pdbe-molstar 3.2.1-beta.1 → 3.2.1-beta.3

package/lib/superposition.js

@@ -1,40 +1,35 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.transform = exports.renderSuperposition = exports.superposeAf = exports.loadAfStructure = exports.initSuperposition = void 0;
+exports.transform = exports.renderSuperposition = exports.superposeAf = exports.loadAfStructure = exports.initSuperposition = exports.getNextColor = exports.SuperpositionColorPalette = void 0;
 var tslib_1 = require("tslib");
-var linear_algebra_1 = require("Molstar/mol-math/linear-algebra");
-var structure_1 = require("Molstar/mol-model/structure");
-var transforms_1 = require("Molstar/mol-plugin-state/transforms");
-var builder_1 = require("Molstar/mol-script/language/builder");
-var script_1 = require("Molstar/mol-script/script");
-var mol_state_1 = require("Molstar/mol-state");
-var mol_task_1 = require("Molstar/mol-task");
-var assets_1 = require("Molstar/mol-util/assets");
-var color_1 = require("Molstar/mol-util/color/color");
-var lists_1 = require("Molstar/mol-util/color/lists");
+var linear_algebra_1 = require("molstar/lib/mol-math/linear-algebra");
+var structure_1 = require("molstar/lib/mol-model/structure");
+var transforms_1 = require("molstar/lib/mol-plugin-state/transforms");
+var builder_1 = require("molstar/lib/mol-script/language/builder");
+var script_1 = require("molstar/lib/mol-script/script");
+var mol_state_1 = require("molstar/lib/mol-state");
+var mol_task_1 = require("molstar/lib/mol-task");
+var assets_1 = require("molstar/lib/mol-util/assets");
+var color_1 = require("molstar/lib/mol-util/color/color");
+var lists_1 = require("molstar/lib/mol-util/color/lists");
 var alphafold_transparency_1 = require("./alphafold-transparency");
 var helpers_1 = require("./helpers");
 var plugin_custom_state_1 = require("./plugin-custom-state");
 var superposition_sifts_mapping_1 = require("./superposition-sifts-mapping");
-function getRandomColor(plugin, segmentIndex) {
-    var clList = lists_1.ColorLists;
+function combinedColorPalette(palettes) {
+    return palettes.flatMap(function (paletteName) { return lists_1.ColorLists[paletteName].list; });
+}
+exports.SuperpositionColorPalette = combinedColorPalette(['dark-2', 'red-yellow-green', 'paired', 'set-1', 'accent', 'set-2', 'rainbow']);
+var DefaultLigandColor = color_1.Color.fromRgb(253, 3, 253);
+function getNextColor(plugin, segmentIndex) {
     var spState = (0, plugin_custom_state_1.PluginCustomState)(plugin).superpositionState;
     if (!spState)
         throw new Error('customState.superpositionState has not been initialized');
-    var palleteIndex = spState.colorState[segmentIndex].palleteIndex;
-    var colorIndex = spState.colorState[segmentIndex].colorIndex;
-    if (clList[spState.colorPalette[palleteIndex]].list[colorIndex + 1]) {
-        colorIndex += 1;
-    }
-    else {
-        colorIndex = 0;
-        palleteIndex = spState.colorPalette[palleteIndex + 1] ? palleteIndex + 1 : 0;
-    }
-    var palleteName = spState.colorPalette[palleteIndex];
-    spState.colorState[segmentIndex].palleteIndex = palleteIndex;
-    spState.colorState[segmentIndex].colorIndex = colorIndex;
-    return clList[palleteName].list[colorIndex];
+    var nextColor = exports.SuperpositionColorPalette[spState.colorCounters[segmentIndex]];
+    spState.colorCounters[segmentIndex] = (spState.colorCounters[segmentIndex] + 1) % exports.SuperpositionColorPalette.length;
+    return nextColor;
 }
+exports.getNextColor = getNextColor;
 function initSuperposition(plugin, completeSubject) {
     var _a;
     return tslib_1.__awaiter(this, void 0, void 0, function () {
@@ -62,8 +57,7 @@ function initSuperposition(plugin, completeSubject) {
                         invalidStruct: [],
                         noMatrixStruct: [],
                         hets: {},
-                        colorPalette: ['dark-2', 'red-yellow-green', 'paired', 'set-1', 'accent', 'set-2', 'rainbow'],
-                        colorState: [],
+                        colorCounters: [],
                         alphafold: {
                             apiData: {
                                 cif: '',
@@ -104,7 +98,7 @@ function initSuperposition(plugin, completeSubject) {
                     segmentData.forEach(function () {
                         customState_1.superpositionState.loadedStructs.push([]);
                         customState_1.superpositionState.visibleRefs.push([]);
-                        customState_1.superpositionState.colorState.push({ palleteIndex: 0, colorIndex: -1 });
+                        customState_1.superpositionState.colorCounters.push(0);
                     });
                     superpositionParams_1 = customState_1.initParams.superpositionParams;
                     segmentIndex = (superpositionParams_1 === null || superpositionParams_1 === void 0 ? void 0 : superpositionParams_1.segment) ? superpositionParams_1.segment - 1 : 0;
@@ -120,7 +114,7 @@ function initSuperposition(plugin, completeSubject) {
                             return;
                         // Add respresentative structure to the list
                         if (superpositionParams_1 === null || superpositionParams_1 === void 0 ? void 0 : superpositionParams_1.superposeAll) {
-                            entryList_1 = entryList_1.concat(cluster);
+                            entryList_1.push.apply(entryList_1, cluster);
                         }
                         else {
                             entryList_1.push(cluster[0]);
@@ -321,36 +315,27 @@ function renderSuperposition(plugin, segmentIndex, entryList) {
             }
             // Load Coordinates and render respresentations
             return [2 /*return*/, plugin.dataTransaction(function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-                    var spState, _a, entryList_2, entryList_2_1, s, request, strUrl, strInstance, modelRef, clearOnFail, polymerInstance, modelInstance, isBinary, _b, model, structure, matrix, chainSel, uniformColor1, uniformColor2, invalidStruct, state, hetInfo, hets, _c, hets_1, hets_1_1, het, ligand, labelTagParams, hetColor, _d, r, g, b, ligandExp, e_2_1, carbEntityCount, allCarbPolymers, polymerChainWithSurroundings, i, _i, _e, carbEntityChainId, carbEntityChain, carbEntityChainInVicinity, data, carbChainSel, carbLigands, carbLigNamesAndCount, carbLigList, _f, _g, carbLigs, ligResDetails, carbVisLabel, branchedEntity, labelTagParams, ligandExp, loadedStructIndex, e_3_1;
-                    var _h, e_3, _j, _k, _l, e_2, _m, _o;
-                    var _p;
-                    return tslib_1.__generator(this, function (_q) {
-                        switch (_q.label) {
+                    var spState, _i, entryList_2, s, request, strUrl, strInstance, modelRef, clearOnFail, polymerInstance, modelInstance, isBinary, _a, model, structure, matrix, chainSel, uniformColor1, uniformColor2, invalidStruct, state, hetInfo, hets, _b, hets_1, hets_1_1, het, ligand, labelTagParams, hetColor, ligandExp, e_2_1, carbEntityCount, allCarbPolymers, polymerChainWithSurroundings, i, _c, _d, carbEntityChainId, carbEntityChain, carbEntityChainInVicinity, data, carbChainSel, carbLigands, carbLigNamesAndCount, carbLigList, _e, _f, carbLigs, ligResDetails, carbVisLabel, branchedEntity, labelTagParams, ligandExp, loadedStructIndex;
+                    var _g, e_2, _h, _j;
+                    var _k;
+                    return tslib_1.__generator(this, function (_l) {
+                        switch (_l.label) {
                             case 0:
                                 if (!customState.initParams)
                                     throw new Error('customState.initParams has not been initialized');
                                 if (!customState.superpositionState)
                                     throw new Error('customState.superpositionState has not been initialized');
                                 spState = customState.superpositionState;
-                                _q.label = 1;
+                                _i = 0, entryList_2 = entryList;
+                                _l.label = 1;
                             case 1:
-                                _q.trys.push([1, 47, 48, 53]);
-                                _a = true, entryList_2 = tslib_1.__asyncValues(entryList);
-                                _q.label = 2;
-                            case 2: return [4 /*yield*/, entryList_2.next()];
-                            case 3:
-                                if (!(entryList_2_1 = _q.sent(), _h = entryList_2_1.done, !_h)) return [3 /*break*/, 46];
-                                _k = entryList_2_1.value;
-                                _a = false;
-                                _q.label = 4;
-                            case 4:
-                                _q.trys.push([4, , 44, 45]);
-                                s = _k;
+                                if (!(_i < entryList_2.length)) return [3 /*break*/, 41];
+                                s = entryList_2[_i];
                                 // 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*/, 45];
+                                    return [3 /*break*/, 40];
                                 }
                                 spState.loadedStructs[segmentIndex].push("".concat(s.pdb_id, "_").concat(s.struct_asym_id));
                                 request = (superpositionParams && superpositionParams.ligandView) ?
@@ -360,26 +345,26 @@ function renderSuperposition(plugin, segmentIndex, entryList) {
                                 strInstance = void 0;
                                 modelRef = void 0;
                                 clearOnFail = true;
-                                if (!(superpositionParams && superpositionParams.ligandView && spState.entries[s.pdb_id])) return [3 /*break*/, 6];
+                                if (!(superpositionParams && superpositionParams.ligandView && spState.entries[s.pdb_id])) return [3 /*break*/, 3];
                                 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 5:
-                                strInstance = _q.sent();
+                            case 2:
+                                strInstance = _l.sent();
                                 clearOnFail = false;
-                                return [3 /*break*/, 8];
-                            case 6:
+                                return [3 /*break*/, 5];
+                            case 3:
                                 isBinary = customState.initParams.encoding === 'bcif' ? true : false;
                                 return [4 /*yield*/, loadStructure(plugin, strUrl, 'mmcif', isBinary)];
-                            case 7:
-                                _b = _q.sent(), model = _b.model, structure = _b.structure;
+                            case 4:
+                                _a = _l.sent(), model = _a.model, structure = _a.structure;
                                 strInstance = structure;
                                 modelRef = model.ref;
-                                _q.label = 8;
-                            case 8:
+                                _l.label = 5;
+                            case 5:
                                 if (!strInstance)
-                                    return [3 /*break*/, 45];
+                                    return [3 /*break*/, 40];
                                 // 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;
@@ -387,107 +372,103 @@ function renderSuperposition(plugin, segmentIndex, entryList) {
                                     spState.entries[s.pdb_id] = strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref;
                                 matrix = linear_algebra_1.Mat4.ofRows(customState.superpositionState.matrixData["".concat(s.pdb_id, "_").concat(s.auth_asym_id)].matrix);
                                 return [4 /*yield*/, transform(plugin, strInstance, matrix)];
-                            case 9:
-                                _q.sent();
+                            case 6:
+                                _l.sent();
                                 chainSel = void 0;
-                                if (!((superpositionParams && superpositionParams.ligandView) && s.is_representative)) return [3 /*break*/, 13];
-                                uniformColor1 = getRandomColor(plugin, segmentIndex);
+                                if (!((superpositionParams && superpositionParams.ligandView) && s.is_representative)) return [3 /*break*/, 10];
+                                uniformColor1 = getNextColor(plugin, segmentIndex);
                                 return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(strInstance, chainSelection(s.struct_asym_id), "Chain-".concat(segmentIndex), { label: "Chain", tags: ["superposition-sel"] })];
-                            case 10:
-                                chainSel = _q.sent();
-                                if (!chainSel) return [3 /*break*/, 12];
+                            case 7:
+                                chainSel = _l.sent();
+                                if (!chainSel) return [3 /*break*/, 9];
                                 return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'uniform', colorParams: { value: uniformColor1 }, size: 'uniform' }, { tag: "superposition-visual" })];
-                            case 11:
-                                _q.sent();
+                            case 8:
+                                _l.sent();
                                 spState.refMaps[chainSel.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
-                                _q.label = 12;
-                            case 12: return [3 /*break*/, 17];
-                            case 13:
-                                if (!((superpositionParams && superpositionParams.ligandView) && !s.is_representative)) return [3 /*break*/, 14];
-                                return [3 /*break*/, 17];
-                            case 14:
-                                uniformColor2 = getRandomColor(plugin, segmentIndex);
+                                _l.label = 9;
+                            case 9: return [3 /*break*/, 14];
+                            case 10:
+                                if (!((superpositionParams && superpositionParams.ligandView) && !s.is_representative)) return [3 /*break*/, 11];
+                                return [3 /*break*/, 14];
+                            case 11:
+                                uniformColor2 = getNextColor(plugin, segmentIndex);
                                 return [4 /*yield*/, plugin.builders.structure.tryCreateComponentStatic(strInstance, 'polymer', { label: "Chain", tags: ["Chain-".concat(segmentIndex), "superposition-sel"] })];
-                            case 15:
-                                chainSel = _q.sent();
-                                if (!chainSel) return [3 /*break*/, 17];
+                            case 12:
+                                chainSel = _l.sent();
+                                if (!chainSel) return [3 /*break*/, 14];
                                 return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'uniform', colorParams: { value: uniformColor2 }, size: 'uniform' }, { tag: "superposition-visual" })];
-                            case 16:
-                                _q.sent();
+                            case 13:
+                                _l.sent();
                                 spState.refMaps[chainSel.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
-                                _q.label = 17;
-                            case 17:
+                                _l.label = 14;
+                            case 14:
                                 invalidStruct = chainSel ? false : true;
-                                if (!(superpositionParams && superpositionParams.ligandView)) return [3 /*break*/, 43];
+                                if (!(superpositionParams && superpositionParams.ligandView)) return [3 /*break*/, 40];
                                 state = plugin.state.data;
                                 return [4 /*yield*/, getLigandNamesFromModelData(plugin, state, modelRef)];
-                            case 18:
-                                hetInfo = _q.sent();
+                            case 15:
+                                hetInfo = _l.sent();
                                 hets = hetInfo ? hetInfo.hetNames : [];
-                                if (!(hets && hets.length > 0)) return [3 /*break*/, 35];
-                                _q.label = 19;
+                                if (!(hets && hets.length > 0)) return [3 /*break*/, 32];
+                                _l.label = 16;
+                            case 16:
+                                _l.trys.push([16, 26, 27, 32]);
+                                _b = true, hets_1 = (e_2 = void 0, tslib_1.__asyncValues(hets));
+                                _l.label = 17;
+                            case 17: return [4 /*yield*/, hets_1.next()];
+                            case 18:
+                                if (!(hets_1_1 = _l.sent(), _g = hets_1_1.done, !_g)) return [3 /*break*/, 25];
+                                _j = hets_1_1.value;
+                                _b = false;
+                                _l.label = 19;
                             case 19:
-                                _q.trys.push([19, 29, 30, 35]);
-                                _c = true, hets_1 = (e_2 = void 0, tslib_1.__asyncValues(hets));
-                                _q.label = 20;
-                            case 20: return [4 /*yield*/, hets_1.next()];
-                            case 21:
-                                if (!(hets_1_1 = _q.sent(), _l = hets_1_1.done, !_l)) return [3 /*break*/, 28];
-                                _o = hets_1_1.value;
-                                _c = false;
-                                _q.label = 22;
-                            case 22:
-                                _q.trys.push([22, , 26, 27]);
-                                het = _o;
+                                _l.trys.push([19, , 23, 24]);
+                                het = _j;
                                 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 === null || superpositionParams === void 0 ? void 0 : superpositionParams.ligandColor) {
-                                    _d = superpositionParams.ligandColor, r = _d.r, g = _d.g, b = _d.b;
-                                    hetColor = color_1.Color.fromRgb(r, g, b);
-                                }
+                                hetColor = (0, helpers_1.normalizeColor)(superpositionParams.ligandColor, DefaultLigandColor);
                                 return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(strInstance, ligand, "".concat(het, "-").concat(segmentIndex), labelTagParams)];
-                            case 23:
-                                ligandExp = _q.sent();
-                                if (!ligandExp) return [3 /*break*/, 25];
+                            case 20:
+                                ligandExp = _l.sent();
+                                if (!ligandExp) return [3 /*break*/, 22];
                                 return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(ligandExp, { type: 'ball-and-stick', color: 'uniform', colorParams: { value: hetColor } }, { tag: "superposition-ligand-visual" })];
-                            case 24:
-                                _q.sent();
+                            case 21:
+                                _l.sent();
                                 spState.refMaps[ligandExp.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
                                 invalidStruct = false;
-                                _q.label = 25;
-                            case 25: return [3 /*break*/, 27];
-                            case 26:
-                                _c = true;
+                                _l.label = 22;
+                            case 22: return [3 /*break*/, 24];
+                            case 23:
+                                _b = true;
                                 return [7 /*endfinally*/];
-                            case 27: return [3 /*break*/, 20];
-                            case 28: return [3 /*break*/, 35];
-                            case 29:
-                                e_2_1 = _q.sent();
+                            case 24: return [3 /*break*/, 17];
+                            case 25: return [3 /*break*/, 32];
+                            case 26:
+                                e_2_1 = _l.sent();
                                 e_2 = { error: e_2_1 };
-                                return [3 /*break*/, 35];
+                                return [3 /*break*/, 32];
+                            case 27:
+                                _l.trys.push([27, , 30, 31]);
+                                if (!(!_b && !_g && (_h = hets_1.return))) return [3 /*break*/, 29];
+                                return [4 /*yield*/, _h.call(hets_1)];
+                            case 28:
+                                _l.sent();
+                                _l.label = 29;
+                            case 29: return [3 /*break*/, 31];
                             case 30:
-                                _q.trys.push([30, , 33, 34]);
-                                if (!(!_c && !_l && (_m = hets_1.return))) return [3 /*break*/, 32];
-                                return [4 /*yield*/, _m.call(hets_1)];
-                            case 31:
-                                _q.sent();
-                                _q.label = 32;
-                            case 32: return [3 /*break*/, 34];
-                            case 33:
                                 if (e_2) throw e_2.error;
                                 return [7 /*endfinally*/];
-                            case 34: return [7 /*endfinally*/];
-                            case 35:
+                            case 31: return [7 /*endfinally*/];
+                            case 32:
                                 carbEntityCount = hetInfo ? hetInfo.carbEntityCount : 0;
-                                if (!(carbEntityCount > 0)) return [3 /*break*/, 42];
+                                if (!(carbEntityCount > 0)) return [3 /*break*/, 39];
                                 return [4 /*yield*/, getCarbPolymerDetailsFromApi(plugin, s.pdb_id)];
-                            case 36:
-                                allCarbPolymers = _q.sent();
+                            case 33:
+                                allCarbPolymers = _l.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']),
@@ -498,11 +479,11 @@ function renderSuperposition(plugin, segmentIndex, entryList) {
                                     'as-whole-residues': true
                                 });
                                 i = 0;
-                                _i = 0, _e = allCarbPolymers.branchedChains;
-                                _q.label = 37;
-                            case 37:
-                                if (!(_i < _e.length)) return [3 /*break*/, 42];
-                                carbEntityChainId = _e[_i];
+                                _c = 0, _d = allCarbPolymers.branchedChains;
+                                _l.label = 34;
+                            case 34:
+                                if (!(_c < _d.length)) return [3 /*break*/, 39];
+                                carbEntityChainId = _d[_c];
                                 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]),
@@ -514,12 +495,12 @@ function renderSuperposition(plugin, segmentIndex, entryList) {
                                 });
                                 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*/, 40];
+                                if (!(carbChainSel && carbChainSel.kind === 'sequence')) return [3 /*break*/, 37];
                                 carbLigands = [];
                                 carbLigNamesAndCount = {};
                                 carbLigList = [];
-                                for (_f = 0, _g = allCarbPolymers.branchedLigands[i]; _f < _g.length; _f++) {
-                                    carbLigs = _g[_f];
+                                for (_e = 0, _f = allCarbPolymers.branchedLigands[i]; _e < _f.length; _e++) {
+                                    carbLigs = _f[_e];
                                     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]]) {
@@ -539,22 +520,22 @@ function renderSuperposition(plugin, segmentIndex, entryList) {
                                 });
                                 labelTagParams = { label: "".concat(carbVisLabel), tags: ["superposition-carb-sel"] };
                                 return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(strInstance, branchedEntity, "".concat(carbLigList.join('-'), "-").concat(segmentIndex), labelTagParams)];
-                            case 38:
-                                ligandExp = _q.sent();
-                                if (!ligandExp) return [3 /*break*/, 40];
+                            case 35:
+                                ligandExp = _l.sent();
+                                if (!ligandExp) return [3 /*break*/, 37];
                                 return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(ligandExp, { type: 'carbohydrate' }, { tag: "superposition-carb-visual" })];
-                            case 39:
-                                _q.sent();
+                            case 36:
+                                _l.sent();
                                 spState.refMaps[ligandExp.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
                                 invalidStruct = false;
-                                _q.label = 40;
-                            case 40:
+                                _l.label = 37;
+                            case 37:
                                 i++;
-                                _q.label = 41;
-                            case 41:
-                                _i++;
-                                return [3 /*break*/, 37];
-                            case 42:
+                                _l.label = 38;
+                            case 38:
+                                _c++;
+                                return [3 /*break*/, 34];
+                            case 39:
                                 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));
@@ -571,33 +552,14 @@ function renderSuperposition(plugin, segmentIndex, entryList) {
                                 else {
                                     // if(interactingHets.length > 0) spState.hets[`${s.pdb_id}_${s.struct_asym_id}`] = interactingHets;
                                 }
-                                _q.label = 43;
-                            case 43: return [3 /*break*/, 45];
-                            case 44:
-                                _a = true;
-                                return [7 /*endfinally*/];
-                            case 45: return [3 /*break*/, 2];
-                            case 46: return [3 /*break*/, 53];
-                            case 47:
-                                e_3_1 = _q.sent();
-                                e_3 = { error: e_3_1 };
-                                return [3 /*break*/, 53];
-                            case 48:
-                                _q.trys.push([48, , 51, 52]);
-                                if (!(!_a && !_h && (_j = entryList_2.return))) return [3 /*break*/, 50];
-                                return [4 /*yield*/, _j.call(entryList_2)];
-                            case 49:
-                                _q.sent();
-                                _q.label = 50;
-                            case 50: return [3 /*break*/, 52];
-                            case 51:
-                                if (e_3) throw e_3.error;
-                                return [7 /*endfinally*/];
-                            case 52: return [7 /*endfinally*/];
-                            case 53:
+                                _l.label = 40;
+                            case 40:
+                                _i++;
+                                return [3 /*break*/, 1];
+                            case 41:
                                 if (busyFlagOn) {
                                     busyFlagOn = false;
-                                    (_p = customState.events) === null || _p === void 0 ? void 0 : _p.isBusy.next(false);
+                                    (_k = customState.events) === null || _k === void 0 ? void 0 : _k.isBusy.next(false);
                                 }
                                 return [2 /*return*/];
                         }
@@ -637,7 +599,7 @@ function getLigandNamesFromModelData(plugin, state, modelRef) {
 }
 function loadStructure(plugin, url, format, isBinary) {
     return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var data, trajectory, model, modelProperties, structure, e_4;
+        var data, trajectory, model, modelProperties, structure, e_3;
         return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -662,7 +624,7 @@ function loadStructure(plugin, url, format, isBinary) {
                     _a.sent();
                     return [2 /*return*/, { data: data, trajectory: trajectory, model: model, structure: structure }];
                 case 7:
-                    e_4 = _a.sent();
+                    e_3 = _a.sent();
                     return [2 /*return*/, { structure: void 0 }];
                 case 8: return [2 /*return*/];
             }
@@ -715,7 +677,7 @@ function afTransform(plugin, s, matrix, coordinateSystem) {
 function getMatrixData(plugin) {
     var _a, _b, _c;
     return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var customState, matrixAccession, clusterRecUrlStr, assetManager, clusterRecUrl, clusterRecData, e_5;
+        var customState, matrixAccession, clusterRecUrlStr, assetManager, clusterRecUrl, clusterRecData, e_4;
         return tslib_1.__generator(this, function (_d) {
             switch (_d.label) {
                 case 0:
@@ -739,7 +701,7 @@ function getMatrixData(plugin) {
                     }
                     return [3 /*break*/, 4];
                 case 3:
-                    e_5 = _d.sent();
+                    e_4 = _d.sent();
                     customState.superpositionError = "Matrix data not available for ".concat(matrixAccession);
                     (_c = customState.events) === null || _c === void 0 ? void 0 : _c.superpositionInit.next(true); // Emit segment API data load event
                     return [3 /*break*/, 4];
@@ -748,10 +710,11 @@ function getMatrixData(plugin) {
         });
     });
 }
+/** Download data about segment clustering and save in plugin custom state */
 function getSegmentData(plugin) {
     var _a;
     return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var customState, segmentsUrl, assetManager, url, result, e_6;
+        var customState, segmentsUrl, assetManager, url, result, e_5;
         return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
@@ -774,7 +737,7 @@ function getSegmentData(plugin) {
                     }
                     return [3 /*break*/, 4];
                 case 3:
-                    e_6 = _b.sent();
+                    e_5 = _b.sent();
                     customState.superpositionError = "Superposition data not available for ".concat(customState.initParams.moleculeId);
                     (_a = customState.events) === null || _a === void 0 ? void 0 : _a.superpositionInit.next(true); // Emit segment API data load event
                     return [3 /*break*/, 4];
@@ -813,7 +776,7 @@ function getChainLigands(carbEntity) {
 }
 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;
+        var customState, apiUrl, assetManager, url, branchedLigands, branchedChains, branchedlabels, result, carbEntities, _i, carbEntities_1, carbEntity, carbLigData, e_6;
         return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -844,7 +807,7 @@ function getCarbPolymerDetailsFromApi(plugin, pdb_id) {
                     }
                     return [3 /*break*/, 4];
                 case 3:
-                    e_7 = _a.sent();
+                    e_6 = _a.sent();
                     return [3 /*break*/, 4];
                 case 4: return [2 /*return*/, {
                         branchedChains: branchedChains,

package/lib/ui/alphafold-superposition.d.ts

@@ -1,5 +1,5 @@
-import { CollapsableControls, PurePluginUIComponent } from 'Molstar/mol-plugin-ui/base';
-import { ParamDefinition as PD } from 'Molstar/mol-util/param-definition';
+import { CollapsableControls, PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
 import { PluginCustomState } from '../plugin-custom-state';
 export declare function InfoIconSvg(): import("react/jsx-runtime").JSX.Element;
 export declare class AlphafoldPaeControls extends CollapsableControls {
@@ -9,7 +9,7 @@ export declare class AlphafoldPaeControls extends CollapsableControls {
         header: string;
         brand: {
             accent: "gray";
-            svg: typeof import("Molstar/mol-plugin-ui/controls/icons").FlipToFrontSvg;
+            svg: typeof import("molstar/lib/mol-plugin-ui/controls/icons").FlipToFrontSvg;
         };
         isHidden: boolean;
     };
@@ -24,7 +24,7 @@ export declare class AlphafoldSuperpositionControls extends CollapsableControls
         header: string;
         brand: {
             accent: "gray";
-            svg: typeof import("Molstar/mol-plugin-ui/controls/icons").FlipToFrontSvg;
+            svg: typeof import("molstar/lib/mol-plugin-ui/controls/icons").FlipToFrontSvg;
         };
         isHidden: boolean;
     };

package/lib/ui/alphafold-superposition.js

@@ -3,17 +3,17 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.AfSuperpositionControls = exports.AlphafoldSuperpositionParams = exports.AlphafoldSuperpositionControls = exports.AlphafoldPaeControls = exports.InfoIconSvg = void 0;
 var tslib_1 = require("tslib");
 var jsx_runtime_1 = require("react/jsx-runtime");
-var react_1 = tslib_1.__importDefault(require("react"));
-var base_1 = require("Molstar/mol-plugin-ui/base");
-var icons_1 = require("Molstar/mol-plugin-ui/controls/icons");
-var common_1 = require("Molstar/mol-plugin-ui/controls/common");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
-var parameters_1 = require("Molstar/mol-plugin-ui/controls/parameters");
-var superposition_1 = require("../superposition");
-var d3_scale_1 = require("d3-scale");
 var d3_axis_1 = require("d3-axis");
+var d3_scale_1 = require("d3-scale");
 var d3_selection_1 = require("d3-selection");
+var base_1 = require("molstar/lib/mol-plugin-ui/base");
+var common_1 = require("molstar/lib/mol-plugin-ui/controls/common");
+var icons_1 = require("molstar/lib/mol-plugin-ui/controls/icons");
+var parameters_1 = require("molstar/lib/mol-plugin-ui/controls/parameters");
+var param_definition_1 = require("molstar/lib/mol-util/param-definition");
+var react_1 = tslib_1.__importDefault(require("react"));
 var plugin_custom_state_1 = require("../plugin-custom-state");
+var superposition_1 = require("../superposition");
 var _InfoIcon = (0, jsx_runtime_1.jsx)("svg", tslib_1.__assign({ width: '24px', height: '24px', viewBox: '0 0 24 24', strokeWidth: '0.1px' }, { children: (0, jsx_runtime_1.jsx)("path", { fill: "currentColor", d: "M11,9H13V7H11M12,20C7.59,20 4,16.41 4,12C4,7.59 7.59,4 12,4C16.41,4 20,7.59 20,12C20,16.41 16.41,20 12,20M12,2A10,10 0 0,0 2,12A10,10 0 0,0 12,22A10,10 0 0,0 22,12A10,10 0 0,0 12,2M11,17H13V11H11V17Z" }) }));
 function InfoIconSvg() { return _InfoIcon; }
 exports.InfoIconSvg = InfoIconSvg;

package/lib/ui/alphafold-tranparency.d.ts

@@ -1,4 +1,4 @@
-import { CollapsableControls } from 'Molstar/mol-plugin-ui/base';
+import { CollapsableControls } from 'molstar/lib/mol-plugin-ui/base';
 export declare class AlphafoldTransparencyControls extends CollapsableControls<{}, {
     transpareny: any;
 }> {
@@ -7,7 +7,7 @@ export declare class AlphafoldTransparencyControls extends CollapsableControls<{
         header: string;
         brand: {
             accent: "gray";
-            svg: typeof import("Molstar/mol-plugin-ui/controls/icons").FlipToFrontSvg;
+            svg: typeof import("molstar/lib/mol-plugin-ui/controls/icons").FlipToFrontSvg;
         };
         isHidden: boolean;
         transpareny: {

package/lib/ui/alphafold-tranparency.js

@@ -3,10 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.AlphafoldTransparencyControls = void 0;
 var tslib_1 = require("tslib");
 var jsx_runtime_1 = require("react/jsx-runtime");
-var base_1 = require("Molstar/mol-plugin-ui/base");
-var icons_1 = require("Molstar/mol-plugin-ui/controls/icons");
-var parameters_1 = require("Molstar/mol-plugin-ui/controls/parameters");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
+var base_1 = require("molstar/lib/mol-plugin-ui/base");
+var icons_1 = require("molstar/lib/mol-plugin-ui/controls/icons");
+var parameters_1 = require("molstar/lib/mol-plugin-ui/controls/parameters");
+var param_definition_1 = require("molstar/lib/mol-util/param-definition");
 var alphafold_transparency_1 = require("../alphafold-transparency");
 var plugin_custom_state_1 = require("../plugin-custom-state");
 var TransparencyParams = {