pdbe-molstar 3.10.0 → 3.11.0

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

@@ -1,6 +1,6 @@
 /**
  * pdbe-molstar
- * @version 3.10.0
+ * @version 3.11.0
  * @link https://github.com/PDBeurope/pdbe-molstar
  * @license Apache 2.0
  */

package/build/pdbe-molstar.css

@@ -1,6 +1,6 @@
 /**
  * pdbe-molstar
- * @version 3.10.0
+ * @version 3.11.0
  * @link https://github.com/PDBeurope/pdbe-molstar
  * @license Apache 2.0
  */

package/lib/helpers.d.ts

@@ -11,6 +11,7 @@ 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';
+import { Transparency } from 'molstar/lib/mol-theme/transparency';
 export type SupportedFormats = 'mmcif' | 'bcif' | 'cif' | 'pdb' | 'sdf';
 export interface LoadParams {
     url: string;
@@ -179,9 +180,14 @@ export declare function normalizeColor(colorVal: AnyColor | null | undefined, de
 /** 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>;
+/** Apply transparency to every representation of every component in a structure.
+ * Excludes representations created as "added representations" by `PDBeMolstarPlugin.visual.select`. */
+export declare function applyTransparency(plugin: PluginContext, structRef: StructureRef, transparencyLayers: Transparency.BundleLayer[]): Promise<void>;
 export declare const Tags: {
     /** Tag needed for `clearStructureOverpaint`; defined in src/mol-plugin-state/helpers/structure-overpaint.ts but private */
     readonly Overpaint: "overpaint-controls";
+    /** Tag needed for `clearStructureTransparency`; defined in src/mol-plugin-state/helpers/structure-transparency.ts but private */
+    readonly Transparency: "transparency-controls";
     /** Marks structure components added by `select` */
     readonly AddedComponent: "pdbe-molstar.added-component";
 };

package/lib/helpers.js

@@ -8,6 +8,7 @@ exports.combineUrl = combineUrl;
 exports.addDefaults = addDefaults;
 exports.normalizeColor = normalizeColor;
 exports.applyOverpaint = applyOverpaint;
+exports.applyTransparency = applyTransparency;
 exports.getComponentTypeFromTags = getComponentTypeFromTags;
 exports.distinct = distinct;
 exports.groupElements = groupElements;
@@ -524,9 +525,39 @@ function applyOverpaint(plugin, structRef, overpaintLayers) {
         yield update.commit();
     });
 }
+/** Apply transparency to every representation of every component in a structure.
+ * Excludes representations created as "added representations" by `PDBeMolstarPlugin.visual.select`. */
+function applyTransparency(plugin, structRef, transparencyLayers) {
+    return tslib_1.__awaiter(this, void 0, void 0, function* () {
+        var _a;
+        if (transparencyLayers.length === 0)
+            return;
+        const update = plugin.build();
+        for (const component of structRef.components) {
+            if ((_a = component.cell.transform.tags) === null || _a === void 0 ? void 0 : _a.includes(exports.Tags.AddedComponent))
+                continue;
+            for (const repr of component.representations) {
+                const currentTransparency = plugin.state.data.select(mol_state_1.StateSelection.Generators
+                    .ofTransformer(transforms_1.StateTransforms.Representation.TransparencyStructureRepresentation3DFromBundle, repr.cell.transform.ref)
+                    .withTag(exports.Tags.Transparency));
+                if (currentTransparency.length === 0) {
+                    // Create a new transparency
+                    update.to(repr.cell.transform.ref).apply(transforms_1.StateTransforms.Representation.TransparencyStructureRepresentation3DFromBundle, { layers: transparencyLayers }, { tags: exports.Tags.Transparency });
+                }
+                else {
+                    // Add layers to existing transparency
+                    update.to(currentTransparency[0]).update(old => ({ layers: old.layers.concat(transparencyLayers) }));
+                }
+            }
+        }
+        yield update.commit();
+    });
+}
 exports.Tags = {
     /** Tag needed for `clearStructureOverpaint`; defined in src/mol-plugin-state/helpers/structure-overpaint.ts but private */
     Overpaint: 'overpaint-controls',
+    /** Tag needed for `clearStructureTransparency`; defined in src/mol-plugin-state/helpers/structure-transparency.ts but private */
+    Transparency: 'transparency-controls',
     /** Marks structure components added by `select` */
     AddedComponent: 'pdbe-molstar.added-component',
 };

package/lib/viewer.d.ts

@@ -135,30 +135,36 @@ export declare class PDBeMolstarPlugin {
         /** Remove any current highlight and reset the highlight color to its default value. */
         clearHighlight: () => Promise<void>;
         /** 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 `opacity`, set opacity accordingly, set opacity to `nonSelectedOpacity` (or 1) for the rest of the structure.
          * 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. */
+         * Remove any previously added coloring, opacity, and/or extra representations, unless `keepColors`, `keepOpacity`, and/or `keepRepresentations` is set. */
         select: (params: {
             data: (QueryParam & {
                 color?: AnyColor;
+                opacity?: number;
                 sideChain?: boolean;
                 representation?: string;
-                representationColor?: any;
+                representationColor?: AnyColor;
+                representationOpacity?: number;
                 focus?: boolean;
             })[];
             nonSelectedColor?: AnyColor;
+            nonSelectedOpacity?: number;
             structureId?: string;
             structureNumber?: number;
             keepColors?: boolean;
+            keepOpacity?: boolean;
             keepRepresentations?: boolean;
         }) => Promise<void>;
         /** Remove any coloring and extra representations previously added by the `select` method.
          * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure;
          * if not provided, will apply to all loaded structures.
-         * If `keepColors`, current residue coloring is preserved. If `keepRepresentations`, current added representations are preserved. */
+         * If `keepColors`, current residue coloring is preserved. If `keepOpacity`, current residue opacity is preserved. If `keepRepresentations`, current added representations are preserved. */
         clearSelection: (structureNumberOrId?: number | string, options?: {
             keepColors?: boolean;
+            keepOpacity?: boolean;
             keepRepresentations?: boolean;
         }) => Promise<void>;
         /** Color the parts of sequence in the sequence panel defined by `data`. Color the rest of the sequence in `nonSelectedColor` if provided.
@@ -233,6 +239,16 @@ export declare class PDBeMolstarPlugin {
                 SupportedVersion: number;
                 fromMVSJ(mvsjString: string): MVSData;
                 toMVSJ(mvsData: MVSData, space?: string | number): string;
+                toMVSX(mvsData: MVSData, options?: {
+                    assets?: {
+                        [uri: string]: Uint8Array<ArrayBuffer> | string;
+                    };
+                    baseUri?: string;
+                    skipExternal?: boolean;
+                    cache?: {
+                        [absoluteUri: string]: Uint8Array<ArrayBuffer> | string;
+                    };
+                }): Promise<Uint8Array<ArrayBuffer>>;
                 isValid(mvsData: MVSData, options?: {
                     noExtra?: boolean;
                 }): boolean;

package/lib/viewer.js

@@ -23,6 +23,7 @@ const state_interpolation_1 = require("molstar/lib/mol-plugin-state/animation/bu
 const state_snapshots_1 = require("molstar/lib/mol-plugin-state/animation/built-in/state-snapshots");
 const structure_overpaint_1 = require("molstar/lib/mol-plugin-state/helpers/structure-overpaint");
 const structure_representation_params_1 = require("molstar/lib/mol-plugin-state/helpers/structure-representation-params");
+const structure_transparency_1 = require("molstar/lib/mol-plugin-state/helpers/structure-transparency");
 const objects_1 = require("molstar/lib/mol-plugin-state/objects");
 const transforms_1 = require("molstar/lib/mol-plugin-state/transforms");
 const model_1 = require("molstar/lib/mol-plugin-state/transforms/model");
@@ -214,14 +215,15 @@ class PDBeMolstarPlugin {
                 }
             }),
             /** 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 `opacity`, set opacity accordingly, set opacity to `nonSelectedOpacity` (or 1) for the rest of the structure.
              * 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. */
+             * Remove any previously added coloring, opacity, and/or extra representations, unless `keepColors`, `keepOpacity`, and/or `keepRepresentations` is set. */
             select: (params) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 var _a, _b, _c, _d;
                 const structureNumberOrId = (_a = params.structureId) !== null && _a !== void 0 ? _a : params.structureNumber;
-                yield this.visual.clearSelection(structureNumberOrId, { keepColors: params.keepColors, keepRepresentations: params.keepRepresentations });
+                yield this.visual.clearSelection(structureNumberOrId, { keepColors: params.keepColors, keepOpacity: params.keepOpacity, keepRepresentations: params.keepRepresentations });
                 // Structure list to apply selection
                 const structures = this.getStructures(structureNumberOrId);
                 // Filter selection items that apply added representations
@@ -260,22 +262,52 @@ class PDBeMolstarPlugin {
                         }
                     }
                     yield (0, helpers_1.applyOverpaint)(this.plugin, struct.structureRef, overpaintLayers);
+                    // Apply opacity to the main representation
+                    const transparencyLayers = selections
+                        .filter(s => s.param.opacity !== undefined)
+                        .map(s => ({
+                        bundle: s.bundle,
+                        value: 1 - s.param.opacity,
+                    }));
+                    if (params.nonSelectedOpacity !== undefined) {
+                        const wholeStructBundle = this.getBundle([{}], struct.number);
+                        if (wholeStructBundle) {
+                            transparencyLayers.unshift({
+                                bundle: wholeStructBundle,
+                                value: 1 - params.nonSelectedOpacity,
+                            });
+                        }
+                    }
+                    yield (0, helpers_1.applyTransparency)(this.plugin, struct.structureRef, transparencyLayers);
                     // Add extra representations
                     for (const repr in addedReprParams) {
                         const bundle = this.getBundle(addedReprParams[repr], struct.number);
                         if (!bundle)
                             continue;
-                        const overpaintLayers = selections.filter(s => s.param.representationColor).map(s => ({
+                        const update = this.plugin.build();
+                        const addedRepr = update.to(struct.structureRef.cell)
+                            .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, (_d = struct.structureRef.cell.obj) === null || _d === void 0 ? void 0 : _d.data, { type: repr }));
+                        const overpaintLayers = selections
+                            .filter(s => s.param.representationColor)
+                            .map(s => ({
                             bundle: s.bundle,
                             color: (0, helpers_1.normalizeColor)(s.param.representationColor),
                             clear: false,
                         }));
-                        yield this.plugin.build()
-                            .to(struct.structureRef.cell)
-                            .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, (_d = struct.structureRef.cell.obj) === null || _d === void 0 ? void 0 : _d.data, { type: repr }))
-                            .apply(transforms_1.StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, { layers: overpaintLayers }, { tags: helpers_1.Tags.Overpaint })
-                            .commit();
+                        if (overpaintLayers.length > 0) {
+                            addedRepr.apply(transforms_1.StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, { layers: overpaintLayers }, { tags: helpers_1.Tags.Overpaint });
+                        }
+                        const transparencyLayers = selections
+                            .filter(s => s.param.representationOpacity !== undefined)
+                            .map(s => ({
+                            bundle: s.bundle,
+                            value: 1 - s.param.representationOpacity,
+                        }));
+                        if (transparencyLayers.length > 0) {
+                            addedRepr.apply(transforms_1.StateTransforms.Representation.TransparencyStructureRepresentation3DFromBundle, { layers: transparencyLayers }, { tags: helpers_1.Tags.Transparency });
+                        }
+                        yield update.commit();
                         // Track that reprs have been added (for later clearSelection)
                         this.addedReprs[struct.number] = true;
                     }
@@ -288,7 +320,7 @@ class PDBeMolstarPlugin {
             /** Remove any coloring and extra representations previously added by the `select` method.
              * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure;
              * if not provided, will apply to all loaded structures.
-             * If `keepColors`, current residue coloring is preserved. If `keepRepresentations`, current added representations are preserved. */
+             * If `keepColors`, current residue coloring is preserved. If `keepOpacity`, current residue opacity is preserved. If `keepRepresentations`, current added representations are preserved. */
             clearSelection: (structureNumberOrId, options) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 // Structure list to apply to
                 const structures = this.getStructures(structureNumberOrId);
@@ -298,6 +330,10 @@ class PDBeMolstarPlugin {
                         const componentsToClear = struct.structureRef.components.filter(c => { var _a; return !((_a = c.cell.transform.tags) === null || _a === void 0 ? void 0 : _a.includes(helpers_1.Tags.AddedComponent)); });
                         yield (0, structure_overpaint_1.clearStructureOverpaint)(this.plugin, componentsToClear);
                     }
+                    if (!(options === null || options === void 0 ? void 0 : options.keepOpacity)) {
+                        const componentsToClear = struct.structureRef.components.filter(c => { var _a; return !((_a = c.cell.transform.tags) === null || _a === void 0 ? void 0 : _a.includes(helpers_1.Tags.AddedComponent)); });
+                        yield (0, structure_transparency_1.clearStructureTransparency)(this.plugin, componentsToClear);
+                    }
                     // Remove added reprs
                     if (!(options === null || options === void 0 ? void 0 : options.keepRepresentations)) {
                         if (this.addedReprs[struct.number]) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "pdbe-molstar",
-  "version": "3.10.0",
+  "version": "3.11.0",
   "description": "Molstar implementation for PDBe",
   "main": "index.js",
   "scripts": {
@@ -26,7 +26,7 @@
   ],
   "repository": {
     "type": "git",
-    "url": "git+https://github.com/PDBeurope/pdbe-molstar.git"
+    "url": "git+https://github.com/molstar/pdbe-molstar.git"
   },
   "keywords": [
     "Molstar",
@@ -41,9 +41,9 @@
   ],
   "license": "Apache-2.0",
   "bugs": {
-    "url": "https://github.com/PDBeurope/pdbe-molstar/issues"
+    "url": "https://github.com/molstar/pdbe-molstar/issues"
   },
-  "homepage": "https://github.com/PDBeurope/pdbe-molstar#readme",
+  "homepage": "https://github.com/molstar/pdbe-molstar#readme",
   "devDependencies": {
     "@babel/core": "^7.17.10",
     "@babel/plugin-transform-runtime": "^7.17.10",
@@ -80,7 +80,7 @@
     "d3-scale": "^4.0.2",
     "d3-selection": "^3.0.0",
     "lit": "^3.1.1",
-    "molstar": "5.6.1",
+    "molstar": "5.7.0",
     "path-browserify": "^1.0.1",
     "stream-browserify": "^3.0.0",
     "vm-browserify": "^1.1.2"