pdbe-molstar 3.2.0-beta.4 → 3.2.1-beta.1

package/lib/index(light).js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Tags = exports.PDBeMolstarPlugin = void 0;
+exports.PDBeMolstarPlugin = void 0;
 var tslib_1 = require("tslib");
 var geo_export_1 = require("Molstar/extensions/geo-export");
 var behavior_1 = require("Molstar/extensions/model-archive/quality-assessment/behavior");
@@ -20,6 +20,7 @@ var state_interpolation_1 = require("Molstar/mol-plugin-state/animation/built-in
 var state_snapshots_1 = require("Molstar/mol-plugin-state/animation/built-in/state-snapshots");
 var structure_overpaint_1 = require("Molstar/mol-plugin-state/helpers/structure-overpaint");
 var structure_representation_params_1 = require("Molstar/mol-plugin-state/helpers/structure-representation-params");
+var objects_1 = require("Molstar/mol-plugin-state/objects");
 var transforms_1 = require("Molstar/mol-plugin-state/transforms");
 var model_1 = require("Molstar/mol-plugin-state/transforms/model");
 var representation_1 = require("Molstar/mol-plugin-state/transforms/representation");
@@ -40,6 +41,7 @@ var names_1 = require("Molstar/mol-util/color/names");
 var rx_event_helper_1 = require("Molstar/mol-util/rx-event-helper");
 var custom_events_1 = require("./custom-events");
 var behavior_4 = require("./domain-annotations/behavior");
+var Foldseek = tslib_1.__importStar(require("./extensions/foldseek"));
 var helpers_1 = require("./helpers");
 var overlay_1 = require("./overlay");
 var plugin_custom_state_1 = require("./plugin-custom-state");
@@ -66,13 +68,15 @@ var PDBeMolstarPlugin = /** @class */ (function () {
         this.isSelectedColorUpdated = false;
         /** Keeps track of representations added by `.visual.select` for each structure. */
         this.addedReprs = {};
+        /** Maps structure IDs (assigned when loading) to cell refs. */
+        this.structureRefMap = new Map();
         this.applyVisualParams = function () {
             var _a;
             var componentGroups = _this.plugin.managers.structure.hierarchy.currentComponentGroups;
             var _loop_1 = function (compGroup) {
                 var compRef = compGroup[compGroup.length - 1];
                 var tag = (_a = compRef.key) !== null && _a !== void 0 ? _a : '';
-                var remove = _this.initParams.hideStructure.some(function (type) { var _a; return (_a = StructureComponentTags[type]) === null || _a === void 0 ? void 0 : _a.includes(tag); });
+                var remove = _this.initParams.hideStructure.some(function (type) { var _a; return (_a = helpers_1.StructureComponentTags[type]) === null || _a === void 0 ? void 0 : _a.includes(tag); });
                 if (remove) {
                     _this.plugin.managers.structure.hierarchy.remove([compRef]);
                 }
@@ -90,17 +94,9 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                 _loop_1(compGroup);
             }
         };
+        /** Helper methods related to canvas and layout */
         this.canvas = {
-            toggleControls: function (isVisible) {
-                if (typeof isVisible === 'undefined')
-                    isVisible = !_this.plugin.layout.state.showControls;
-                commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { showControls: isVisible } });
-            },
-            toggleExpanded: function (isExpanded) {
-                if (typeof isExpanded === 'undefined')
-                    isExpanded = !_this.plugin.layout.state.isExpanded;
-                commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { isExpanded: isExpanded } });
-            },
+            /** Set canvas background color. */
             setBgColor: function (color) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                 return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
@@ -114,6 +110,18 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                     }
                 });
             }); },
+            /** Set controls panel visibility. Without `isVisible` parameter, toggle controls panel visibility. */
+            toggleControls: function (isVisible) {
+                if (typeof isVisible === 'undefined')
+                    isVisible = !_this.plugin.layout.state.showControls;
+                commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { showControls: isVisible } });
+            },
+            /** Set full-screen mode on or off. Without `isExpanded` parameter, toggle full-screen mode. */
+            toggleExpanded: function (isExpanded) {
+                if (typeof isExpanded === 'undefined')
+                    isExpanded = !_this.plugin.layout.state.isExpanded;
+                commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { isExpanded: isExpanded } });
+            },
             applySettings: function (settings) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                 var renderer;
                 return tslib_1.__generator(this, function (_a) {
@@ -138,54 +146,187 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                 });
             }); },
         };
+        /** Helper methods related to 3D visuals */
         this.visual = {
-            highlight: function (params) {
-                var loci = _this.getLociForParams(params.data, params.structureNumber);
-                if (loci_1.Loci.isEmpty(loci))
-                    return;
-                if (params.color) {
-                    _this.visual.setColor({ highlight: params.color });
-                }
-                _this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci: loci });
-                if (params.focus)
-                    _this.plugin.managers.camera.focusLoci(loci);
-            },
-            clearHighlight: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            /** Change the visibility of individual entity visuals */
+            visibility: function (data) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var _a, _b, _c, _i, visual, requiredVisibility, tags, _d, tags_1, tag, componentRef, compVisual, currentlyVisible;
+                var _e;
+                return tslib_1.__generator(this, function (_f) {
+                    switch (_f.label) {
+                        case 0:
+                            if (!data)
+                                return [2 /*return*/];
+                            _a = data;
+                            _b = [];
+                            for (_c in _a)
+                                _b.push(_c);
+                            _i = 0;
+                            _f.label = 1;
+                        case 1:
+                            if (!(_i < _b.length)) return [3 /*break*/, 6];
+                            _c = _b[_i];
+                            if (!(_c in _a)) return [3 /*break*/, 5];
+                            visual = _c;
+                            requiredVisibility = data[visual];
+                            if (requiredVisibility === undefined)
+                                return [3 /*break*/, 5];
+                            tags = (_e = helpers_1.StructureComponentTags[visual]) !== null && _e !== void 0 ? _e : [];
+                            _d = 0, tags_1 = tags;
+                            _f.label = 2;
+                        case 2:
+                            if (!(_d < tags_1.length)) return [3 /*break*/, 5];
+                            tag = tags_1[_d];
+                            componentRef = mol_state_1.StateSelection.findTagInSubtree(this.plugin.state.data.tree, mol_state_1.StateTransform.RootRef, tag);
+                            if (!componentRef) return [3 /*break*/, 4];
+                            compVisual = this.plugin.state.data.select(componentRef)[0];
+                            if (!(compVisual && compVisual.obj)) return [3 /*break*/, 4];
+                            currentlyVisible = !(compVisual.state && compVisual.state.isHidden);
+                            if (!(currentlyVisible !== requiredVisibility)) return [3 /*break*/, 4];
+                            return [4 /*yield*/, commands_1.PluginCommands.State.ToggleVisibility(this.plugin, { state: this.state, ref: componentRef })];
+                        case 3:
+                            _f.sent();
+                            _f.label = 4;
+                        case 4:
+                            _d++;
+                            return [3 /*break*/, 2];
+                        case 5:
+                            _i++;
+                            return [3 /*break*/, 1];
+                        case 6: return [2 /*return*/];
+                    }
+                });
+            }); },
+            /** Change the visibility of a structure.
+             * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure.
+             * If `visibility` is undefined, toggle current visibility state. */
+            structureVisibility: function (structureNumberOrId, visibility) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var struct, currentVisibility;
+                return tslib_1.__generator(this, function (_a) {
+                    switch (_a.label) {
+                        case 0:
+                            struct = this.getStructure(structureNumberOrId);
+                            if (!struct) {
+                                console.error("Cannot change visibility of structure ".concat(structureNumberOrId, ": structure not found."));
+                                return [2 /*return*/];
+                            }
+                            currentVisibility = !struct.cell.state.isHidden;
+                            if (!(visibility !== currentVisibility)) return [3 /*break*/, 2];
+                            return [4 /*yield*/, commands_1.PluginCommands.State.ToggleVisibility(this.plugin, { state: this.state, ref: struct.cell.transform.ref })];
+                        case 1:
+                            _a.sent();
+                            _a.label = 2;
+                        case 2: return [2 /*return*/];
+                    }
+                });
+            }); },
+            /** With `isSpinning` parameter, switch visual rotation on or off. Without `isSpinning` parameter, toggle rotation. If `resetCamera`, also reset the camera zoom. */
+            toggleSpin: function (isSpinning, resetCamera) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var trackball, toggleSpinParam;
                 return tslib_1.__generator(this, function (_a) {
-                    this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci: loci_1.EmptyLoci });
-                    if (this.isHighlightColorUpdated)
-                        this.visual.reset({ highlightColor: true });
+                    switch (_a.label) {
+                        case 0:
+                            if (!this.plugin.canvas3d)
+                                return [2 /*return*/];
+                            trackball = this.plugin.canvas3d.props.trackball;
+                            toggleSpinParam = trackball.animate.name === 'spin' ? { name: 'off', params: {} } : { name: 'spin', params: { speed: 1 } };
+                            if (typeof isSpinning !== 'undefined') {
+                                toggleSpinParam = { name: 'off', params: {} };
+                                if (isSpinning)
+                                    toggleSpinParam = { name: 'spin', params: { speed: 1 } };
+                            }
+                            return [4 /*yield*/, commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: tslib_1.__assign(tslib_1.__assign({}, trackball), { animate: toggleSpinParam }) } })];
+                        case 1:
+                            _a.sent();
+                            if (!resetCamera) return [3 /*break*/, 3];
+                            return [4 /*yield*/, commands_1.PluginCommands.Camera.Reset(this.plugin, {})];
+                        case 2:
+                            _a.sent();
+                            _a.label = 3;
+                        case 3: return [2 /*return*/];
+                    }
+                });
+            }); },
+            /** Focus (zoom) on the part of the structure defined by `selection`.
+             * If `selection` contains more items, focus on the union of those.
+             * If `structureNumber` is provided, use the specified structure (numbered from 1!); otherwise use the last added structure. */
+            focus: function (selection, structureNumber) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var loci;
+                return tslib_1.__generator(this, function (_a) {
+                    loci = this.getLociForParams(selection, structureNumber);
+                    this.plugin.managers.camera.focusLoci(loci);
                     return [2 /*return*/];
                 });
             }); },
-            /** `structureNumber` counts from 1; if not provided, select will be applied to all loaded structures.
-             * Use `keepColors` and/or `keepRepresentations` to preserve currently active selection.
-             */
+            /** Trigger highlight on the part of the structure defined by `data`
+             * (this will look the same as when the user hovers over a part of the structure).
+             * If `focus`, also zoom on the highlighted part.
+             * If `structureNumber` is provided, use the specified structure (numbered from 1!); otherwise use the last added structure. */
+            highlight: function (params) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var loci;
+                return tslib_1.__generator(this, function (_a) {
+                    switch (_a.label) {
+                        case 0:
+                            loci = this.getLociForParams(params.data, params.structureNumber);
+                            if (loci_1.Loci.isEmpty(loci))
+                                return [2 /*return*/];
+                            if (!params.color) return [3 /*break*/, 2];
+                            return [4 /*yield*/, this.visual.setColor({ highlight: params.color })];
+                        case 1:
+                            _a.sent();
+                            _a.label = 2;
+                        case 2:
+                            this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci: loci });
+                            if (params.focus)
+                                this.plugin.managers.camera.focusLoci(loci);
+                            return [2 /*return*/];
+                    }
+                });
+            }); },
+            /** Remove any current highlight and reset the highlight color to its default value. */
+            clearHighlight: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                return tslib_1.__generator(this, function (_a) {
+                    switch (_a.label) {
+                        case 0:
+                            this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci: loci_1.EmptyLoci });
+                            if (!this.isHighlightColorUpdated) return [3 /*break*/, 2];
+                            return [4 /*yield*/, this.visual.reset({ highlightColor: true })];
+                        case 1:
+                            _a.sent();
+                            _a.label = 2;
+                        case 2: return [2 /*return*/];
+                    }
+                });
+            }); },
+            /** Color the parts of the structure defined by `data`. Color the rest of the structure in `nonSelectedColor` if provided.
+             * If any items in `data` contain `focus`, zoom to the union of these items.
+             * If any items in `data` contain `sideChain` or `representation`, add extra representations to them (colored in `representationColor` if provided).
+             * If `structureNumber` is provided, apply to the specified structure (numbered from 1!); otherwise apply to all loaded structures.
+             * Remove any previously added coloring and extra representations, unless `keepColors` and/or `keepRepresentations` is set. */
             select: function (params) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-                var structures, addedReprParams, _i, _a, param, repr, DefaultSelectColor, focusLoci, _b, structures_1, struct, selections, _c, selections_1, selection, overpaintLayers, wholeStructBundle, _d, _e, _f, _g, repr, bundle, overpaintLayers_1;
+                var structureNumberOrId, structures, addedReprParams, _i, _a, param, repr, DefaultSelectColor, focusLoci, _b, structures_1, struct, selections, _c, selections_1, selection, overpaintLayers, wholeStructBundle, _d, _e, _f, _g, repr, bundle, overpaintLayers_1;
                 var _this = this;
-                var _h, _j, _k;
-                return tslib_1.__generator(this, function (_l) {
-                    switch (_l.label) {
-                        case 0: return [4 /*yield*/, this.visual.clearSelection(params.structureNumber, { keepColors: params.keepColors, keepRepresentations: params.keepRepresentations })];
+                var _h, _j, _k, _l;
+                return tslib_1.__generator(this, function (_m) {
+                    switch (_m.label) {
+                        case 0:
+                            structureNumberOrId = (_h = params.structureId) !== null && _h !== void 0 ? _h : params.structureNumber;
+                            return [4 /*yield*/, this.visual.clearSelection(structureNumberOrId, { keepColors: params.keepColors, keepRepresentations: params.keepRepresentations })];
                         case 1:
-                            _l.sent();
-                            structures = this.plugin.managers.structure.hierarchy.current.structures.map(function (structureRef, i) { return ({ structureRef: structureRef, number: i + 1 }); });
-                            if (params.structureNumber !== undefined) {
-                                structures = [structures[params.structureNumber - 1]];
-                            }
+                            _m.sent();
+                            structures = this.getStructures(structureNumberOrId);
                             addedReprParams = {};
                             for (_i = 0, _a = params.data; _i < _a.length; _i++) {
                                 param = _a[_i];
-                                repr = (_h = param.representation) !== null && _h !== void 0 ? _h : (param.sideChain ? 'ball-and-stick' : undefined);
+                                repr = (_j = param.representation) !== null && _j !== void 0 ? _j : (param.sideChain ? 'ball-and-stick' : undefined);
                                 if (repr) {
-                                    ((_j = addedReprParams[repr]) !== null && _j !== void 0 ? _j : (addedReprParams[repr] = [])).push(param);
+                                    ((_k = addedReprParams[repr]) !== null && _k !== void 0 ? _k : (addedReprParams[repr] = [])).push(param);
                                 }
                             }
                             DefaultSelectColor = color_1.Color.fromRgb(255, 112, 3);
                             focusLoci = [];
                             _b = 0, structures_1 = structures;
-                            _l.label = 2;
+                            _m.label = 2;
                         case 2:
                             if (!(_b < structures_1.length)) return [3 /*break*/, 8];
                             struct = structures_1[_b];
@@ -215,13 +356,13 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                             }
                             return [4 /*yield*/, (0, helpers_1.applyOverpaint)(this.plugin, struct.structureRef, overpaintLayers)];
                         case 3:
-                            _l.sent();
+                            _m.sent();
                             _d = addedReprParams;
                             _e = [];
                             for (_f in _d)
                                 _e.push(_f);
                             _g = 0;
-                            _l.label = 4;
+                            _m.label = 4;
                         case 4:
                             if (!(_g < _e.length)) return [3 /*break*/, 7];
                             _f = _e[_g];
@@ -237,15 +378,15 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                             }); });
                             return [4 /*yield*/, this.plugin.build()
                                     .to(struct.structureRef.cell)
-                                    .apply(model_1.StructureComponent, { type: { name: 'bundle', params: bundle }, label: repr }, { tags: exports.Tags.AddedComponent })
-                                    .apply(representation_1.StructureRepresentation3D, (0, structure_representation_params_1.createStructureRepresentationParams)(this.plugin, (_k = struct.structureRef.cell.obj) === null || _k === void 0 ? void 0 : _k.data, { type: repr }))
-                                    .apply(transforms_1.StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, { layers: overpaintLayers_1 }, { tags: exports.Tags.Overpaint })
+                                    .apply(model_1.StructureComponent, { type: { name: 'bundle', params: bundle }, label: repr }, { tags: helpers_1.Tags.AddedComponent })
+                                    .apply(representation_1.StructureRepresentation3D, (0, structure_representation_params_1.createStructureRepresentationParams)(this.plugin, (_l = struct.structureRef.cell.obj) === null || _l === void 0 ? void 0 : _l.data, { type: repr }))
+                                    .apply(transforms_1.StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, { layers: overpaintLayers_1 }, { tags: helpers_1.Tags.Overpaint })
                                     .commit()];
                         case 5:
-                            _l.sent();
+                            _m.sent();
                             // Track that reprs have been added (for later clearSelection)
                             this.addedReprs[struct.number] = true;
-                            _l.label = 6;
+                            _m.label = 6;
                         case 6:
                             _g++;
                             return [3 /*break*/, 4];
@@ -261,25 +402,22 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                     }
                 });
             }); },
-            /** Clear any currently active "selection" (i.e. colored residues and added representations via `select`).
-             * `structureNumber` counts from 1; if not provided, clearSelection will be applied to all loaded structures.
-             * If `keepColors`, curent residue coloring is preserved. If `keepRepresentations`, current added representations are preserved. */
-            clearSelection: function (structureNumber, options) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            /** Remove any coloring and extra representations previously added by the `select` method.
+             * If `structureNumber` is provided, apply to the specified structure (numbered from 1!); otherwise apply to all loaded structures.
+             * If `keepColors`, current residue coloring is preserved. If `keepRepresentations`, current added representations are preserved. */
+            clearSelection: function (structureNumberOrId, options) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                 var structures, _i, structures_2, struct, componentsToClear, componentsToDelete, update, _a, componentsToDelete_1, comp;
                 return tslib_1.__generator(this, function (_b) {
                     switch (_b.label) {
                         case 0:
-                            structures = this.plugin.managers.structure.hierarchy.current.structures.map(function (structureRef, i) { return ({ structureRef: structureRef, number: i + 1 }); });
-                            if (structureNumber !== undefined) {
-                                structures = [structures[structureNumber - 1]];
-                            }
+                            structures = this.getStructures(structureNumberOrId);
                             _i = 0, structures_2 = structures;
                             _b.label = 1;
                         case 1:
                             if (!(_i < structures_2.length)) return [3 /*break*/, 6];
                             struct = structures_2[_i];
                             if (!!(options === null || options === void 0 ? void 0 : options.keepColors)) return [3 /*break*/, 3];
-                            componentsToClear = struct.structureRef.components.filter(function (c) { var _a; return !((_a = c.cell.transform.tags) === null || _a === void 0 ? void 0 : _a.includes(exports.Tags.AddedComponent)); });
+                            componentsToClear = struct.structureRef.components.filter(function (c) { var _a; return !((_a = c.cell.transform.tags) === null || _a === void 0 ? void 0 : _a.includes(helpers_1.Tags.AddedComponent)); });
                             return [4 /*yield*/, (0, structure_overpaint_1.clearStructureOverpaint)(this.plugin, componentsToClear)];
                         case 2:
                             _b.sent();
@@ -287,7 +425,7 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                         case 3:
                             if (!!(options === null || options === void 0 ? void 0 : options.keepRepresentations)) return [3 /*break*/, 5];
                             if (!this.addedReprs[struct.number]) return [3 /*break*/, 5];
-                            componentsToDelete = struct.structureRef.components.filter(function (comp) { var _a; return (_a = comp.cell.transform.tags) === null || _a === void 0 ? void 0 : _a.includes(exports.Tags.AddedComponent); });
+                            componentsToDelete = struct.structureRef.components.filter(function (comp) { var _a; return (_a = comp.cell.transform.tags) === null || _a === void 0 ? void 0 : _a.includes(helpers_1.Tags.AddedComponent); });
                             update = this.plugin.build();
                             for (_a = 0, componentsToDelete_1 = componentsToDelete; _a < componentsToDelete_1.length; _a++) {
                                 comp = componentsToDelete_1[_a];
@@ -305,148 +443,99 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                     }
                 });
             }); },
-            update: function (options, fullLoad) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-                var validationIssues, dataSource;
-                return tslib_1.__generator(this, function (_a) {
-                    switch (_a.label) {
-                        case 0:
-                            console.debug('Updating PDBeMolstarPlugin instance with options:', options);
-                            // Validate options
-                            if (!options) {
-                                console.error('Missing `options` argument to `PDBeMolstarPlugin.visual.update');
-                                return [2 /*return*/];
-                            }
-                            validationIssues = (0, spec_2.validateInitParams)(options);
-                            if (validationIssues) {
-                                console.error('Invalid PDBeMolstarPlugin options:', options);
-                                return [2 /*return*/];
-                            }
-                            this.initParams = (0, helpers_1.addDefaults)(options, spec_2.DefaultParams);
-                            if (!this.initParams.moleculeId && !this.initParams.customData)
-                                return [2 /*return*/, false];
-                            if (this.initParams.customData && this.initParams.customData.url && !this.initParams.customData.format)
-                                return [2 /*return*/, false];
-                            (0, plugin_custom_state_1.PluginCustomState)(this.plugin).initParams = this.initParams;
-                            // Show/hide buttons in the viewport control panel
-                            this.plugin.config.set(config_1.PluginConfig.Viewport.ShowExpand, !this.initParams.hideCanvasControls.includes('expand'));
-                            this.plugin.config.set(config_1.PluginConfig.Viewport.ShowSelectionMode, !this.initParams.hideCanvasControls.includes('selection'));
-                            this.plugin.config.set(config_1.PluginConfig.Viewport.ShowAnimation, !this.initParams.hideCanvasControls.includes('animation'));
-                            this.plugin.config.set(config_1.PluginConfig.Viewport.ShowControls, !this.initParams.hideCanvasControls.includes('controlToggle'));
-                            this.plugin.config.set(config_1.PluginConfig.Viewport.ShowSettings, !this.initParams.hideCanvasControls.includes('controlInfo'));
-                            if (!(this.initParams.bgColor || this.initParams.lighting)) return [3 /*break*/, 2];
-                            return [4 /*yield*/, this.canvas.applySettings({ color: this.initParams.bgColor, lighting: this.initParams.lighting })];
-                        case 1:
-                            _a.sent();
-                            _a.label = 2;
-                        case 2:
-                            dataSource = this.getMoleculeSrcUrl();
-                            if (!dataSource) return [3 /*break*/, 4];
-                            return [4 /*yield*/, this.load({ url: dataSource.url, format: dataSource.format, assemblyId: this.initParams.assemblyId, isBinary: dataSource.isBinary }, fullLoad)];
-                        case 3:
-                            _a.sent();
-                            _a.label = 4;
-                        case 4: return [2 /*return*/];
-                    }
-                });
-            }); },
-            visibility: function (data) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-                var _a, _b, _c, _i, visual, tags, _d, tags_1, tag, componentRef, compVisual, currentlyVisible;
-                var _e;
-                return tslib_1.__generator(this, function (_f) {
-                    switch (_f.label) {
+            /** Add interactive tooltips to parts of the structure. The added tooltips will be shown on a separate line in the tooltip box.
+             * Repeated call to this function removes any previously added tooltips.
+             * `structureNumber` counts from 1; if not provided, tooltips will be applied to all loaded structures.
+             * Example: `await this.visual.tooltips({ data: [{ struct_asym_id: 'A', tooltip: 'Chain A' }, { struct_asym_id: 'B', tooltip: 'Chain B' }] });`. */
+            tooltips: function (params) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var structures, _loop_2, this_1, _i, structures_3, struct;
+                var _a;
+                return tslib_1.__generator(this, function (_b) {
+                    switch (_b.label) {
                         case 0:
-                            if (!data)
-                                return [2 /*return*/];
-                            _a = data;
-                            _b = [];
-                            for (_c in _a)
-                                _b.push(_c);
-                            _i = 0;
-                            _f.label = 1;
+                            structures = this.getStructures((_a = params.structureId) !== null && _a !== void 0 ? _a : params.structureNumber);
+                            _loop_2 = function (struct) {
+                                var selections, customTooltipProps, structRef, customPropsCells;
+                                return tslib_1.__generator(this, function (_c) {
+                                    switch (_c.label) {
+                                        case 0:
+                                            selections = this_1.getSelections(params.data, struct.number);
+                                            customTooltipProps = {
+                                                tooltips: selections.map(function (s) { var _a; return ({ text: (_a = s.param.tooltip) !== null && _a !== void 0 ? _a : '', selector: { name: 'bundle', params: s.bundle } }); }),
+                                            };
+                                            structRef = struct.structureRef.cell.transform.ref;
+                                            customPropsCells = this_1.plugin.state.data.select(mol_state_1.StateSelection.Generators.ofTransformer(model_1.CustomStructureProperties, structRef));
+                                            if (!(customPropsCells.length === 0)) return [3 /*break*/, 2];
+                                            return [4 /*yield*/, this_1.plugin.build().to(structRef).apply(model_1.CustomStructureProperties).commit()];
+                                        case 1:
+                                            _c.sent();
+                                            customPropsCells = this_1.plugin.state.data.select(mol_state_1.StateSelection.Generators.ofTransformer(model_1.CustomStructureProperties, structRef));
+                                            _c.label = 2;
+                                        case 2: return [4 /*yield*/, this_1.plugin.build().to(customPropsCells[0]).update(function (old) {
+                                                var _a;
+                                                return ({
+                                                    properties: tslib_1.__assign(tslib_1.__assign({}, old.properties), (_a = {}, _a[custom_tooltips_prop_1.CustomTooltipsProvider.descriptor.name] = customTooltipProps, _a)),
+                                                    autoAttach: old.autoAttach.includes(custom_tooltips_prop_1.CustomTooltipsProvider.descriptor.name) ?
+                                                        old.autoAttach
+                                                        : tslib_1.__spreadArray(tslib_1.__spreadArray([], old.autoAttach, true), [custom_tooltips_prop_1.CustomTooltipsProvider.descriptor.name], false),
+                                                });
+                                            }).commit()];
+                                        case 3:
+                                            _c.sent();
+                                            return [2 /*return*/];
+                                    }
+                                });
+                            };
+                            this_1 = this;
+                            _i = 0, structures_3 = structures;
+                            _b.label = 1;
                         case 1:
-                            if (!(_i < _b.length)) return [3 /*break*/, 6];
-                            _c = _b[_i];
-                            if (!(_c in _a)) return [3 /*break*/, 5];
-                            visual = _c;
-                            tags = (_e = StructureComponentTags[visual]) !== null && _e !== void 0 ? _e : [];
-                            _d = 0, tags_1 = tags;
-                            _f.label = 2;
+                            if (!(_i < structures_3.length)) return [3 /*break*/, 4];
+                            struct = structures_3[_i];
+                            return [5 /*yield**/, _loop_2(struct)];
                         case 2:
-                            if (!(_d < tags_1.length)) return [3 /*break*/, 5];
-                            tag = tags_1[_d];
-                            componentRef = mol_state_1.StateSelection.findTagInSubtree(this.plugin.state.data.tree, mol_state_1.StateTransform.RootRef, tag);
-                            if (!componentRef) return [3 /*break*/, 4];
-                            compVisual = this.plugin.state.data.select(componentRef)[0];
-                            if (!(compVisual && compVisual.obj)) return [3 /*break*/, 4];
-                            currentlyVisible = (compVisual.state && compVisual.state.isHidden) ? false : true;
-                            if (!(data[visual] !== currentlyVisible)) return [3 /*break*/, 4];
-                            return [4 /*yield*/, commands_1.PluginCommands.State.ToggleVisibility(this.plugin, { state: this.state, ref: componentRef })];
+                            _b.sent();
+                            _b.label = 3;
                         case 3:
-                            _f.sent();
-                            _f.label = 4;
-                        case 4:
-                            _d++;
-                            return [3 /*break*/, 2];
-                        case 5:
                             _i++;
                             return [3 /*break*/, 1];
-                        case 6: return [2 /*return*/];
+                        case 4: return [2 /*return*/];
                     }
                 });
             }); },
-            toggleSpin: function (isSpinning, resetCamera) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-                var trackball, toggleSpinParam;
+            /** Remove any custom tooltips added by the `tooltips` method. */
+            clearTooltips: function (structureNumberOrId) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                 return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
-                        case 0:
-                            if (!this.plugin.canvas3d)
-                                return [2 /*return*/];
-                            trackball = this.plugin.canvas3d.props.trackball;
-                            toggleSpinParam = trackball.animate.name === 'spin' ? { name: 'off', params: {} } : { name: 'spin', params: { speed: 1 } };
-                            if (typeof isSpinning !== 'undefined') {
-                                toggleSpinParam = { name: 'off', params: {} };
-                                if (isSpinning)
-                                    toggleSpinParam = { name: 'spin', params: { speed: 1 } };
-                            }
-                            return [4 /*yield*/, commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: tslib_1.__assign(tslib_1.__assign({}, trackball), { animate: toggleSpinParam }) } })];
+                        case 0: return [4 /*yield*/, this.visual.tooltips({ data: [], structureId: structureNumberOrId })];
                         case 1:
                             _a.sent();
-                            if (!resetCamera) return [3 /*break*/, 3];
-                            return [4 /*yield*/, commands_1.PluginCommands.Camera.Reset(this.plugin, {})];
-                        case 2:
-                            _a.sent();
-                            _a.label = 3;
-                        case 3: return [2 /*return*/];
+                            return [2 /*return*/];
                     }
                 });
             }); },
-            focus: function (params, structureNumber) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-                var loci;
-                return tslib_1.__generator(this, function (_a) {
-                    loci = this.getLociForParams(params, structureNumber);
-                    this.plugin.managers.camera.focusLoci(loci);
-                    return [2 /*return*/];
-                });
-            }); },
-            setColor: function (param) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            /** Set highlight and/or selection color.
+             * Highlight color is used when the user hovers over a part of the structure or when applying the `highlight` method.
+             * Selection color is used when creating selections with Selection Mode (the mouse cursor icon) and is not related to the color used by the `select` method. */
+            setColor: function (params) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                 var renderer, marking;
                 return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
                             if (!this.plugin.canvas3d)
                                 return [2 /*return*/];
-                            if (!param.highlight && !param.select)
+                            if (!params.highlight && !params.select)
                                 return [2 /*return*/];
                             renderer = tslib_1.__assign({}, this.plugin.canvas3d.props.renderer);
                             marking = tslib_1.__assign({}, this.plugin.canvas3d.props.marking);
-                            if (param.highlight) {
-                                renderer.highlightColor = this.normalizeColor(param.highlight);
-                                marking.highlightEdgeColor = color_1.Color.darken(this.normalizeColor(param.highlight), 1);
+                            if (params.highlight) {
+                                renderer.highlightColor = this.normalizeColor(params.highlight);
+                                marking.highlightEdgeColor = color_1.Color.darken(this.normalizeColor(params.highlight), 1);
                                 this.isHighlightColorUpdated = true;
                             }
-                            if (param.select) {
-                                renderer.selectColor = this.normalizeColor(param.select);
-                                marking.selectEdgeColor = color_1.Color.darken(this.normalizeColor(param.select), 1);
+                            if (params.select) {
+                                renderer.selectColor = this.normalizeColor(params.select);
+                                marking.selectEdgeColor = color_1.Color.darken(this.normalizeColor(params.select), 1);
                                 this.isSelectedColorUpdated = true;
                             }
                             return [4 /*yield*/, commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: renderer, marking: marking } })];
@@ -456,6 +545,10 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                     }
                 });
             }); },
+            /** Reset various settings to defaults:
+             * `camera` resets camera position (i.e. zooms on the whole scene).
+             * `theme` resets color theme for visual representations.
+             * `highlightColor` and `selectColor` reset colors previously set by the `setColor` method. */
             reset: function (params) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                 var defaultTheme, componentGroups, _i, componentGroups_2, compGrp, renderer, marking;
                 return tslib_1.__generator(this, function (_a) {
@@ -506,76 +599,51 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                     }
                 });
             }); },
-            /** Add interactive tooltips to parts of the structure. The added tooltips will be shown on a separate line in the tooltip box.
-             * Repeated call to this function removes any previously added tooltips.
-             * `structureNumber` counts from 1; if not provided, tooltips will be applied to all loaded structures.
-             * Example: `await this.visual.tooltips({ data: [{ struct_asym_id: 'A', tooltip: 'Chain A' }, { struct_asym_id: 'B', tooltip: 'Chain B' }] });`. */
-            tooltips: function (params) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-                var structures, _loop_2, this_1, _i, structures_3, struct;
+            /** Change parameters of the plugin instance.
+             * Can be used to load a different structure.
+             * If `fullLoad`, remove currently loaded structure before loading the new one;
+             * otherwise add the new structure to existing structures. */
+            update: function (options, fullLoad) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var validationIssues, dataSource;
                 return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
-                            structures = this.plugin.managers.structure.hierarchy.current.structures.map(function (structureRef, i) { return ({ structureRef: structureRef, number: i + 1 }); });
-                            if (params.structureNumber !== undefined) {
-                                structures = [structures[params.structureNumber - 1]];
+                            console.debug('Updating PDBeMolstarPlugin instance with options:', options);
+                            // Validate options
+                            if (!options) {
+                                console.error('Missing `options` argument to `PDBeMolstarPlugin.visual.update');
+                                return [2 /*return*/, false];
                             }
-                            _loop_2 = function (struct) {
-                                var selections, customTooltipProps, structRef, customPropsCells;
-                                return tslib_1.__generator(this, function (_b) {
-                                    switch (_b.label) {
-                                        case 0:
-                                            selections = this_1.getSelections(params.data, struct.number);
-                                            customTooltipProps = {
-                                                tooltips: selections.map(function (s) { var _a; return ({ text: (_a = s.param.tooltip) !== null && _a !== void 0 ? _a : '', selector: { name: 'bundle', params: s.bundle } }); }),
-                                            };
-                                            structRef = struct.structureRef.cell.transform.ref;
-                                            customPropsCells = this_1.plugin.state.data.select(mol_state_1.StateSelection.Generators.ofTransformer(model_1.CustomStructureProperties, structRef));
-                                            if (!(customPropsCells.length === 0)) return [3 /*break*/, 2];
-                                            return [4 /*yield*/, this_1.plugin.build().to(structRef).apply(model_1.CustomStructureProperties).commit()];
-                                        case 1:
-                                            _b.sent();
-                                            customPropsCells = this_1.plugin.state.data.select(mol_state_1.StateSelection.Generators.ofTransformer(model_1.CustomStructureProperties, structRef));
-                                            _b.label = 2;
-                                        case 2: return [4 /*yield*/, this_1.plugin.build().to(customPropsCells[0]).update(function (old) {
-                                                var _a;
-                                                return ({
-                                                    properties: tslib_1.__assign(tslib_1.__assign({}, old.properties), (_a = {}, _a[custom_tooltips_prop_1.CustomTooltipsProvider.descriptor.name] = customTooltipProps, _a)),
-                                                    autoAttach: old.autoAttach.includes(custom_tooltips_prop_1.CustomTooltipsProvider.descriptor.name) ?
-                                                        old.autoAttach
-                                                        : tslib_1.__spreadArray(tslib_1.__spreadArray([], old.autoAttach, true), [custom_tooltips_prop_1.CustomTooltipsProvider.descriptor.name], false),
-                                                });
-                                            }).commit()];
-                                        case 3:
-                                            _b.sent();
-                                            return [2 /*return*/];
-                                    }
-                                });
-                            };
-                            this_1 = this;
-                            _i = 0, structures_3 = structures;
-                            _a.label = 1;
+                            validationIssues = (0, spec_2.validateInitParams)(options);
+                            if (validationIssues) {
+                                console.error('Invalid PDBeMolstarPlugin options:', options);
+                                return [2 /*return*/, false];
+                            }
+                            this.initParams = (0, helpers_1.addDefaults)(options, spec_2.DefaultParams);
+                            if (!this.initParams.moleculeId && !this.initParams.customData)
+                                return [2 /*return*/, false];
+                            if (this.initParams.customData && this.initParams.customData.url && !this.initParams.customData.format)
+                                return [2 /*return*/, false];
+                            (0, plugin_custom_state_1.PluginCustomState)(this.plugin).initParams = this.initParams;
+                            // Show/hide buttons in the viewport control panel
+                            this.plugin.config.set(config_1.PluginConfig.Viewport.ShowExpand, !this.initParams.hideCanvasControls.includes('expand'));
+                            this.plugin.config.set(config_1.PluginConfig.Viewport.ShowSelectionMode, !this.initParams.hideCanvasControls.includes('selection'));
+                            this.plugin.config.set(config_1.PluginConfig.Viewport.ShowAnimation, !this.initParams.hideCanvasControls.includes('animation'));
+                            this.plugin.config.set(config_1.PluginConfig.Viewport.ShowControls, !this.initParams.hideCanvasControls.includes('controlToggle'));
+                            this.plugin.config.set(config_1.PluginConfig.Viewport.ShowSettings, !this.initParams.hideCanvasControls.includes('controlInfo'));
+                            if (!(this.initParams.bgColor || this.initParams.lighting)) return [3 /*break*/, 2];
+                            return [4 /*yield*/, this.canvas.applySettings({ color: this.initParams.bgColor, lighting: this.initParams.lighting })];
                         case 1:
-                            if (!(_i < structures_3.length)) return [3 /*break*/, 4];
-                            struct = structures_3[_i];
-                            return [5 /*yield**/, _loop_2(struct)];
-                        case 2:
                             _a.sent();
-                            _a.label = 3;
+                            _a.label = 2;
+                        case 2:
+                            dataSource = this.getMoleculeSrcUrl();
+                            if (!dataSource) return [3 /*break*/, 4];
+                            return [4 /*yield*/, this.load({ url: dataSource.url, format: dataSource.format, assemblyId: this.initParams.assemblyId, isBinary: dataSource.isBinary }, fullLoad)];
                         case 3:
-                            _i++;
-                            return [3 /*break*/, 1];
-                        case 4: return [2 /*return*/];
-                    }
-                });
-            }); },
-            /** Remove any tooltips added by `this.visual.tooltips`. */
-            clearTooltips: function (structureNumber) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-                return tslib_1.__generator(this, function (_a) {
-                    switch (_a.label) {
-                        case 0: return [4 /*yield*/, this.visual.tooltips({ data: [], structureNumber: structureNumber })];
-                        case 1:
                             _a.sent();
-                            return [2 /*return*/];
+                            _a.label = 4;
+                        case 4: return [2 /*return*/, true];
                     }
                 });
             }); },
@@ -735,7 +803,14 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                                 if (this.initParams.loadingOverlay) {
                                     new overlay_1.LoadingOverlay(this.targetElement, { resize: (_e = (_d = this.plugin) === null || _d === void 0 ? void 0 : _d.canvas3d) === null || _e === void 0 ? void 0 : _e.resized, hide: this.events.loadComplete }).show();
                                 }
-                                this.load({ url: dataSource.url, format: dataSource.format, assemblyId: this.initParams.assemblyId, isBinary: dataSource.isBinary, progressMessage: "Loading ".concat((_f = this.initParams.moleculeId) !== null && _f !== void 0 ? _f : '', " ...") });
+                                this.load({
+                                    url: dataSource.url,
+                                    format: dataSource.format,
+                                    assemblyId: this.initParams.assemblyId,
+                                    isBinary: dataSource.isBinary,
+                                    progressMessage: "Loading ".concat((_f = this.initParams.moleculeId) !== null && _f !== void 0 ? _f : '', " ..."),
+                                    id: 'main',
+                                });
                             }
                             // Binding to other PDB Component events
                             if (this.initParams.subscribeEvents) {
@@ -886,14 +961,14 @@ var PDBeMolstarPlugin = /** @class */ (function () {
         });
     };
     PDBeMolstarPlugin.prototype.load = function (_a, fullLoad) {
-        var url = _a.url, _b = _a.format, format = _b === void 0 ? 'mmcif' : _b, _c = _a.isBinary, isBinary = _c === void 0 ? false : _c, _d = _a.assemblyId, assemblyId = _d === void 0 ? '' : _d, progressMessage = _a.progressMessage;
+        var url = _a.url, _b = _a.format, format = _b === void 0 ? 'mmcif' : _b, _c = _a.isBinary, isBinary = _c === void 0 ? false : _c, _d = _a.assemblyId, assemblyId = _d === void 0 ? '' : _d, progressMessage = _a.progressMessage, id = _a.id;
         if (fullLoad === void 0) { fullLoad = true; }
         return tslib_1.__awaiter(this, void 0, void 0, function () {
             var _this = this;
             return tslib_1.__generator(this, function (_e) {
                 switch (_e.label) {
                     case 0: return [4 /*yield*/, (0, helpers_1.runWithProgressMessage)(this.plugin, progressMessage, function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-                            var success, isHetView, downloadOptions, isBranchedView, data, trajectory, model, pivotIndex, pivot, asm, defaultMapParams, pdbeMapParams;
+                            var success, isHetView, downloadOptions, isBranchedView, data_1, trajectory, structRef, model, structure, pivotIndex, pivot, asm, defaultMapParams, pdbeMapParams;
                             return tslib_1.__generator(this, function (_a) {
                                 switch (_a.label) {
                                     case 0:
@@ -916,10 +991,11 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                                         }
                                         return [4 /*yield*/, this.plugin.builders.data.download({ url: assets_1.Asset.Url(url, downloadOptions), isBinary: isBinary }, { state: { isGhost: true } })];
                                     case 4:
-                                        data = _a.sent();
-                                        return [4 /*yield*/, this.plugin.builders.structure.parseTrajectory(data, format)];
+                                        data_1 = _a.sent();
+                                        return [4 /*yield*/, this.plugin.builders.structure.parseTrajectory(data_1, format)];
                                     case 5:
                                         trajectory = _a.sent();
+                                        structRef = void 0;
                                         if (!!isHetView) return [3 /*break*/, 7];
                                         return [4 /*yield*/, this.plugin.builders.structure.hierarchy.applyPreset(trajectory, this.initParams.defaultPreset, {
                                                 structure: assemblyId ? (assemblyId === 'preferred') ? void 0 : { name: 'assembly', params: { id: assemblyId } } : { name: 'model', params: {} },
@@ -928,6 +1004,7 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                                             })];
                                     case 6:
                                         _a.sent();
+                                        structRef = this.plugin.state.data.selectQ(function (q) { return q.byRef(data_1.ref).subtree().ofType(objects_1.PluginStateObject.Molecule.Structure); })[0].transform.ref;
                                         if (this.initParams.hideStructure.length > 0 || this.initParams.visualStyle) {
                                             this.applyVisualParams();
                                         }
@@ -937,9 +1014,13 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                                         model = _a.sent();
                                         return [4 /*yield*/, this.plugin.builders.structure.createStructure(model, { name: 'model', params: {} })];
                                     case 9:
-                                        _a.sent();
+                                        structure = _a.sent();
+                                        structRef = structure.ref;
                                         _a.label = 10;
                                     case 10:
+                                        if (id) {
+                                            this.structureRefMap.set(id, structRef);
+                                        }
                                         // show selection if param is set
                                         if (this.initParams.selection) {
                                             this.visual.select(this.initParams.selection);
@@ -984,6 +1065,56 @@ var PDBeMolstarPlugin = /** @class */ (function () {
             });
         });
     };
+    /** Remove loaded structure(s).
+     * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure.
+     * If `structureNumberOrId` is undefined, remove all structures.
+     * You will likely need to call `await this.visual.reset({ camera: true })` afterwards. */
+    PDBeMolstarPlugin.prototype.deleteStructure = function (structureNumberOrId) {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var structs, _loop_3, this_2, _i, structs_1, struct;
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        structs = this.getStructures(structureNumberOrId);
+                        if (structureNumberOrId !== undefined && structs.length === 0) {
+                            console.error("Cannot delete structure: there is no structure with number or id ".concat(structureNumberOrId, "."));
+                        }
+                        _loop_3 = function (struct) {
+                            var dataNode;
+                            return tslib_1.__generator(this, function (_b) {
+                                switch (_b.label) {
+                                    case 0:
+                                        dataNode = this_2.plugin.state.data.selectQ(function (q) { return q.byRef(struct.structureRef.cell.transform.ref).ancestorOfType([objects_1.PluginStateObject.Data.String, objects_1.PluginStateObject.Data.Binary]); })[0];
+                                        if (!dataNode) return [3 /*break*/, 2];
+                                        return [4 /*yield*/, this_2.plugin.build().delete(dataNode).commit()];
+                                    case 1:
+                                        _b.sent();
+                                        _b.label = 2;
+                                    case 2: return [2 /*return*/];
+                                }
+                            });
+                        };
+                        this_2 = this;
+                        _i = 0, structs_1 = structs;
+                        _a.label = 1;
+                    case 1:
+                        if (!(_i < structs_1.length)) return [3 /*break*/, 4];
+                        struct = structs_1[_i];
+                        return [5 /*yield**/, _loop_3(struct)];
+                    case 2:
+                        _a.sent();
+                        _a.label = 3;
+                    case 3:
+                        _i++;
+                        return [3 /*break*/, 1];
+                    case 4: return [2 /*return*/];
+                }
+            });
+        });
+    };
+    /** Get loci corresponding to a selection within a structure.
+     * If `params` contains more items, return loci for the union of the selections.
+     * If `structureNumber` is provided, use the specified structure (numbered from 1!); otherwise use the last added structure. */
     PDBeMolstarPlugin.prototype.getLociForParams = function (params, structureNumber) {
         var assemblyRef = this.assemblyRef;
         if (structureNumber) {
@@ -1029,7 +1160,7 @@ var PDBeMolstarPlugin = /** @class */ (function () {
     };
     PDBeMolstarPlugin.prototype.normalizeColor = function (colorVal, defaultColor) {
         var _a, _b, _c;
-        defaultColor !== null && defaultColor !== void 0 ? defaultColor : (defaultColor = color_1.Color.fromRgb(170, 170, 170));
+        if (defaultColor === void 0) { defaultColor = color_1.Color.fromRgb(170, 170, 170); }
         try {
             if (colorVal === undefined || colorVal === null)
                 return defaultColor;
@@ -1047,6 +1178,39 @@ var PDBeMolstarPlugin = /** @class */ (function () {
         }
         return defaultColor;
     };
+    /** Get structure ref for a structure with given `structureNumberOrId`.
+     * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure.
+     * If `structureNumberOrId` is undefined, return refs for all loaded structures. */
+    PDBeMolstarPlugin.prototype.getStructures = function (structureNumberOrId) {
+        var allStructures = this.plugin.managers.structure.hierarchy.current.structures.map(function (structureRef, i) { return ({ structureRef: structureRef, number: i + 1 }); });
+        if (typeof structureNumberOrId === 'number') {
+            var theStructure = allStructures[structureNumberOrId - 1];
+            return theStructure ? [theStructure] : [];
+        }
+        else if (typeof structureNumberOrId === 'string') {
+            var structRef_1 = this.structureRefMap.get(structureNumberOrId);
+            if (structRef_1 === undefined) {
+                return [];
+            }
+            var found = allStructures.find(function (s) { return s.structureRef.cell.transform.ref === structRef_1; });
+            if (found) {
+                return [found];
+            }
+            else {
+                this.structureRefMap.delete(structureNumberOrId); // remove outdated record
+                return [];
+            }
+        }
+        else {
+            return allStructures;
+        }
+    };
+    /** Get StructureRef for a structure with given `structureNumberOrId`.
+     * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure. */
+    PDBeMolstarPlugin.prototype.getStructure = function (structureNumberOrId) {
+        var _a;
+        return (_a = this.getStructures(structureNumberOrId)[0]) === null || _a === void 0 ? void 0 : _a.structureRef;
+    };
     PDBeMolstarPlugin.prototype.clear = function () {
         return tslib_1.__awaiter(this, void 0, void 0, function () {
             return tslib_1.__generator(this, function (_a) {
@@ -1063,22 +1227,11 @@ var PDBeMolstarPlugin = /** @class */ (function () {
             });
         });
     };
+    /** Helper functions related to specific views or use cases */
+    PDBeMolstarPlugin.extensions = {
+        foldseek: Foldseek,
+    };
     return PDBeMolstarPlugin;
 }());
 exports.PDBeMolstarPlugin = PDBeMolstarPlugin;
-exports.Tags = {
-    /** Tag needed for `clearStructureOverpaint`; defined in src/mol-plugin-state/helpers/structure-overpaint.ts but private */
-    Overpaint: 'overpaint-controls',
-    /** Marks structure components added by `select` */
-    AddedComponent: 'pdbe-molstar.added-component',
-};
-var StructureComponentTags = {
-    polymer: ['structure-component-static-polymer'],
-    het: ['structure-component-static-ligand', 'structure-component-static-ion'],
-    water: ['structure-component-static-water'],
-    carbs: ['structure-component-static-branched'],
-    nonStandard: ['structure-component-static-non-standard'],
-    coarse: ['structure-component-static-coarse'],
-    maps: ['volume-streaming-info'],
-};
 window.PDBeMolstarPlugin = PDBeMolstarPlugin;