure, e_4;
-        return tslib_1.__generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    _a.trys.push([0, 7, , 8]);
-                    return [4 /*yield*/, plugin.builders.data.download({ url: assets_1.Asset.Url(url), isBinary: isBinary })];
-                case 1:
-                    data = _a.sent();
-                    return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data, format)];
-                case 2:
-                    trajectory = _a.sent();
-                    return [4 /*yield*/, plugin.builders.structure.createModel(trajectory)];
-                case 3:
-                    model = _a.sent();
-                    return [4 /*yield*/, plugin.builders.structure.insertModelProperties(model)];
-                case 4:
-                    modelProperties = _a.sent();
-                    return [4 /*yield*/, plugin.builders.structure.createStructure(modelProperties || model, { name: 'model', params: {} })];
-                case 5:
-                    structure = _a.sent();
-                    return [4 /*yield*/, plugin.builders.structure.insertStructureProperties(structure)];
-                case 6:
-                    _a.sent();
-                    return [2 /*return*/, { data: data, trajectory: trajectory, model: model, structure: structure }];
-                case 7:
-                    e_4 = _a.sent();
-                    return [2 /*return*/, { structure: void 0 }];
-                case 8: return [2 /*return*/];
-            }
-        });
-    });
+exports.renderSuperposition = renderSuperposition;
+async function getLigandNamesFromModelData(plugin, state, modelRef) {
+    const cell = state.select(modelRef)[0];
+    if (!cell || !cell.obj)
+        return void 0;
+    const model = cell.obj.data;
+    if (!model)
+        return;
+    const structures = [];
+    for (const s of plugin.managers.structure.hierarchy.selection.structures) {
+        const structure = s.cell.obj?.data;
+        if (structure)
+            structures.push(structure);
+    }
+    const info = await helpers_1.ModelInfo.get(model, structures);
+    return info;
+}
+async function loadStructure(plugin, url, format, isBinary) {
+    try {
+        const data = await plugin.builders.data.download({ url: assets_1.Asset.Url(url), isBinary: isBinary });
+        const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
+        const model = await plugin.builders.structure.createModel(trajectory);
+        const modelProperties = await plugin.builders.structure.insertModelProperties(model);
+        const structure = await plugin.builders.structure.createStructure(modelProperties || model, { name: 'model', params: {} });
+        await plugin.builders.structure.insertStructureProperties(structure);
+        return { data, trajectory, model, structure };
+    }
+    catch (e) {
+        return { structure: void 0 };
+    }
 }
 function chainSelection(struct_asym_id) {
     return builder_1.MolScriptBuilder.struct.generator.atomGroups({
@@ -626,169 +445,114 @@ function chainSelection(struct_asym_id) {
     });
 }
 function transform(plugin, s, matrix) {
-    var b = plugin.state.data.build().to(s)
+    const b = plugin.state.data.build().to(s)
         .insert(transforms_1.StateTransforms.Model.TransformStructureConformation, { transform: { name: 'matrix', params: { data: matrix, transpose: false } } });
     return plugin.runTask(plugin.state.data.updateTree(b));
 }
-function afTransform(plugin, s, matrix, coordinateSystem) {
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var r, o, transform, params, b;
-        return tslib_1.__generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    r = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, s);
-                    if (!r)
-                        return [2 /*return*/];
-                    o = plugin.state.data.selectQ(function (q) { return q.byRef(r.transform.ref).subtree().withTransformer(transforms_1.StateTransforms.Model.TransformStructureConformation); })[0];
-                    transform = coordinateSystem && !linear_algebra_1.Mat4.isIdentity(coordinateSystem.matrix)
-                        ? linear_algebra_1.Mat4.mul((0, linear_algebra_1.Mat4)(), coordinateSystem.matrix, matrix)
-                        : matrix;
-                    params = {
-                        transform: {
-                            name: 'matrix',
-                            params: { data: transform, transpose: false }
-                        }
-                    };
-                    b = o
-                        ? plugin.state.data.build().to(o).update(params)
-                        : plugin.state.data.build().to(s)
-                            .insert(transforms_1.StateTransforms.Model.TransformStructureConformation, params, { tags: 'SuperpositionTransform' });
-                    return [4 /*yield*/, plugin.runTask(plugin.state.data.updateTree(b))];
-                case 1:
-                    _a.sent();
-                    return [2 /*return*/];
-            }
-        });
-    });
+async function afTransform(plugin, s, matrix, coordinateSystem) {
+    const r = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, s);
+    if (!r)
+        return;
+    const o = plugin.state.data.selectQ(q => q.byRef(r.transform.ref).subtree().withTransformer(transforms_1.StateTransforms.Model.TransformStructureConformation))[0];
+    const transform = coordinateSystem && !linear_algebra_1.Mat4.isIdentity(coordinateSystem.matrix)
+        ? linear_algebra_1.Mat4.mul((0, linear_algebra_1.Mat4)(), coordinateSystem.matrix, matrix)
+        : matrix;
+    const params = {
+        transform: {
+            name: 'matrix',
+            params: { data: transform, transpose: false }
+        }
+    };
+    const b = o
+        ? plugin.state.data.build().to(o).update(params)
+        : plugin.state.data.build().to(s)
+            .insert(transforms_1.StateTransforms.Model.TransformStructureConformation, params, { tags: 'SuperpositionTransform' });
+    await plugin.runTask(plugin.state.data.updateTree(b));
 }
-function getMatrixData(plugin) {
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var customState, matrixAccession, clusterRecUrlStr, assetManager, clusterRecUrl, clusterRecData, e_5;
-        return tslib_1.__generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    customState = plugin.customState;
-                    matrixAccession = customState.initParams.superpositionParams.matrixAccession ? customState.initParams.superpositionParams.matrixAccession : customState.initParams.moleculeId;
-                    clusterRecUrlStr = "".concat(customState.initParams.pdbeUrl, "static/superpose/matrices/").concat(matrixAccession);
-                    assetManager = plugin.managers.asset;
-                    clusterRecUrl = assets_1.Asset.getUrlAsset(assetManager, clusterRecUrlStr);
-                    _a.label = 1;
-                case 1:
-                    _a.trys.push([1, 3, , 4]);
-                    return [4 /*yield*/, plugin.runTask(assetManager.resolve(clusterRecUrl, 'json', false))];
-                case 2:
-                    clusterRecData = _a.sent();
-                    if (clusterRecData && clusterRecData.data) {
-                        plugin.customState.superpositionState.matrixData = clusterRecData.data;
-                    }
-                    return [3 /*break*/, 4];
-                case 3:
-                    e_5 = _a.sent();
-                    customState['superpositionError'] = "Matrix data not available for ".concat(matrixAccession);
-                    plugin.customState.events.superpositionInit.next(true); // Emit segment API data load event
-                    return [3 /*break*/, 4];
-                case 4: return [2 /*return*/];
-            }
-        });
-    });
+async function getMatrixData(plugin) {
+    const customState = plugin.customState;
+    const matrixAccession = customState.initParams.superpositionParams.matrixAccession ? customState.initParams.superpositionParams.matrixAccession : customState.initParams.moleculeId;
+    const clusterRecUrlStr = `${customState.initParams.pdbeUrl}static/superpose/matrices/${matrixAccession}`;
+    const assetManager = plugin.managers.asset;
+    const clusterRecUrl = assets_1.Asset.getUrlAsset(assetManager, clusterRecUrlStr);
+    try {
+        const clusterRecData = await plugin.runTask(assetManager.resolve(clusterRecUrl, 'json', false));
+        if (clusterRecData && clusterRecData.data) {
+            plugin.customState.superpositionState.matrixData = clusterRecData.data;
+        }
+    }
+    catch (e) {
+        customState['superpositionError'] = `Matrix data not available for ${matrixAccession}`;
+        plugin.customState.events.superpositionInit.next(true); // Emit segment API data load event
+    }
 }
-function getSegmentData(plugin) {
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var customState, segmentsUrl, assetManager, url, result, e_6;
-        return tslib_1.__generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    customState = plugin.customState;
-                    segmentsUrl = "".concat(customState.initParams.pdbeUrl, "graph-api/uniprot/superposition/").concat(customState.initParams.moleculeId);
-                    assetManager = plugin.managers.asset;
-                    url = assets_1.Asset.getUrlAsset(assetManager, segmentsUrl);
-                    _a.label = 1;
-                case 1:
-                    _a.trys.push([1, 3, , 4]);
-                    return [4 /*yield*/, plugin.runTask(assetManager.resolve(url, 'json', false))];
-                case 2:
-                    result = _a.sent();
-                    if (result && result.data) {
-                        customState.superpositionState.segmentData = result.data[customState.initParams.moleculeId];
-                    }
-                    return [3 /*break*/, 4];
-                case 3:
-                    e_6 = _a.sent();
-                    customState['superpositionError'] = "Superposition data not available for ".concat(customState.initParams.moleculeId);
-                    plugin.customState.events.superpositionInit.next(true); // Emit segment API data load event
-                    return [3 /*break*/, 4];
-                case 4: return [2 /*return*/];
-            }
-        });
-    });
+async function getSegmentData(plugin) {
+    const customState = plugin.customState;
+    // Get Data
+    const segmentsUrl = `${customState.initParams.pdbeUrl}graph-api/uniprot/superposition/${customState.initParams.moleculeId}`;
+    const assetManager = plugin.managers.asset;
+    const url = assets_1.Asset.getUrlAsset(assetManager, segmentsUrl);
+    try {
+        const result = await plugin.runTask(assetManager.resolve(url, 'json', false));
+        if (result && result.data) {
+            customState.superpositionState.segmentData = result.data[customState.initParams.moleculeId];
+        }
+    }
+    catch (e) {
+        customState['superpositionError'] = `Superposition data not available for ${customState.initParams.moleculeId}`;
+        plugin.customState.events.superpositionInit.next(true); // Emit segment API data load event
+    }
 }
 function getChainLigands(carbEntity) {
-    var ligandChain = [];
-    var ligandLabels = [];
-    var ligands = [];
-    var labelValueArr = [];
-    var ligNameStr = '';
-    for (var _i = 0, _a = carbEntity.chem_comp_list; _i < _a.length; _i++) {
-        var chemComp = _a[_i];
-        labelValueArr.push("".concat(chemComp.chem_comp_id, " (").concat(chemComp.count, ")"));
+    const ligandChain = [];
+    const ligandLabels = [];
+    const ligands = [];
+    const labelValueArr = [];
+    let ligNameStr = '';
+    for (const chemComp of carbEntity.chem_comp_list) {
+        labelValueArr.push(`${chemComp.chem_comp_id} (${chemComp.count})`);
     }
     ligNameStr = labelValueArr.join(', ');
-    for (var _b = 0, _c = carbEntity.chains; _b < _c.length; _b++) {
-        var chain = _c[_b];
+    for (const chain of carbEntity.chains) {
         ligandChain.push(chain.chain_id);
         ligandLabels.push(ligNameStr);
-        var chainLigands = [];
-        for (var _d = 0, _e = chain.residues; _d < _e.length; _d++) {
-            var residue = _e[_d];
+        const chainLigands = [];
+        for (const residue of chain.residues) {
             chainLigands.push(residue.chem_comp_id + '-' + residue.residue_number);
         }
         ligands.push(chainLigands);
     }
     return {
-        ligands: ligands,
-        ligandChain: ligandChain,
-        ligandLabels: ligandLabels
+        ligands,
+        ligandChain,
+        ligandLabels
     };
 }
-function getCarbPolymerDetailsFromApi(plugin, pdb_id) {
-    return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var customState, apiUrl, assetManager, url, branchedLigands, branchedChains, branchedlabels, result, carbEntities, _i, carbEntities_1, carbEntity, carbLigData, e_7;
-        return tslib_1.__generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    customState = plugin.customState;
-                    apiUrl = "".concat(customState.initParams.pdbeUrl, "api/pdb/entry/carbohydrate_polymer/").concat(pdb_id);
-                    assetManager = plugin.managers.asset;
-                    url = assets_1.Asset.getUrlAsset(assetManager, apiUrl);
-                    branchedLigands = [];
-                    branchedChains = [];
-                    branchedlabels = [];
-                    _a.label = 1;
-                case 1:
-                    _a.trys.push([1, 3, , 4]);
-                    return [4 /*yield*/, plugin.runTask(assetManager.resolve(url, 'json', false))];
-                case 2:
-                    result = _a.sent();
-                    if (result && result.data) {
-                        carbEntities = result.data[pdb_id];
-                        for (_i = 0, carbEntities_1 = carbEntities; _i < carbEntities_1.length; _i++) {
-                            carbEntity = carbEntities_1[_i];
-                            carbLigData = getChainLigands(carbEntity);
-                            branchedLigands = branchedLigands.concat(carbLigData.ligands);
-                            branchedChains = branchedChains.concat(carbLigData.ligandChain);
-                            branchedlabels = branchedlabels.concat(carbLigData.ligandLabels);
-                        }
-                    }
-                    return [3 /*break*/, 4];
-                case 3:
-                    e_7 = _a.sent();
-                    return [3 /*break*/, 4];
-                case 4: return [2 /*return*/, {
-                        branchedChains: branchedChains,
-                        branchedLigands: branchedLigands,
-                        branchedlabels: branchedlabels
-                    }];
+async function getCarbPolymerDetailsFromApi(plugin, pdb_id) {
+    const customState = plugin.customState;
+    // Get Data
+    const apiUrl = `${customState.initParams.pdbeUrl}api/pdb/entry/carbohydrate_polymer/${pdb_id}`;
+    const assetManager = plugin.managers.asset;
+    const url = assets_1.Asset.getUrlAsset(assetManager, apiUrl);
+    let branchedLigands = [];
+    let branchedChains = [];
+    let branchedlabels = [];
+    try {
+        const result = await plugin.runTask(assetManager.resolve(url, 'json', false));
+        if (result && result.data) {
+            const carbEntities = result.data[pdb_id];
+            for (const carbEntity of carbEntities) {
+                const carbLigData = getChainLigands(carbEntity);
+                branchedLigands = branchedLigands.concat(carbLigData.ligands);
+                branchedChains = branchedChains.concat(carbLigData.ligandChain);
+                branchedlabels = branchedlabels.concat(carbLigData.ligandLabels);
             }
-        });
-    });
+        }
+    }
+    catch (e) { }
+    return {
+        branchedChains,
+        branchedLigands,
+        branchedlabels
+    };
 }