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

package/lib/labels.d.ts

@@ -1,2 +1,2 @@
-import { PluginBehavior } from 'Molstar/mol-plugin/behavior';
+import { PluginBehavior } from 'molstar/lib/mol-plugin/behavior';
 export declare const PDBeLociLabelProvider: import("molstar/lib/mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;

package/lib/labels.js

@@ -1,9 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PDBeLociLabelProvider = void 0;
-var behavior_1 = require("Molstar/mol-plugin/behavior");
-var structure_1 = require("Molstar/mol-model/structure");
-var label_1 = require("Molstar/mol-theme/label");
+var structure_1 = require("molstar/lib/mol-model/structure");
+var behavior_1 = require("molstar/lib/mol-plugin/behavior");
+var label_1 = require("molstar/lib/mol-theme/label");
 var plugin_custom_state_1 = require("./plugin-custom-state");
 exports.PDBeLociLabelProvider = behavior_1.PluginBehavior.create({
     name: 'pdbe-loci-label-provider',

package/lib/loci-details.d.ts

@@ -1,5 +1,5 @@
-import { Bond } from 'Molstar/mol-model/structure';
-import { Loci } from 'Molstar/mol-model/loci';
+import { Loci } from 'molstar/lib/mol-model/loci';
+import { Bond } from 'molstar/lib/mol-model/structure';
 export type EventDetail = {
     models?: string[];
     entity_id?: string;

package/lib/loci-details.js

@@ -2,9 +2,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports._bundleLabel = exports.bondLabel = exports.lociDetails = void 0;
 var tslib_1 = require("tslib");
-var structure_1 = require("Molstar/mol-model/structure");
-var int_1 = require("Molstar/mol-data/int");
-var sifts_mapping_1 = require("Molstar/mol-model-props/sequence/sifts-mapping");
+var int_1 = require("molstar/lib/mol-data/int");
+var sifts_mapping_1 = require("molstar/lib/mol-model-props/sequence/sifts-mapping");
+var structure_1 = require("molstar/lib/mol-model/structure");
 function lociDetails(loci) {
     switch (loci.kind) {
         case 'structure-loci':

package/lib/plugin-custom-state.d.ts

@@ -1,7 +1,7 @@
-import { SymmetryOperator } from 'Molstar/mol-math/geometry';
-import { Mat4 } from 'Molstar/mol-math/linear-algebra';
-import { PluginContext } from 'Molstar/mol-plugin/context';
-import { StateSelection, StateTransform } from 'Molstar/mol-state';
+import { SymmetryOperator } from 'molstar/lib/mol-math/geometry';
+import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { StateSelection, StateTransform } from 'molstar/lib/mol-state';
 import { Subject } from 'rxjs';
 import { InitParams } from './spec';
 export interface PluginCustomState {
@@ -35,11 +35,8 @@ export interface PluginCustomState {
         hets: {
             [key: string]: unknown[];
         };
-        colorPalette: ['dark-2', 'red-yellow-green', 'paired', 'set-1', 'accent', 'set-2', 'rainbow'];
-        colorState: {
-            palleteIndex: number;
-            colorIndex: number;
-        }[];
+        /** Counts how many colors have been assigned, per segment */
+        colorCounters: number[];
         alphafold: {
             apiData: {
                 cif: string;

package/lib/sifts-mapping.d.ts

@@ -1,6 +1,6 @@
-import { Model } from 'Molstar/mol-model/structure';
-import { StructureElement } from 'Molstar/mol-model/structure/structure';
-import { CustomModelProperty } from 'Molstar/mol-model-props/common/custom-model-property';
+import { CustomModelProperty } from 'molstar/lib/mol-model-props/common/custom-model-property';
+import { Model } from 'molstar/lib/mol-model/structure';
+import { StructureElement } from 'molstar/lib/mol-model/structure/structure';
 export { SIFTSMapping as SIFTSMapping };
 export interface SIFTSMappingMapping {
     readonly dbName: string[];

package/lib/sifts-mapping.js

@@ -2,10 +2,10 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SIFTSMapping = void 0;
 var tslib_1 = require("tslib");
-var db_1 = require("Molstar/mol-data/db");
-var mmcif_1 = require("Molstar/mol-model-formats/structure/mmcif");
-var custom_property_1 = require("Molstar/mol-model/custom-property");
-var custom_model_property_1 = require("Molstar/mol-model-props/common/custom-model-property");
+var db_1 = require("molstar/lib/mol-data/db");
+var mmcif_1 = require("molstar/lib/mol-model-formats/structure/mmcif");
+var custom_model_property_1 = require("molstar/lib/mol-model-props/common/custom-model-property");
+var custom_property_1 = require("molstar/lib/mol-model/custom-property");
 var SIFTSMapping;
 (function (SIFTSMapping) {
     var _this = this;

package/lib/sifts-mappings-behaviour.d.ts

@@ -1,4 +1,4 @@
-import { PluginBehavior } from 'Molstar/mol-plugin/behavior';
+import { PluginBehavior } from 'molstar/lib/mol-plugin/behavior';
 export declare const PDBeSIFTSMapping: import("molstar/lib/mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
     autoAttach: boolean;
     showTooltip: boolean;

package/lib/sifts-mappings-behaviour.js

@@ -2,12 +2,12 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PDBeSIFTSMapping = void 0;
 var tslib_1 = require("tslib");
-var int_1 = require("Molstar/mol-data/int");
-var sifts_mapping_1 = require("./sifts-mapping");
-var sifts_mapping_2 = require("Molstar/mol-model-props/sequence/themes/sifts-mapping");
-var structure_1 = require("Molstar/mol-model/structure");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
-var behavior_1 = require("Molstar/mol-plugin/behavior");
+var int_1 = require("molstar/lib/mol-data/int");
+var sifts_mapping_1 = require("molstar/lib/mol-model-props/sequence/themes/sifts-mapping");
+var structure_1 = require("molstar/lib/mol-model/structure");
+var behavior_1 = require("molstar/lib/mol-plugin/behavior");
+var param_definition_1 = require("molstar/lib/mol-util/param-definition");
+var sifts_mapping_2 = require("./sifts-mapping");
 exports.PDBeSIFTSMapping = behavior_1.PluginBehavior.create({
     name: 'pdbe-sifts-mapping-prop',
     category: 'custom-props',
@@ -16,7 +16,7 @@ exports.PDBeSIFTSMapping = behavior_1.PluginBehavior.create({
         tslib_1.__extends(class_1, _super);
         function class_1() {
             var _this = _super !== null && _super.apply(this, arguments) || this;
-            _this.provider = sifts_mapping_1.SIFTSMapping.Provider;
+            _this.provider = sifts_mapping_2.SIFTSMapping.Provider;
             _this.labelProvider = {
                 label: function (loci) {
                     if (!_this.params.showTooltip)
@@ -36,12 +36,12 @@ exports.PDBeSIFTSMapping = behavior_1.PluginBehavior.create({
         };
         class_1.prototype.register = function () {
             this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
-            this.ctx.representation.structure.themes.colorThemeRegistry.add(sifts_mapping_2.SIFTSMappingColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(sifts_mapping_1.SIFTSMappingColorThemeProvider);
             this.ctx.managers.lociLabels.addProvider(this.labelProvider);
         };
         class_1.prototype.unregister = function () {
             this.ctx.customModelProperties.unregister(this.provider.descriptor.name);
-            this.ctx.representation.structure.themes.colorThemeRegistry.remove(sifts_mapping_2.SIFTSMappingColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(sifts_mapping_1.SIFTSMappingColorThemeProvider);
             this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
         };
         return class_1;
@@ -59,6 +59,6 @@ function PDBeBestDatabaseSequenceMappingLabel(loci) {
         var e = loci.elements[0];
         var u = e.unit;
         var se = structure_1.StructureElement.Location.create(loci.structure, u, u.elements[int_1.OrderedSet.getAt(e.indices, 0)]);
-        return sifts_mapping_1.SIFTSMapping.getLabel(se);
+        return sifts_mapping_2.SIFTSMapping.getLabel(se);
     }
 }

package/lib/spec.d.ts

@@ -1,8 +1,9 @@
-import { Loci } from 'Molstar/mol-model/loci';
-import { PluginUISpec } from 'Molstar/mol-plugin-ui/spec';
-import { DefaultFocusLociBindings } from 'Molstar/mol-plugin/behavior/dynamic/camera';
-import { DefaultSelectLociBindings } from 'Molstar/mol-plugin/behavior/dynamic/representation';
-import { PluginSpec } from 'Molstar/mol-plugin/spec';
+import { Loci } from 'molstar/lib/mol-model/loci';
+import { StructureRepresentationBuiltInProps } from 'molstar/lib/mol-plugin-state/helpers/structure-representation-params';
+import { PluginUISpec } from 'molstar/lib/mol-plugin-ui/spec';
+import { DefaultFocusLociBindings } from 'molstar/lib/mol-plugin/behavior/dynamic/camera';
+import { DefaultSelectLociBindings } from 'molstar/lib/mol-plugin/behavior/dynamic/representation';
+import { PluginSpec } from 'molstar/lib/mol-plugin/spec';
 import { LigandQueryParam, MapParams, QueryParam } from './helpers';
 export declare const DefaultPluginSpec: () => PluginSpec;
 export declare const DefaultPluginUISpec: () => PluginUISpec;
@@ -12,12 +13,29 @@ export interface ColorParams {
     g: number;
     b: number;
 }
+/** Color name (e.g. 'yellow') or hexcode (e.g. '#ffff00') or Molstar color encoding (e.g. 16776960) or RGB color object (e.g. { r: 255, g: 255, b: 0 }) */
+export type AnyColor = ColorParams | string | number;
 export declare const Preset: readonly ["default", "unitcell", "all-models", "supercell"];
 export type Preset = (typeof Preset)[number];
 export declare const Lighting: readonly ["flat", "matte", "glossy", "metallic", "plastic"];
 export type Lighting = (typeof Lighting)[number];
+/** Structure component type ('het' includes Molstar types 'ligand' and 'ion') */
+export declare const ComponentType: readonly ["polymer", "het", "water", "carbs", "nonStandard", "coarse"];
+export type ComponentType = (typeof ComponentType)[number];
+/** Structure representation type */
 export declare const VisualStyle: readonly ["cartoon", "ball-and-stick", "carbohydrate", "ellipsoid", "gaussian-surface", "molecular-surface", "point", "putty", "spacefill"];
 export type VisualStyle = (typeof VisualStyle)[number];
+/** Specification of visual style for a single component visual, e.g. `'cartoon'` or `{type: 'putty', size: 'uniform'}` */
+type ComponentVisualStyleSpec = VisualStyle | StructureRepresentationBuiltInProps;
+/** Specification of visual styles for individual component types, e.g. `'cartoon'` (all components as cartoon) or `{polymer: {type: 'putty', size: 'uniform'}, ligand: 'ball-and-stick'}` */
+export type VisualStylesSpec = ComponentVisualStyleSpec | {
+    [component in ComponentType]?: ComponentVisualStyleSpec;
+};
+/** Normalize a `VisualStylesSpec` to a form {polymer?:{...},het?:{...},...} */
+export declare function resolveVisualStyleSpec(spec: VisualStylesSpec): {
+    [component in ComponentType]?: StructureRepresentationBuiltInProps;
+};
+/** Structure file format */
 export declare const Encoding: readonly ["cif", "bcif"];
 export type Encoding = (typeof Encoding)[number];
 /** Options for initializing `PDBeMolstarPlugin` */
@@ -50,15 +68,15 @@ export interface InitParams {
         superposeCompleteCluster?: boolean;
         ligandView?: boolean;
         superposeAll?: boolean;
-        ligandColor?: ColorParams;
+        ligandColor?: AnyColor;
     };
     /** Specify parts of the structure to highlight with different colors */
     selection?: {
         data: QueryParam[];
-        nonSelectedColor?: ColorParams;
+        nonSelectedColor?: AnyColor;
     };
     /** Leave `undefined` to keep both cartoon and ball-and-sticks based on component type */
-    visualStyle?: VisualStyle;
+    visualStyle?: VisualStylesSpec;
     /** Molstar renders multiple visuals (polymer, ligand, water...) visuals by default. This option is to exclude any of these default visuals */
     hideStructure: ('polymer' | 'het' | 'water' | 'carbs' | 'nonStandard' | 'coarse')[];
     /** Load electron density (or EM) maps from Volume Server if value is set to true */
@@ -66,11 +84,11 @@ export interface InitParams {
     /** Customize map style (opacity and solid/wireframe) */
     mapSettings?: MapParams;
     /** Canvas background color */
-    bgColor: ColorParams;
+    bgColor: AnyColor;
     /** Color appearing on mouse-over */
-    highlightColor?: ColorParams;
+    highlightColor?: AnyColor;
     /** Color for marking the selected part of structure (when Selection Mode is active) */
-    selectColor?: ColorParams;
+    selectColor?: AnyColor;
     /** Default lighting (I don't think it really works) */
     lighting?: Lighting;
     /** Load Validation Report Annotations. Adds 'Annotations' control in the menu */
@@ -104,6 +122,12 @@ export interface InitParams {
     hideCanvasControls: ('expand' | 'selection' | 'animation' | 'controlToggle' | 'controlInfo')[];
     /** Display Sequence panel */
     sequencePanel: boolean;
+    /** Display Left control panel */
+    leftPanel: boolean;
+    /** Display Right control panel */
+    rightPanel: boolean;
+    /** Display Log panel */
+    logPanel: boolean;
     /** Display PDBe entry link in top right corner of the canvas */
     pdbeLink: boolean;
     /** Show overlay with PDBe logo while the initial structure is being loaded */
@@ -119,3 +143,4 @@ export interface InitParams {
 export declare const DefaultParams: InitParams;
 /** Return `undefined` if `params` are valid, an error message otherwise. */
 export declare function validateInitParams(params: Partial<InitParams>): string | undefined;
+export {};

package/lib/spec.js

@@ -1,13 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.validateInitParams = exports.DefaultParams = exports.Encoding = exports.VisualStyle = exports.Lighting = exports.Preset = exports.DefaultPluginUISpec = exports.DefaultPluginSpec = void 0;
+exports.validateInitParams = exports.DefaultParams = exports.Encoding = exports.resolveVisualStyleSpec = exports.VisualStyle = exports.ComponentType = exports.Lighting = exports.Preset = exports.DefaultPluginUISpec = exports.DefaultPluginSpec = void 0;
 var tslib_1 = require("tslib");
-var actions_1 = require("Molstar/mol-plugin-state/actions");
-var volume_1 = require("Molstar/mol-plugin-ui/custom/volume");
-var behavior_1 = require("Molstar/mol-plugin/behavior");
-var transformers_1 = require("Molstar/mol-plugin/behavior/dynamic/volume-streaming/transformers");
-var config_1 = require("Molstar/mol-plugin/config");
-var spec_1 = require("Molstar/mol-plugin/spec");
+var actions_1 = require("molstar/lib/mol-plugin-state/actions");
+var volume_1 = require("molstar/lib/mol-plugin-ui/custom/volume");
+var behavior_1 = require("molstar/lib/mol-plugin/behavior");
+var transformers_1 = require("molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers");
+var config_1 = require("molstar/lib/mol-plugin/config");
+var spec_1 = require("molstar/lib/mol-plugin/spec");
 var labels_1 = require("./labels");
 var sifts_mappings_behaviour_1 = require("./sifts-mappings-behaviour");
 var DefaultPluginSpec = function () { return ({
@@ -42,7 +42,35 @@ var DefaultPluginUISpec = function () { return (tslib_1.__assign(tslib_1.__assig
 exports.DefaultPluginUISpec = DefaultPluginUISpec;
 exports.Preset = ['default', 'unitcell', 'all-models', 'supercell'];
 exports.Lighting = ['flat', 'matte', 'glossy', 'metallic', 'plastic'];
+/** Structure component type ('het' includes Molstar types 'ligand' and 'ion') */
+exports.ComponentType = ['polymer', 'het', 'water', 'carbs', 'nonStandard', 'coarse'];
+/** Structure representation type */
 exports.VisualStyle = ['cartoon', 'ball-and-stick', 'carbohydrate', 'ellipsoid', 'gaussian-surface', 'molecular-surface', 'point', 'putty', 'spacefill'];
+/** Normalize a `VisualStylesSpec` to a form {polymer?:{...},het?:{...},...} */
+function resolveVisualStyleSpec(spec) {
+    if (spec === undefined) {
+        return {};
+    }
+    if (typeof spec === 'string' || 'type' in spec) {
+        var commonStyle_1 = resolveComponentVisualStyleSpec(spec);
+        return Object.fromEntries(exports.ComponentType.map(function (type) { return [type, commonStyle_1]; }));
+    }
+    return Object.fromEntries(Object.entries(spec).map(function (_a) {
+        var type = _a[0], compSpec = _a[1];
+        return [type, resolveComponentVisualStyleSpec(compSpec)];
+    }));
+}
+exports.resolveVisualStyleSpec = resolveVisualStyleSpec;
+function resolveComponentVisualStyleSpec(spec) {
+    if (spec === undefined)
+        return undefined;
+    if (typeof spec === 'string')
+        return { type: spec };
+    if ('type' in spec)
+        return spec;
+    throw new Error('TypeError');
+}
+/** Structure file format */
 exports.Encoding = ['cif', 'bcif'];
 /** Default values for `InitParams` */
 exports.DefaultParams = {
@@ -77,6 +105,9 @@ exports.DefaultParams = {
     hideControls: false,
     hideCanvasControls: [],
     sequencePanel: false,
+    leftPanel: true,
+    rightPanel: true,
+    logPanel: false,
     pdbeLink: true,
     loadingOverlay: false,
     expanded: false,

package/lib/{overlay.scss → styles/index.scss}

@@ -1,3 +1,5 @@
+/** Styles for PDBe Molstar (in addition to styles imported from core Molstar) */
+
 .pdbemolstar-overlay {
     z-index: 1000;
     position: fixed;
@@ -48,3 +50,12 @@ svg.pdbe-animated-logo {
     border: solid 1px transparent;
     background-clip: content-box;
 }
+
+
+.msp-plugin .msp-layout-static {
+    container-type: size; // define container to reference in .msp-viewport-controls-panel-controls
+}
+
+.msp-plugin .msp-viewport-controls-panel .msp-viewport-controls-panel-controls {
+    max-height: calc(100cqh - 41px - 24px - 10px); // 100cqh = viewport container, 41px = control buttons offset, 24px = header, 10px = space below
+}

package/lib/superposition-export.d.ts

@@ -1,4 +1,4 @@
-import { PluginContext } from 'Molstar/mol-plugin/context';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
 export declare function superpositionExportHierarchy(plugin: PluginContext, options?: {
     format?: 'cif' | 'bcif';
 }): Promise<void>;

package/lib/superposition-export.js

@@ -2,13 +2,13 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.superpositionExportHierarchy = void 0;
 var tslib_1 = require("tslib");
-var utf8_1 = require("Molstar/mol-io/common/utf8");
-var structure_1 = require("Molstar/mol-model/structure");
-var mol_task_1 = require("Molstar/mol-task");
-var date_1 = require("Molstar/mol-util/date");
-var download_1 = require("Molstar/mol-util/download");
-var zip_1 = require("Molstar/mol-util/zip/zip");
-var commands_1 = require("Molstar/mol-plugin/commands");
+var utf8_1 = require("molstar/lib/mol-io/common/utf8");
+var structure_1 = require("molstar/lib/mol-model/structure");
+var commands_1 = require("molstar/lib/mol-plugin/commands");
+var mol_task_1 = require("molstar/lib/mol-task");
+var date_1 = require("molstar/lib/mol-util/date");
+var download_1 = require("molstar/lib/mol-util/download");
+var zip_1 = require("molstar/lib/mol-util/zip/zip");
 var plugin_custom_state_1 = require("./plugin-custom-state");
 function superpositionExportHierarchy(plugin, options) {
     return tslib_1.__awaiter(this, void 0, void 0, function () {

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

@@ -1,6 +1,6 @@
-import { PluginBehavior } from 'Molstar/mol-plugin/behavior';
-import { ParamDefinition as PD } from 'Molstar/mol-util/param-definition';
-import { PluginContext } from 'Molstar/mol-plugin/context';
+import { PluginBehavior } from 'molstar/lib/mol-plugin/behavior';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
 declare const SuperpositionFocusRepresentationParams: (plugin: PluginContext) => {
     expandRadius: PD.Numeric;
     surroundingsParams: PD.Group<PD.Normalize<{

package/lib/superposition-focus-representation.js

@@ -2,14 +2,14 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SuperpositionFocusRepresentation = exports.SuperpositionFocusRepresentationTags = void 0;
 var tslib_1 = require("tslib");
-var structure_1 = require("Molstar/mol-model/structure");
-var structure_representation_params_1 = require("Molstar/mol-plugin-state/helpers/structure-representation-params");
-var transforms_1 = require("Molstar/mol-plugin-state/transforms");
-var behavior_1 = require("Molstar/mol-plugin/behavior");
-var builder_1 = require("Molstar/mol-script/language/builder");
-var mol_state_1 = require("Molstar/mol-state");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
-var commands_1 = require("Molstar/mol-plugin/commands");
+var structure_1 = require("molstar/lib/mol-model/structure");
+var structure_representation_params_1 = require("molstar/lib/mol-plugin-state/helpers/structure-representation-params");
+var transforms_1 = require("molstar/lib/mol-plugin-state/transforms");
+var behavior_1 = require("molstar/lib/mol-plugin/behavior");
+var commands_1 = require("molstar/lib/mol-plugin/commands");
+var builder_1 = require("molstar/lib/mol-script/language/builder");
+var mol_state_1 = require("molstar/lib/mol-state");
+var param_definition_1 = require("molstar/lib/mol-util/param-definition");
 var loci_details_1 = require("./loci-details");
 var SuperpositionFocusRepresentationParams = function (plugin) {
     var reprParams = transforms_1.StateTransforms.Representation.StructureRepresentation3D.definition.params(void 0, plugin);

package/lib/superposition-sifts-mapping.d.ts

@@ -1,8 +1,8 @@
-import { MinimizeRmsd } from 'Molstar/mol-math/linear-algebra/3d/minimize-rmsd';
-import { ElementIndex, ResidueIndex } from 'Molstar/mol-model/structure/model/indexing';
-import { StructureElement } from 'Molstar/mol-model/structure/structure/element';
-import { Structure } from 'Molstar/mol-model/structure';
-import { Unit } from 'Molstar/mol-model/structure/structure/unit';
+import { MinimizeRmsd } from 'molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd';
+import { Structure } from 'molstar/lib/mol-model/structure';
+import { ElementIndex, ResidueIndex } from 'molstar/lib/mol-model/structure/model/indexing';
+import { StructureElement } from 'molstar/lib/mol-model/structure/structure/element';
+import { Unit } from 'molstar/lib/mol-model/structure/structure/unit';
 export interface AlignmentResultEntry {
     transform: MinimizeRmsd.Result;
     pivot: number;

package/lib/superposition-sifts-mapping.js

@@ -1,10 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.alignAndSuperposeWithSIFTSMapping = void 0;
-var int_1 = require("Molstar/mol-data/int");
-var minimize_rmsd_1 = require("Molstar/mol-math/linear-algebra/3d/minimize-rmsd");
+var int_1 = require("molstar/lib/mol-data/int");
+var minimize_rmsd_1 = require("molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd");
+var element_1 = require("molstar/lib/mol-model/structure/structure/element");
 var sifts_mapping_1 = require("./sifts-mapping");
-var element_1 = require("Molstar/mol-model/structure/structure/element");
 function alignAndSuperposeWithSIFTSMapping(structures, options) {
     var _a, _b;
     var indexMap = new Map();

package/lib/superposition.d.ts

@@ -1,9 +1,12 @@
-import { Mat4 } from 'Molstar/mol-math/linear-algebra';
-import { PluginStateObject as PSO } from 'Molstar/mol-plugin-state/objects';
-import { PluginContext } from 'Molstar/mol-plugin/context';
-import { StateObjectRef, StateObjectSelector } from 'Molstar/mol-state';
+import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
+import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin-state/objects';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { StateObjectRef, StateObjectSelector } from 'molstar/lib/mol-state';
+import { ColorListEntry } from 'molstar/lib/mol-util/color/color';
 import { Subject } from 'rxjs';
 import { ClusterMember } from './plugin-custom-state';
+export declare const SuperpositionColorPalette: ColorListEntry[];
+export declare function getNextColor(plugin: PluginContext, segmentIndex: number): ColorListEntry;
 export declare function initSuperposition(plugin: PluginContext, completeSubject?: Subject<boolean>): Promise<void>;
 export declare function loadAfStructure(plugin: PluginContext): Promise<string | false>;
 export declare function superposeAf(plugin: PluginContext, traceOnly: boolean, segmentIndex?: number): Promise<true | undefined>;