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

package/build/pdbe-molstar-plugin.js.LICENSE.txt

@@ -1,6 +1,6 @@
 /**
  * pdbe-molstar
- * @version 3.2.1-beta.1
+ * @version 3.2.1-beta.3
  * @link https://github.com/PDBeurope/pdbe-molstar
  * @license Apache 2.0
  */

package/build/pdbe-molstar.css

@@ -1,9 +1,9 @@
 /**
  * pdbe-molstar
- * @version 3.2.1-beta.1
+ * @version 3.2.1-beta.3
  * @link https://github.com/PDBeurope/pdbe-molstar
  * @license Apache 2.0
  */
 
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)}.msp-plugin .msp-plugin-content{color:#ccd4e0}.msp-plugin .msp-plugin-init-error{white-space:pre;margin:10px}
-.pdbemolstar-overlay{z-index:1000;position:fixed;top:0px;bottom:0px;left:0px;right:0px;display:flex;justify-content:center;align-items:center;pointer-events:none}.pdbemolstar-overlay-box{width:25%;height:25%}svg.pdbe-animated-logo{background-color:rgba(0,0,0,0);width:100%;height:100%;opacity:80%}svg.pdbe-animated-logo .path-fg{stroke-dasharray:1812 250;stroke-dashoffset:-250;animation:dash linear normal infinite;animation-duration:5s;animation-delay:1s}@keyframes dash{0%{stroke-dashoffset:1812}80%{stroke-dashoffset:-250}100%{stroke-dashoffset:-250}}.msp-plugin ::-webkit-scrollbar-thumb{background-color:rgba(128,128,128,.5019607843);border-radius:10px;border:solid 1px rgba(0,0,0,0);background-clip:content-box}
+.pdbemolstar-overlay{z-index:1000;position:fixed;top:0px;bottom:0px;left:0px;right:0px;display:flex;justify-content:center;align-items:center;pointer-events:none}.pdbemolstar-overlay-box{width:25%;height:25%}svg.pdbe-animated-logo{background-color:rgba(0,0,0,0);width:100%;height:100%;opacity:80%}svg.pdbe-animated-logo .path-fg{stroke-dasharray:1812 250;stroke-dashoffset:-250;animation:dash linear normal infinite;animation-duration:5s;animation-delay:1s}@keyframes dash{0%{stroke-dashoffset:1812}80%{stroke-dashoffset:-250}100%{stroke-dashoffset:-250}}.msp-plugin ::-webkit-scrollbar-thumb{background-color:rgba(128,128,128,.5019607843);border-radius:10px;border:solid 1px rgba(0,0,0,0);background-clip:content-box}.msp-plugin .msp-layout-static{container-type:size}.msp-plugin .msp-viewport-controls-panel .msp-viewport-controls-panel-controls{max-height:calc(100cqh - 41px - 24px - 10px)}

package/lib/alphafold-transparency.d.ts

@@ -1,6 +1,6 @@
-import { StructureElement } from 'Molstar/mol-model/structure';
-import { PluginContext } from 'Molstar/mol-plugin/context';
-import { StructureComponentRef, StructureRef } from 'Molstar/mol-plugin-state/manager/structure/hierarchy-state';
+import { StructureElement } from 'molstar/lib/mol-model/structure';
+import { StructureComponentRef, StructureRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
 export declare function applyAFTransparency(plugin: PluginContext, structure: Readonly<StructureRef>, transparency: number, pLDDT?: number): Promise<void>;
 export declare function setStructureTransparency(plugin: PluginContext, components: StructureComponentRef[], value: number, loci: StructureElement.Loci, types?: string[]): Promise<void>;
 export declare function clearStructureTransparency(plugin: PluginContext, components: StructureComponentRef[], types?: string[]): Promise<void>;

package/lib/alphafold-transparency.js

@@ -2,15 +2,14 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.clearStructureTransparency = exports.setStructureTransparency = exports.applyAFTransparency = void 0;
 var tslib_1 = require("tslib");
-var structure_1 = require("Molstar/mol-model/structure");
-var transforms_1 = require("Molstar/mol-plugin-state/transforms");
-var mol_state_1 = require("Molstar/mol-state");
-var loci_1 = require("Molstar/mol-model/loci");
-var transparency_1 = require("Molstar/mol-theme/transparency");
-var builder_1 = require("Molstar/mol-script/language/builder");
-var prop_1 = require("Molstar/extensions/model-archive/quality-assessment/prop");
-var compiler_1 = require("Molstar/mol-script/runtime/query/compiler");
-var structure_2 = require("Molstar/mol-model/structure");
+var prop_1 = require("molstar/lib/extensions/model-archive/quality-assessment/prop");
+var loci_1 = require("molstar/lib/mol-model/loci");
+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 compiler_1 = require("molstar/lib/mol-script/runtime/query/compiler");
+var mol_state_1 = require("molstar/lib/mol-state");
+var transparency_1 = require("molstar/lib/mol-theme/transparency");
 var TransparencyManagerTag = 'transparency-controls';
 function getLociByPLDDT(score, contextData) {
     var queryExp = builder_1.MolScriptBuilder.struct.modifier.union([
@@ -24,8 +23,8 @@ function getLociByPLDDT(score, contextData) {
         ])
     ]);
     var query = (0, compiler_1.compile)(queryExp);
-    var sel = query(new structure_2.QueryContext(contextData));
-    return structure_2.StructureSelection.toLociWithSourceUnits(sel);
+    var sel = query(new structure_1.QueryContext(contextData));
+    return structure_1.StructureSelection.toLociWithSourceUnits(sel);
 }
 function applyAFTransparency(plugin, structure, transparency, pLDDT) {
     if (pLDDT === void 0) { pLDDT = 70; }

package/lib/custom-events.d.ts

@@ -1,4 +1,4 @@
-import { PluginContext } from 'Molstar/mol-plugin/context';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
 export declare namespace CustomEvents {
     function add(plugin: PluginContext, targetElement: HTMLElement): void;
 }

package/lib/custom-events.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.CustomEvents = void 0;
-var loci_details_1 = require("./loci-details");
 var operators_1 = require("rxjs/operators");
+var loci_details_1 = require("./loci-details");
 var CustomEvents;
 (function (CustomEvents) {
     function create(eventTypeArr) {

package/lib/domain-annotations/behavior.d.ts

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

package/lib/domain-annotations/behavior.js

@@ -2,10 +2,10 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PDBeDomainAnnotations = void 0;
 var tslib_1 = require("tslib");
-var prop_1 = require("./prop");
+var behavior_1 = require("molstar/lib/mol-plugin/behavior");
+var param_definition_1 = require("molstar/lib/mol-util/param-definition");
 var color_1 = require("./color");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
-var behavior_1 = require("Molstar/mol-plugin/behavior");
+var prop_1 = require("./prop");
 exports.PDBeDomainAnnotations = behavior_1.PluginBehavior.create({
     name: 'pdbe-domain-annotations-prop',
     category: 'custom-props',

package/lib/domain-annotations/color.d.ts

@@ -1,6 +1,6 @@
-import { ColorTheme } from 'Molstar/mol-theme/color';
-import { ThemeDataContext } from 'Molstar/mol-theme/theme';
-import { ParamDefinition as PD } from 'Molstar/mol-util/param-definition';
+import { ColorTheme } from 'molstar/lib/mol-theme/color';
+import { ThemeDataContext } from 'molstar/lib/mol-theme/theme';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
 export declare const DomainAnnotationsColorThemeParams: {
     type: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "">>;
 };

package/lib/domain-annotations/color.js

@@ -1,11 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DomainAnnotationsColorThemeProvider = exports.DomainAnnotationsColorTheme = exports.DomainAnnotationsColorThemeParams = void 0;
+var structure_1 = require("molstar/lib/mol-model/structure");
+var color_1 = require("molstar/lib/mol-theme/color");
+var color_2 = require("molstar/lib/mol-util/color");
+var param_definition_1 = require("molstar/lib/mol-util/param-definition");
 var prop_1 = require("./prop");
-var structure_1 = require("Molstar/mol-model/structure");
-var color_1 = require("Molstar/mol-theme/color");
-var color_2 = require("Molstar/mol-util/color");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
 var DomainColors = [
     color_2.Color.fromRgb(170, 170, 170),
     color_2.Color.fromRgb(255, 112, 3)

package/lib/domain-annotations/prop.d.ts

@@ -1,9 +1,9 @@
-import { Model, IndexedCustomProperty } from 'Molstar/mol-model/structure';
-import { StructureElement, Structure } from 'Molstar/mol-model/structure/structure';
-import { PropertyWrapper } from 'Molstar/mol-model-props/common/wrapper';
-import { CustomModelProperty } from 'Molstar/mol-model-props/common/custom-model-property';
-import { ParamDefinition as PD } from 'Molstar/mol-util/param-definition';
-import { CustomProperty } from 'Molstar/mol-model-props/common/custom-property';
+import { CustomModelProperty } from 'molstar/lib/mol-model-props/common/custom-model-property';
+import { CustomProperty } from 'molstar/lib/mol-model-props/common/custom-property';
+import { PropertyWrapper } from 'molstar/lib/mol-model-props/common/wrapper';
+import { IndexedCustomProperty, Model } from 'molstar/lib/mol-model/structure';
+import { Structure, StructureElement } from 'molstar/lib/mol-model/structure/structure';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
 export { DomainAnnotations };
 type DomainAnnotations = PropertyWrapper<{
     domains: IndexedCustomProperty.Residue<string[]>;

package/lib/domain-annotations/prop.js

@@ -2,13 +2,13 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DomainAnnotationsProvider = exports.DomainAnnotationsParams = exports.DomainAnnotations = void 0;
 var tslib_1 = require("tslib");
-var structure_1 = require("Molstar/mol-model/structure");
-var wrapper_1 = require("Molstar/mol-model-props/common/wrapper");
-var custom_model_property_1 = require("Molstar/mol-model-props/common/custom-model-property");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
-var array_1 = require("Molstar/mol-util/array");
-var assets_1 = require("Molstar/mol-util/assets");
-var custom_property_1 = require("Molstar/mol-model/custom-property");
+var custom_model_property_1 = require("molstar/lib/mol-model-props/common/custom-model-property");
+var wrapper_1 = require("molstar/lib/mol-model-props/common/wrapper");
+var custom_property_1 = require("molstar/lib/mol-model/custom-property");
+var structure_1 = require("molstar/lib/mol-model/structure");
+var array_1 = require("molstar/lib/mol-util/array");
+var assets_1 = require("molstar/lib/mol-util/assets");
+var param_definition_1 = require("molstar/lib/mol-util/param-definition");
 var DomainAnnotations;
 (function (DomainAnnotations) {
     DomainAnnotations.DefaultServerUrl = 'https://www.ebi.ac.uk/pdbe/api/mappings';

package/lib/extensions/foldseek.d.ts

@@ -1,5 +1,5 @@
 /** Helper functions to allow visualizing Foldseek results and superposing them on the query structure */
-import { Mat4 } from 'Molstar/mol-math/linear-algebra';
+import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
 import { PDBeMolstarPlugin } from '..';
 export interface FoldseekApiData {
     query: string;

package/lib/extensions/foldseek.js

@@ -3,8 +3,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.exportModels = exports.loadFoldseekSuperposition = void 0;
 var tslib_1 = require("tslib");
-var export_1 = require("Molstar/extensions/model-export/export");
-var minimize_rmsd_1 = require("Molstar/mol-math/linear-algebra/3d/minimize-rmsd");
+var export_1 = require("molstar/lib/extensions/model-export/export");
+var minimize_rmsd_1 = require("molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd");
 var superposition_1 = require("../superposition");
 /** Load target structure as defined by `apiData`
  * and superpose it on the already loaded query structure. */

package/lib/helpers.d.ts

@@ -1,10 +1,11 @@
-import { Model, Structure } from 'Molstar/mol-model/structure';
-import { BuiltInTrajectoryFormat } from 'Molstar/mol-plugin-state/formats/trajectory';
-import { StructureRef } from 'Molstar/mol-plugin-state/manager/structure/hierarchy-state';
-import { PluginContext } from 'Molstar/mol-plugin/context';
-import Expression from 'Molstar/mol-script/language/expression';
-import { Overpaint } from 'Molstar/mol-theme/overpaint';
-import { InitParams } from './spec';
+import { Model, Structure } from 'molstar/lib/mol-model/structure';
+import { BuiltInTrajectoryFormat } from 'molstar/lib/mol-plugin-state/formats/trajectory';
+import { StructureRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { Expression } from 'molstar/lib/mol-script/language/expression';
+import { Overpaint } from 'molstar/lib/mol-theme/overpaint';
+import { Color } from 'molstar/lib/mol-util/color';
+import { AnyColor, InitParams } from './spec';
 export type SupportedFormats = 'mmcif' | 'bcif' | 'cif' | 'pdb' | 'sdf';
 export type LoadParams = {
     url: string;
@@ -44,12 +45,12 @@ export type LigandQueryParam = {
 };
 export declare namespace LigandView {
     function query(ligandViewParams: LigandQueryParam): {
-        core: Expression.Expression;
-        surroundings: Expression.Expression;
+        core: Expression;
+        surroundings: Expression;
     };
     function branchedQuery(params: any): {
-        core: Expression.Expression;
-        surroundings: Expression.Expression;
+        core: Expression;
+        surroundings: Expression;
     };
 }
 export type QueryParam = {
@@ -83,9 +84,9 @@ export type QueryParam = {
     end_uniprot_residue_number?: number;
 };
 export declare namespace QueryHelper {
-    function getQueryObject(params: QueryParam[], contextData: Structure): Expression.Expression;
+    function getQueryObject(params: QueryParam[], contextData: Structure): Expression;
     function getInteractivityLoci(params: QueryParam[], contextData: Structure): import("molstar/lib/mol-model/structure/structure/element/loci").Loci;
-    function getHetLoci(queryExp: Expression.Expression, contextData: Structure): import("molstar/lib/mol-model/structure/structure/element/loci").Loci;
+    function getHetLoci(queryExp: Expression, contextData: Structure): import("molstar/lib/mol-model/structure/structure/element/loci").Loci;
 }
 export interface ModelInfo {
     hetNames: string[];
@@ -107,6 +108,10 @@ export interface ModelServerRequest {
 export declare function getStructureUrl(initParams: InitParams, request: ModelServerRequest): string;
 /** Create a copy of object `object`, fill in missing/undefined keys using `defaults` */
 export declare function addDefaults<T extends {}>(object: Partial<T> | undefined, defaults: T): T;
+/** Convert `colorVal` from any of supported color formats (e.g. 'yellow', '#ffff00', {r:255,g:255,b:0}) to `Color`.
+ * Return default color (gray) if `colorVal` is undefined or null.
+*/
+export declare function normalizeColor(colorVal: AnyColor | null | undefined, defaultColor?: Color): Color;
 /** Apply overpaint to every representation of every component in a structure.
  * Excludes representations created as "added representations" by `PDBeMolstarPlugin.visual.select`. */
 export declare function applyOverpaint(plugin: PluginContext, structRef: StructureRef, overpaintLayers: Overpaint.BundleLayer[]): Promise<void>;
@@ -125,4 +130,6 @@ export declare const StructureComponentTags: {
     coarse: string[];
     maps: string[];
 };
+/** Return component type based on the component's PluginStateObject tags */
+export declare function getComponentTypeFromTags(tags: string[] | undefined): keyof typeof StructureComponentTags | undefined;
 export {};

package/lib/helpers.js

@@ -1,17 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StructureComponentTags = exports.Tags = exports.applyOverpaint = exports.addDefaults = exports.getStructureUrl = exports.runWithProgressMessage = exports.ModelInfo = exports.QueryHelper = exports.LigandView = exports.AlphafoldView = exports.PDBeVolumes = void 0;
+exports.getComponentTypeFromTags = exports.StructureComponentTags = exports.Tags = exports.applyOverpaint = exports.normalizeColor = exports.addDefaults = exports.getStructureUrl = exports.runWithProgressMessage = exports.ModelInfo = exports.QueryHelper = exports.LigandView = exports.AlphafoldView = exports.PDBeVolumes = void 0;
 var tslib_1 = require("tslib");
-var prop_1 = require("Molstar/extensions/model-archive/quality-assessment/prop");
-var structure_1 = require("Molstar/mol-model/structure");
-var query_1 = require("Molstar/mol-model/structure/query/query");
-var transforms_1 = require("Molstar/mol-plugin-state/transforms");
-var transformers_1 = require("Molstar/mol-plugin/behavior/dynamic/volume-streaming/transformers");
-var commands_1 = require("Molstar/mol-plugin/commands");
-var builder_1 = require("Molstar/mol-script/language/builder");
-var compiler_1 = require("Molstar/mol-script/runtime/query/compiler");
-var mol_state_1 = require("Molstar/mol-state");
-var mol_task_1 = require("Molstar/mol-task");
+var prop_1 = require("molstar/lib/extensions/model-archive/quality-assessment/prop");
+var structure_1 = require("molstar/lib/mol-model/structure");
+var query_1 = require("molstar/lib/mol-model/structure/query/query");
+var transforms_1 = require("molstar/lib/mol-plugin-state/transforms");
+var transformers_1 = require("molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers");
+var commands_1 = require("molstar/lib/mol-plugin/commands");
+var builder_1 = require("molstar/lib/mol-script/language/builder");
+var compiler_1 = require("molstar/lib/mol-script/runtime/query/compiler");
+var mol_state_1 = require("molstar/lib/mol-state");
+var mol_task_1 = require("molstar/lib/mol-task");
+var color_1 = require("molstar/lib/mol-util/color");
+var names_1 = require("molstar/lib/mol-util/color/names");
 var sifts_mapping_1 = require("./sifts-mapping");
 var PDBeVolumes;
 (function (PDBeVolumes) {
@@ -341,6 +343,30 @@ function addDefaults(object, defaults) {
     return result;
 }
 exports.addDefaults = addDefaults;
+/** Convert `colorVal` from any of supported color formats (e.g. 'yellow', '#ffff00', {r:255,g:255,b:0}) to `Color`.
+ * Return default color (gray) if `colorVal` is undefined or null.
+*/
+function normalizeColor(colorVal, defaultColor) {
+    var _a, _b, _c;
+    if (defaultColor === void 0) { defaultColor = color_1.Color.fromRgb(170, 170, 170); }
+    try {
+        if (colorVal === undefined || colorVal === null)
+            return defaultColor;
+        if (typeof colorVal === 'number')
+            return (0, color_1.Color)(colorVal);
+        if (typeof colorVal === 'string' && colorVal[0] === '#')
+            return (0, color_1.Color)(Number("0x".concat(colorVal.substring(1))));
+        if (typeof colorVal === 'string' && colorVal in names_1.ColorNames)
+            return names_1.ColorNames[colorVal];
+        if (typeof colorVal === 'object')
+            return color_1.Color.fromRgb((_a = colorVal.r) !== null && _a !== void 0 ? _a : 0, (_b = colorVal.g) !== null && _b !== void 0 ? _b : 0, (_c = colorVal.b) !== null && _c !== void 0 ? _c : 0);
+    }
+    catch (_d) {
+        // do nothing
+    }
+    return defaultColor;
+}
+exports.normalizeColor = normalizeColor;
 /** Apply overpaint to every representation of every component in a structure.
  * Excludes representations created as "added representations" by `PDBeMolstarPlugin.visual.select`. */
 function applyOverpaint(plugin, structRef, overpaintLayers) {
@@ -396,3 +422,15 @@ exports.StructureComponentTags = {
     coarse: ['structure-component-static-coarse'],
     maps: ['volume-streaming-info'],
 };
+/** Return component type based on the component's PluginStateObject tags */
+function getComponentTypeFromTags(tags) {
+    var type;
+    for (type in exports.StructureComponentTags) {
+        var typeTags = exports.StructureComponentTags[type];
+        if (typeTags.some(function (tag) { return tags === null || tags === void 0 ? void 0 : tags.includes(tag); })) {
+            return type;
+        }
+    }
+    return undefined;
+}
+exports.getComponentTypeFromTags = getComponentTypeFromTags;