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

package/lib/overlay.scss

@@ -41,3 +41,10 @@ svg.pdbe-animated-logo {
         }
     }
 }
+
+.msp-plugin ::-webkit-scrollbar-thumb {
+    background-color: #80808080;
+    border-radius: 10px;
+    border: solid 1px transparent;
+    background-clip: content-box;
+}

package/lib/spec-from-html.js

@@ -13,6 +13,7 @@ function initParamsFromHtmlAttributes(element) {
 exports.initParamsFromHtmlAttributes = initParamsFromHtmlAttributes;
 /** Actions for loading individual HTML attributes into InitParams object */
 var InitParamsLoadingActions = {
+    // DATA
     'molecule-id': setString('moleculeId'),
     'custom-data-url': function (value, params) { var _a; ((_a = params.customData) !== null && _a !== void 0 ? _a : (params.customData = defaultCustomData())).url = value; },
     'custom-data-format': function (value, params) { var _a; ((_a = params.customData) !== null && _a !== void 0 ? _a : (params.customData = defaultCustomData())).format = value; },
@@ -25,6 +26,7 @@ var InitParamsLoadingActions = {
     'ligand-auth-seq-id': function (value, params) { var _a; ((_a = params.ligandView) !== null && _a !== void 0 ? _a : (params.ligandView = {})).auth_seq_id = Number(value); },
     'ligand-show-all': function (value, params) { var _a; ((_a = params.ligandView) !== null && _a !== void 0 ? _a : (params.ligandView = {})).show_all = parseBool(value); },
     'alphafold-view': setBool('alphafoldView'),
+    // APPEARANCE
     'visual-style': setLiteral(spec_1.VisualStyle, 'visualStyle'),
     'hide-polymer': pushItem('hideStructure', 'polymer'),
     'hide-water': pushItem('hideStructure', 'water'),
@@ -43,6 +45,7 @@ var InitParamsLoadingActions = {
     'select-color-g': setColorComponent('selectColor', 'g'),
     'select-color-b': setColorComponent('selectColor', 'b'),
     'lighting': setLiteral(spec_1.Lighting, 'lighting'),
+    // BEHAVIOR
     'validation-annotation': setBool('validationAnnotation'),
     'domain-annotation': setBool('domainAnnotation'),
     'symmetry-annotation': setBool('symmetryAnnotation'),
@@ -51,6 +54,7 @@ var InitParamsLoadingActions = {
     'low-precision': setBool('lowPrecisionCoords'),
     'select-interaction': setBool('selectInteraction'),
     'subscribe-events': setBool('subscribeEvents'),
+    // INTERFACE
     'hide-controls': setBool('hideControls'),
     'hide-expand-icon': pushItem('hideCanvasControls', 'expand'),
     'hide-selection-icon': pushItem('hideCanvasControls', 'selection'),

package/lib/spec.d.ts

@@ -56,7 +56,6 @@ export interface InitParams {
     selection?: {
         data: QueryParam[];
         nonSelectedColor?: ColorParams;
-        clearPrevious?: boolean;
     };
     /** Leave `undefined` to keep both cartoon and ball-and-sticks based on component type */
     visualStyle?: VisualStyle;

package/lib/superposition.d.ts

@@ -1,7 +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 { Subject } from 'rxjs';
 import { ClusterMember } from './plugin-custom-state';
 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>;
 export declare function renderSuperposition(plugin: PluginContext, segmentIndex: number, entryList: ClusterMember[]): Promise<void>;
+/** Apply tranformation to a structure. Only use once per structure, combining multiple transformations is not implemented. */
+export declare function transform(plugin: PluginContext, s: StateObjectRef<PSO.Molecule.Structure>, matrix: Mat4): Promise<StateObjectSelector<PSO.Molecule.Structure, import("molstar/lib/mol-state/transformer").StateTransformer<import("molstar/lib/mol-state/object").StateObject<any, import("molstar/lib/mol-state/object").StateObject.Type<any>>, import("molstar/lib/mol-state/object").StateObject<any, import("molstar/lib/mol-state/object").StateObject.Type<any>>, any>>>;

package/lib/superposition.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderSuperposition = exports.superposeAf = exports.loadAfStructure = exports.initSuperposition = void 0;
+exports.transform = exports.renderSuperposition = exports.superposeAf = exports.loadAfStructure = exports.initSuperposition = void 0;
 var tslib_1 = require("tslib");
 var linear_algebra_1 = require("Molstar/mol-math/linear-algebra");
 var structure_1 = require("Molstar/mol-model/structure");
@@ -674,11 +674,13 @@ function chainSelection(struct_asym_id) {
         'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.label_asym_id(), struct_asym_id])
     });
 }
+/** Apply tranformation to a structure. Only use once per structure, combining multiple transformations is not implemented. */
 function transform(plugin, s, matrix) {
     var b = plugin.state.data.build().to(s)
         .insert(transforms_1.StateTransforms.Model.TransformStructureConformation, { transform: { name: 'matrix', params: { data: matrix, transpose: false } } });
     return plugin.runTask(plugin.state.data.updateTree(b));
 }
+exports.transform = transform;
 function afTransform(plugin, s, matrix, coordinateSystem) {
     return tslib_1.__awaiter(this, void 0, void 0, function () {
         var r, o, transform, params, b;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "pdbe-molstar",
-  "version": "3.2.0-beta.4",
+  "version": "3.2.1-beta.1",
   "description": "Molstar implementation for PDBe",
   "main": "index.js",
   "scripts": {