molstar 4.2.0 → 4.4.0

package/lib/apps/viewer/app.js

@@ -3,6 +3,7 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Neli Fonseca <neli@ebi.ac.uk>
  */
 import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
 import { Backgrounds } from '../../extensions/backgrounds';
@@ -20,7 +21,7 @@ import { MVSData } from '../../extensions/mvs/mvs-data';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBValidationReport } from '../../extensions/rcsb';
 import { AssemblySymmetry, AssemblySymmetryConfig } from '../../extensions/assembly-symmetry';
-import { SbNcbrPartialCharges, SbNcbrPartialChargesPreset, SbNcbrPartialChargesPropertyProvider } from '../../extensions/sb-ncbr';
+import { SbNcbrPartialCharges, SbNcbrPartialChargesPreset, SbNcbrPartialChargesPropertyProvider, SbNcbrTunnels } from '../../extensions/sb-ncbr';
 import { Volseg, VolsegVolumeServerConfig } from '../../extensions/volumes-and-segmentations';
 import { wwPDBChemicalComponentDictionary } from '../../extensions/wwpdb/ccd/behavior';
 import { wwPDBStructConnExtensionFunctions } from '../../extensions/wwpdb/struct-conn';
@@ -41,6 +42,7 @@ import { PluginSpec } from '../../mol-plugin/spec';
 import { StateObjectRef } from '../../mol-state';
 import { Task } from '../../mol-task';
 import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
 import '../../mol-util/polyfill';
 import { ObjectKeys } from '../../mol-util/type-helpers';
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
@@ -65,6 +67,7 @@ export const ExtensionMap = {
     'sb-ncbr-partial-charges': PluginSpec.Behavior(SbNcbrPartialCharges),
     'wwpdb-chemical-component-dictionary': PluginSpec.Behavior(wwPDBChemicalComponentDictionary),
     'mvs': PluginSpec.Behavior(MolViewSpec),
+    'tunnels': PluginSpec.Behavior(SbNcbrTunnels),
 };
 const DefaultViewerOptions = {
     customFormats: CustomFormats,
@@ -384,6 +387,32 @@ export class Viewer {
             await repr.commit();
         });
     }
+    loadFullResolutionEMDBMap(emdbId, options) {
+        const plugin = this.plugin;
+        const numericId = parseInt(emdbId.toUpperCase().replace('EMD-', ''));
+        const url = `https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-${numericId}/map/emd_${numericId}.map.gz`;
+        return plugin.dataTransaction(async () => {
+            var _a, _b, _c;
+            const data = await plugin.build().toRoot()
+                .apply(StateTransforms.Data.Download, { url, isBinary: true, label: emdbId }, { state: { isGhost: true } })
+                .apply(StateTransforms.Data.DeflateData)
+                .commit();
+            const parsed = await plugin.dataFormats.get('ccp4').parse(plugin, data, { entryId: emdbId });
+            const firstVolume = (parsed.volume || parsed.volumes[0]);
+            if (!(firstVolume === null || firstVolume === void 0 ? void 0 : firstVolume.isOk))
+                throw new Error('Failed to parse any volume.');
+            const volume = (_b = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[0]) !== null && _b !== void 0 ? _b : parsed.volume;
+            await plugin.build()
+                .to(volume)
+                .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data, {
+                type: 'isosurface',
+                typeParams: { alpha: 1, isoValue: options.isoValue },
+                color: 'uniform',
+                colorParams: { value: (_c = options.color) !== null && _c !== void 0 ? _c : Color(0x33BB33) }
+            }))
+                .commit();
+        });
+    }
     /**
      * @example
      *  viewer.loadTrajectory({

package/lib/commonjs/apps/docking-viewer/viewport.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/apps/docking-viewer/viewport.js

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.ViewportComponent = exports.ShowButtons = exports.IllustrativePreset = exports.StructurePreset = void 0;
 const jsx_runtime_1 = require("react/jsx-runtime");
 /**
- * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -45,6 +45,7 @@ function occlusionStyle(plugin) {
                 ...plugin.canvas3d.props.postprocessing,
                 occlusion: { name: 'on', params: {
                         blurKernelSize: 15,
+                        blurDepthBias: 0.5,
                         multiScale: { name: 'off', params: {} },
                         radius: 5,
                         bias: 0.8,

package/lib/commonjs/apps/mesoscale-explorer/app.d.ts

@@ -24,12 +24,13 @@ export type MesoscaleExplorerState = {
     examples?: ExampleEntry[];
     graphicsMode: GraphicsMode;
     stateRef?: string;
+    driver?: any;
     stateCache: {
         [k: string]: any;
     };
 };
 declare const DefaultMesoscaleExplorerOptions: {
-    customFormats: [string, DataFormatProvider<any, any, any>][];
+    customFormats: [string, DataFormatProvider][];
     extensions: ("mp4-export" | "backgrounds")[];
     layoutIsExpanded: boolean;
     layoutShowControls: boolean;
@@ -60,6 +61,7 @@ declare const DefaultMesoscaleExplorerOptions: {
     emdbProvider: import("../../mol-plugin-state/actions/volume").EmdbDownloadProvider | undefined;
     saccharideCompIdMapType: SaccharideCompIdMapType;
     graphicsMode: GraphicsMode;
+    driver: undefined;
 };
 type MesoscaleExplorerOptions = typeof DefaultMesoscaleExplorerOptions;
 export declare class MesoscaleExplorer {

package/lib/commonjs/apps/mesoscale-explorer/app.js

@@ -27,6 +27,7 @@ const assets_1 = require("../../mol-util/assets");
 const camera_spin_1 = require("../../mol-plugin-state/animation/built-in/camera-spin");
 const camera_rock_1 = require("../../mol-plugin-state/animation/built-in/camera-rock");
 const state_snapshots_1 = require("../../mol-plugin-state/animation/built-in/state-snapshots");
+const entities_1 = require("./ui/entities");
 var version_1 = require("../../mol-plugin/version");
 Object.defineProperty(exports, "version", { enumerable: true, get: function () { return version_1.PLUGIN_VERSION; } });
 var debug_1 = require("../../mol-util/debug");
@@ -70,7 +71,8 @@ const DefaultMesoscaleExplorerOptions = {
     pdbProvider: config_1.PluginConfig.Download.DefaultPdbProvider.defaultValue,
     emdbProvider: config_1.PluginConfig.Download.DefaultEmdbProvider.defaultValue,
     saccharideCompIdMapType: 'default',
-    graphicsMode: 'quality'
+    graphicsMode: 'quality',
+    driver: undefined
 };
 class MesoscaleExplorer {
     constructor(plugin) {
@@ -142,6 +144,9 @@ class MesoscaleExplorer {
                     right: panels_1.RightPanel,
                 },
                 remoteState: 'none',
+                viewport: {
+                    snapshotDescription: entities_1.MesoViewportSnapshotDescription,
+                }
             },
             config: [
                 [config_1.PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
@@ -179,6 +184,11 @@ class MesoscaleExplorer {
                 let examples = undefined;
                 try {
                     examples = await plugin.fetch({ url: './examples/list.json', type: 'json' }).run();
+                    // extend the array with file tour.json if it exists
+                    const tour = await plugin.fetch({ url: './examples/tour.json', type: 'json' }).run();
+                    if (tour) {
+                        examples = examples === null || examples === void 0 ? void 0 : examples.concat(tour);
+                    }
                 }
                 catch (e) {
                     console.log(e);
@@ -186,6 +196,7 @@ class MesoscaleExplorer {
                 plugin.customState = {
                     examples,
                     graphicsMode: o.graphicsMode,
+                    driver: o.driver,
                     stateCache: {},
                 };
                 await state_1.MesoscaleState.init(plugin);

package/lib/commonjs/apps/mesoscale-explorer/behavior/camera.d.ts

@@ -6,6 +6,17 @@
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginBehavior } from '../../../mol-plugin/behavior';
 import { Binding } from '../../../mol-util/binding';
+export declare const MesoFocusLociParams: {
+    minRadius: PD.Numeric;
+    extraRadius: PD.Numeric;
+    durationMs: PD.Numeric;
+    centerOnly: PD.BooleanParam;
+    bindings: PD.Value<{
+        clickCenter: Binding;
+        clickCenterFocus: Binding;
+        keyCenterOnly: Binding;
+    }>;
+};
 export declare const MesoFocusLoci: import("../../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, PD.Values<{
     minRadius: PD.Numeric;
     extraRadius: PD.Numeric;
@@ -14,5 +25,6 @@ export declare const MesoFocusLoci: import("../../../mol-state").StateTransforme
     bindings: PD.Value<{
         clickCenter: Binding;
         clickCenterFocus: Binding;
+        keyCenterOnly: Binding;
     }>;
 }>>;

package/lib/commonjs/apps/mesoscale-explorer/behavior/camera.js

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MesoFocusLoci = void 0;
+exports.MesoFocusLoci = exports.MesoFocusLociParams = void 0;
 const loci_1 = require("../../../mol-model/loci");
 const param_definition_1 = require("../../../mol-util/param-definition");
 const behavior_1 = require("../../../mol-plugin/behavior");
@@ -13,9 +13,11 @@ const input_observer_1 = require("../../../mol-util/input/input-observer");
 const binding_1 = require("../../../mol-util/binding");
 const commands_1 = require("../../../mol-plugin/commands");
 const geometry_1 = require("../../../mol-math/geometry");
+const structure_1 = require("../../../mol-model/structure");
 const B = input_observer_1.ButtonsType;
 const M = input_observer_1.ModifiersKeys;
 const Trigger = binding_1.Binding.Trigger;
+const Key = binding_1.Binding.TriggerKey;
 const DefaultMesoFocusLociBindings = {
     clickCenter: (0, binding_1.Binding)([
         Trigger(B.Flag.Primary, M.create()),
@@ -23,8 +25,9 @@ const DefaultMesoFocusLociBindings = {
     clickCenterFocus: (0, binding_1.Binding)([
         Trigger(B.Flag.Secondary, M.create()),
     ], 'Camera center and focus', 'Click element using ${triggers}'),
+    keyCenterOnly: (0, binding_1.Binding)([Key('C')], 'Center Only Toggle', 'Press ${triggers}'),
 };
-const MesoFocusLociParams = {
+exports.MesoFocusLociParams = {
     minRadius: param_definition_1.ParamDefinition.Numeric(8, { min: 1, max: 50, step: 1 }),
     extraRadius: param_definition_1.ParamDefinition.Numeric(4, { min: 1, max: 50, step: 1 }, { description: 'Value added to the bounding-sphere radius of the Loci' }),
     durationMs: param_definition_1.ParamDefinition.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'Camera transition duration' }),
@@ -43,27 +46,50 @@ exports.MesoFocusLoci = behavior_1.PluginBehavior.create({
                 const loci = loci_1.Loci.normalize(current.loci, this.ctx.managers.interactivity.props.granularity);
                 const sphere = loci_1.Loci.getBoundingSphere(loci) || (0, geometry_1.Sphere3D)();
                 const { clickCenter, clickCenterFocus } = this.params.bindings;
-                const { durationMs, extraRadius, minRadius } = this.params;
+                const { durationMs, extraRadius, minRadius, centerOnly } = this.params;
                 const radius = Math.max(sphere.radius + extraRadius, minRadius);
                 if (binding_1.Binding.match(clickCenter, button, modifiers)) {
+                    // left mouse button
                     if (loci_1.Loci.isEmpty(current.loci)) {
                         commands_1.PluginCommands.Camera.Reset(this.ctx, {});
                         return;
                     }
-                    const snapshot = canvas3d.camera.getCenter(sphere.center);
-                    canvas3d.requestCameraReset({ durationMs, snapshot });
+                    if (structure_1.StructureElement.Loci.is(current.loci)) {
+                        if (centerOnly) {
+                            const snapshot = canvas3d.camera.getCenter(sphere.center);
+                            canvas3d.requestCameraReset({ durationMs, snapshot });
+                        }
+                        else {
+                            this.ctx.managers.camera.focusSphere(sphere, this.params);
+                        }
+                    }
                 }
                 else if (binding_1.Binding.match(clickCenterFocus, button, modifiers)) {
+                    // right mouse button
                     if (loci_1.Loci.isEmpty(current.loci)) {
                         commands_1.PluginCommands.Camera.Reset(this.ctx, {});
                         return;
                     }
-                    const snapshot = canvas3d.camera.getCenter(sphere.center, radius);
-                    canvas3d.requestCameraReset({ durationMs, snapshot });
+                    if (centerOnly) {
+                        const snapshot = canvas3d.camera.getCenter(sphere.center, radius);
+                        canvas3d.requestCameraReset({ durationMs, snapshot });
+                    }
+                    else {
+                        this.ctx.managers.camera.focusSphere(sphere, this.params);
+                    }
+                }
+            });
+            this.subscribeObservable(this.ctx.behaviors.interaction.key, ({ code, key, modifiers }) => {
+                if (!this.ctx.canvas3d)
+                    return;
+                const b = { ...DefaultMesoFocusLociBindings, ...this.params.bindings };
+                const { centerOnly } = this.params;
+                if (binding_1.Binding.matchKey(b.keyCenterOnly, code, modifiers, key)) {
+                    this.params.centerOnly = !centerOnly;
                 }
             });
         }
     },
-    params: () => MesoFocusLociParams,
+    params: () => exports.MesoFocusLociParams,
     display: { name: 'Camera Meso Focus Loci on Canvas' }
 });

package/lib/commonjs/apps/mesoscale-explorer/behavior/select.d.ts

@@ -8,6 +8,7 @@ import { PluginBehavior } from '../../../mol-plugin/behavior';
 import { Binding } from '../../../mol-util/binding';
 export declare const MesoSelectLoci: import("../../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, PD.Values<{
     bindings: PD.Value<{
+        click: Binding;
         clickToggleSelect: Binding;
         hoverHighlightOnly: Binding;
     }>;

package/lib/commonjs/apps/mesoscale-explorer/behavior/select.js

@@ -16,10 +16,14 @@ const structure_1 = require("../../../mol-model/structure");
 const mol_state_1 = require("../../../mol-state");
 const spine_1 = require("../../../mol-state/tree/spine");
 const marker_action_1 = require("../../../mol-util/marker-action");
+const state_1 = require("../data/state");
 const B = input_observer_1.ButtonsType;
 const M = input_observer_1.ModifiersKeys;
 const Trigger = binding_1.Binding.Trigger;
 const DefaultMesoSelectLociBindings = {
+    click: (0, binding_1.Binding)([
+        Trigger(B.Flag.Primary, M.create())
+    ], 'Click', 'Click element using ${triggers}'),
     clickToggleSelect: (0, binding_1.Binding)([
         Trigger(B.Flag.Primary, M.create({ shift: true })),
         Trigger(B.Flag.Primary, M.create({ control: true })),
@@ -52,9 +56,10 @@ exports.MesoSelectLoci = behavior_1.PluginBehavior.create({
         }
         register() {
             this.subscribeObservable(this.ctx.behaviors.interaction.click, ({ current, button, modifiers }) => {
+                var _a, _b, _c, _d, _e;
                 if (!this.ctx.canvas3d || this.ctx.isBusy)
                     return;
-                const { clickToggleSelect } = this.params.bindings;
+                const { click, clickToggleSelect } = this.params.bindings;
                 if (binding_1.Binding.match(clickToggleSelect, button, modifiers)) {
                     if (loci_1.Loci.isEmpty(current.loci)) {
                         this.ctx.managers.interactivity.lociSelects.deselectAll();
@@ -62,11 +67,34 @@ exports.MesoSelectLoci = behavior_1.PluginBehavior.create({
                     }
                     const loci = loci_1.Loci.normalize(current.loci, modifiers.control ? 'entity' : 'chain');
                     this.ctx.managers.interactivity.lociSelects.toggle({ loci }, false);
+                    if (structure_1.StructureElement.Loci.is(current.loci)) {
+                        const cell = this.ctx.helpers.substructureParent.get(current.loci.structure);
+                        const d = (0, state_1.getCellDescription)(cell);
+                        state_1.MesoscaleState.set(this.ctx, { focusInfo: `${d}` });
+                    }
+                }
+                if (binding_1.Binding.match(click, button, modifiers)) {
+                    if (loci_1.Loci.isEmpty(current.loci)) {
+                        state_1.MesoscaleState.set(this.ctx, { focusInfo: '', filter: '' });
+                        return;
+                    }
+                    const snapshotKey = (_d = (_c = (_b = (_a = current.repr) === null || _a === void 0 ? void 0 : _a.props) === null || _b === void 0 ? void 0 : _b.snapshotKey) === null || _c === void 0 ? void 0 : _c.trim()) !== null && _d !== void 0 ? _d : '';
+                    if (snapshotKey) {
+                        this.ctx.managers.snapshot.applyKey(snapshotKey);
+                    }
+                    else {
+                        if (structure_1.StructureElement.Loci.is(current.loci)) {
+                            const cell = this.ctx.helpers.substructureParent.get(current.loci.structure);
+                            const d = (0, state_1.getCellDescription)(cell);
+                            state_1.MesoscaleState.set(this.ctx, { focusInfo: `${d}`, filter: `${(_e = cell === null || cell === void 0 ? void 0 : cell.obj) === null || _e === void 0 ? void 0 : _e.label}` });
+                            (0, state_1.expandAllGroups)(this.ctx);
+                        }
+                    }
                 }
             });
             this.ctx.managers.interactivity.lociSelects.addProvider(this.lociMarkProvider);
             this.subscribeObservable(this.ctx.behaviors.interaction.hover, ({ current, button, modifiers }) => {
-                var _a, _b;
+                var _a, _b, _c, _d, _e;
                 if (!this.ctx.canvas3d || this.ctx.isBusy)
                     return;
                 const pointerLock = !!((_a = this.ctx.canvas3dContext) === null || _a === void 0 ? void 0 : _a.input.pointerLock);
@@ -76,22 +104,43 @@ exports.MesoSelectLoci = behavior_1.PluginBehavior.create({
                         this.ctx.managers.interactivity.lociHighlights.clearHighlights();
                         return;
                     }
-                    if (modifiers.control) {
-                        this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: loci_1.EveryLoci }, false);
-                    }
-                    else {
-                        const loci = loci_1.Loci.normalize(current.loci, 'chain');
-                        this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci }, false);
+                    if (structure_1.StructureElement.Loci.is(current.loci)) {
+                        if (modifiers.control) {
+                            this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: loci_1.EveryLoci }, false);
+                        }
+                        else {
+                            const loci = loci_1.Loci.normalize(current.loci, 'chain');
+                            this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci }, false);
+                        }
                     }
                 }
                 if (loci_1.Loci.isEmpty(current.loci)) {
                     this.ctx.behaviors.labels.highlight.next({ labels: [] });
+                    (_b = this.ctx.canvas3d) === null || _b === void 0 ? void 0 : _b.mark({ loci: loci_1.EveryLoci }, marker_action_1.MarkerAction.RemoveHighlight);
                 }
                 else {
                     const labels = [];
                     if (structure_1.StructureElement.Loci.is(current.loci)) {
                         const cell = this.ctx.helpers.substructureParent.get(current.loci.structure);
-                        labels.push(((_b = cell === null || cell === void 0 ? void 0 : cell.obj) === null || _b === void 0 ? void 0 : _b.label) || 'Unknown');
+                        const d = (0, state_1.getCellDescription)(cell);
+                        labels.push(d);
+                    }
+                    else {
+                        const loci = loci_1.Loci.normalize(current.loci, this.ctx.managers.interactivity.props.granularity);
+                        if (loci.kind === 'group-loci') {
+                            if ('shape' in current.loci && current.loci.shape.geometry.kind === 'text') {
+                                const qname = (_c = current.repr) === null || _c === void 0 ? void 0 : _c.props.customText;
+                                // highlight protein with same name
+                                const entities = (0, state_1.getEveryEntity)(this.ctx, qname);
+                                for (const r of entities) {
+                                    const repr = (_d = r.obj) === null || _d === void 0 ? void 0 : _d.data.repr;
+                                    if (repr) {
+                                        (_e = this.ctx.canvas3d) === null || _e === void 0 ? void 0 : _e.mark({ repr, loci: loci_1.EveryLoci }, marker_action_1.MarkerAction.Highlight);
+                                    }
+                                }
+                            }
+                            labels.push(loci.shape.getLabel(0, 0));
+                        }
                     }
                     this.ctx.behaviors.labels.highlight.next({ labels });
                 }

package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/model.js

@@ -138,13 +138,11 @@ const CellpackStructure = objects_1.PluginStateTransform.BuiltIn({
             const idx = entities.getEntityIndex(params.entityId);
             const unitsByEntity = getUnitsByEntity(parent);
             const units = unitsByEntity.get(idx) || [];
-            // if (!unitsByEntity.get(idx)) {
-            //     console.log(entities.data.pdbx_description.value(idx));
-            // }
             const structure = structure_1.Structure.create(units);
-            const description = entities.data.pdbx_description.value(idx)[0] || 'model';
-            const label = description.split('.').at(-1) || a.label;
-            return new objects_1.PluginStateObject.Molecule.Structure(structure, { label, description: `${a.description}` });
+            const description_label = entities.data.pdbx_description.value(idx)[0] || 'model';
+            const label = description_label.split('.').at(-1) || a.label;
+            const description = entities.data.pdbx_parent_entity_id.value(idx) || label;
+            return new objects_1.PluginStateObject.Molecule.Structure(structure, { label, description: description }); // `${a.description}`
         });
     },
     dispose({ b }) {

package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/preset.js

@@ -6,7 +6,7 @@
  * @author Ludovic Autin <ludovic.autin@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createCellpackHierarchy = void 0;
+exports.createCellpackHierarchy = createCellpackHierarchy;
 const representation_1 = require("../../../../mol-plugin-state/transforms/representation");
 const spacefill_1 = require("../../../../mol-repr/structure/representation/spacefill");
 const names_1 = require("../../../../mol-util/color/names");
@@ -86,11 +86,11 @@ async function createCellpackHierarchy(plugin, trajectory) {
         .commit();
     const compRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:comp:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `comp:`, label: 'compartment', color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:comp:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged('group:comp:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `comp:`, label: 'compartment', color: { type: 'custom', illustrative: false, value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:comp:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
     const funcRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:func:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `func:`, label: 'function', color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:func:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged('group:func:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `func:`, label: 'function', color: { type: 'custom', illustrative: false, value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:func:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
     if (entities._rowCount > 1) {
         for (let i = 0; i < entities._rowCount; i++) {
@@ -140,7 +140,7 @@ async function createCellpackHierarchy(plugin, trajectory) {
                     parent.cell.state.isCollapsed = false;
                     const group = await state.build()
                         .to(parent)
-                        .applyOrUpdateTagged(`group:comp:${n}`, state_1.MesoscaleGroup, { ...groupParams, root: parent === compRoot, index: colorIdx, tag: `comp:${n}`, label, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `comp:${p}`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                        .applyOrUpdateTagged(`group:comp:${n}`, state_1.MesoscaleGroup, { ...groupParams, root: parent === compRoot, index: colorIdx, tag: `comp:${n}`, label, color: { type: 'generate', illustrative: false, value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `comp:${p}`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
                         .commit({ revertOnError: true });
                     compGroups.set(n, group);
                 }
@@ -151,7 +151,7 @@ async function createCellpackHierarchy(plugin, trajectory) {
                 const color = colorIdx !== undefined ? baseFuncColors[colorIdx] : names_1.ColorNames.white;
                 const group = await state.build()
                     .to(funcRoot)
-                    .applyOrUpdateTagged(`group:func:${f}`, state_1.MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `func:${f}`, label: f, color: { type: 'custom', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'func:', state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                    .applyOrUpdateTagged(`group:func:${f}`, state_1.MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `func:${f}`, label: f, color: { type: 'custom', illustrative: false, value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'func:', state: { isCollapsed: true, isHidden: groupParams.hidden } })
                     .commit({ revertOnError: true });
                 funcGroups.set(f, group);
             }
@@ -176,6 +176,9 @@ async function createCellpackHierarchy(plugin, trajectory) {
                         .apply(representation_1.StructureRepresentation3D, getSpacefillParams(color, sizeFactor, graphicsMode), { tags: [`comp:${n}`, `func:${f}`] });
                 }
                 await build.commit();
+                const values = { type: 'group-generate', value: names_1.ColorNames.white, lightness: 0, alpha: 1 };
+                const options = { ignoreLight: true, materialStyle: { metalness: 0, roughness: 1.0, bumpiness: 0 }, celShaded: true, };
+                await (0, state_1.updateColors)(plugin, values, options);
             }
             catch (e) {
                 console.error(e);
@@ -199,4 +202,3 @@ async function createCellpackHierarchy(plugin, trajectory) {
             .commit();
     }
 }
-exports.createCellpackHierarchy = createCellpackHierarchy;

package/lib/commonjs/apps/mesoscale-explorer/data/generic/model.d.ts

@@ -13,5 +13,6 @@ type StructureFromGeneric = typeof StructureFromGeneric;
 declare const StructureFromGeneric: StateTransformer<SO.Molecule.Model, SO.Molecule.Structure, PD.Normalize<{
     instances: GenericInstances<Asset>;
     label: string | undefined;
+    description: string | undefined;
     cellSize: number;
 }>>;

package/lib/commonjs/apps/mesoscale-explorer/data/generic/model.js

@@ -65,6 +65,7 @@ const StructureFromGeneric = objects_1.PluginStateTransform.BuiltIn({
     params: {
         instances: param_definition_1.ParamDefinition.Value(EmptyInstances),
         label: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Text('')),
+        description: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Text('')),
         cellSize: param_definition_1.ParamDefinition.Numeric(500, { min: 0, max: 10000, step: 100 }),
     }
 })({
@@ -100,7 +101,7 @@ const StructureFromGeneric = objects_1.PluginStateTransform.BuiltIn({
                 }
                 structure = assembler.getStructure();
             }
-            const props = { label, description: structure_1.Structure.elementDescription(structure) };
+            const props = { label, description: params.description || structure_1.Structure.elementDescription(structure) };
             return new objects_1.PluginStateObject.Molecule.Structure(structure, props);
         });
     },

package/lib/commonjs/apps/mesoscale-explorer/data/generic/preset.js

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getTransforms = exports.createGenericHierarchy = void 0;
+exports.createGenericHierarchy = createGenericHierarchy;
+exports.getTransforms = getTransforms;
 const mat4_1 = require("../../../../mol-math/linear-algebra/3d/mat4");
 const spacefill_1 = require("../../../../mol-repr/structure/representation/spacefill");
 const utf8_1 = require("../../../../mol-io/common/utf8");
@@ -118,7 +119,7 @@ async function createGenericHierarchy(plugin, file) {
     async function addGroup(g, cell, parent) {
         const group = await state.build()
             .to(cell)
-            .apply(state_1.MesoscaleGroup, { ...groupParams, index: undefined, tag: `${g.root}:${g.id}`, label: g.label || g.id, color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: [`group:${g.root}:${g.id}`, g.root === parent ? `${g.root}:` : `${g.root}:${parent}`], state: { isCollapsed: true, isHidden: groupParams.hidden } })
+            .apply(state_1.MesoscaleGroup, { ...groupParams, index: undefined, tag: `${g.root}:${g.id}`, label: g.label || g.id, description: g.description, color: { type: 'custom', illustrative: false, value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: [`group:${g.root}:${g.id}`, g.root === parent ? `${g.root}:` : `${g.root}:${parent}`], state: { isCollapsed: true, isHidden: groupParams.hidden } })
             .commit();
         if (g.children) {
             for (const c of g.children) {
@@ -129,7 +130,7 @@ async function createGenericHierarchy(plugin, file) {
     for (const r of manifest.roots) {
         const root = await state.build()
             .toRoot()
-            .apply(state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `${r.id}:`, label: r.label || r.id, color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `group:${r.id}:`, state: { isCollapsed: false, isHidden: groupParams.hidden } })
+            .apply(state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `${r.id}:`, label: r.label || r.id, description: r.description, color: { type: 'custom', illustrative: false, value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `group:${r.id}:`, state: { isCollapsed: false, isHidden: groupParams.hidden } })
             .commit();
         if (r.children) {
             for (const c of r.children) {
@@ -179,10 +180,11 @@ async function createGenericHierarchy(plugin, file) {
                 const t = isBinary ? d : (0, utf8_1.utf8Read)(d, 0, d.length);
                 const file = assets_1.Asset.File(new File([t], ent.file));
                 const color = names_1.ColorNames.skyblue;
-                const label = ent.label || ent.file.split('.')[0];
                 const sizeFactor = ent.sizeFactor || 1;
                 const tags = ent.groups.map(({ id, root }) => `${root}:${id}`);
                 const instances = ent.instances && getAssetInstances(ent.instances);
+                const description = ent.description;
+                const label = ent.label || ent.file.split('.')[0];
                 build = build
                     .toRoot()
                     .apply(data_1.ReadFile, { file, label, isBinary });
@@ -222,7 +224,7 @@ async function createGenericHierarchy(plugin, file) {
                     }
                     build = build
                         .apply(model_1.ModelFromTrajectory, { modelIndex: 0 })
-                        .apply(model_2.StructureFromGeneric, { instances, label })
+                        .apply(model_2.StructureFromGeneric, { instances, label, description })
                         .apply(representation_1.StructureRepresentation3D, getSpacefillParams(color, sizeFactor, graphicsMode, clipVariant), { tags });
                 }
                 else if (['ply'].includes(info.ext)) {
@@ -240,9 +242,9 @@ async function createGenericHierarchy(plugin, file) {
                 }
             }
             await build.commit();
-            const rootId = `${manifest.roots[0].id}:`;
             const values = { type: 'group-generate', value: names_1.ColorNames.white, lightness: 0, alpha: 1 };
-            await (0, state_1.updateColors)(plugin, values, rootId, '');
+            const options = { ignoreLight: true, materialStyle: { metalness: 0, roughness: 1.0, bumpiness: 0 }, celShaded: true, };
+            await (0, state_1.updateColors)(plugin, values, options);
         }
         catch (e) {
             console.error(e);
@@ -254,7 +256,6 @@ async function createGenericHierarchy(plugin, file) {
     }).run();
     asset.dispose();
 }
-exports.createGenericHierarchy = createGenericHierarchy;
 //
 const p = (0, linear_algebra_1.Vec3)();
 const q = (0, linear_algebra_1.Quat)();
@@ -319,7 +320,6 @@ async function getTransforms(plugin, instances) {
     }
     return transforms;
 }
-exports.getTransforms = getTransforms;
 function martiniToGeneric(martini) {
     const functionRoot = {
         id: 'function',

package/lib/commonjs/apps/mesoscale-explorer/data/mmcif/model.js

@@ -165,8 +165,10 @@ const MmcifStructure = objects_1.PluginStateTransform.BuiltIn({
             else {
                 structure = structure_1.Structure.create(units);
             }
+            // could also use _struct_ref.pdbx_db_accession to point to uniprot with _struct_ref.db_name == UNP
             const label = entities.data.pdbx_description.value(idx).join(', ') || 'model';
-            return new objects_1.PluginStateObject.Molecule.Structure(structure, { label, description: `${a.description}` });
+            const description = `*Entity id* ${entities.data.id.value(idx)} *src_method* ${entities.data.src_method.value(idx)} *type* ${entities.data.type.value(idx)}`;
+            return new objects_1.PluginStateObject.Molecule.Structure(structure, { label, description: description });
         });
     },
     update({ newParams, oldParams }) {

package/lib/commonjs/apps/mesoscale-explorer/data/mmcif/preset.js

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createMmcifHierarchy = void 0;
+exports.createMmcifHierarchy = createMmcifHierarchy;
 const mmcif_1 = require("../../../../mol-model-formats/structure/mmcif");
 const representation_1 = require("../../../../mol-plugin-state/transforms/representation");
 const spacefill_1 = require("../../../../mol-repr/structure/representation/spacefill");
@@ -103,7 +103,7 @@ async function createMmcifHierarchy(plugin, trajectory) {
     const clipVariant = willBeMerged ? 'pixel' : 'instance';
     const entRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:ent:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged('group:ent:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'custom', illustrative: false, value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
     const getEntityType = (i) => {
         if (entities.type.value(i) === 'water')
@@ -133,7 +133,7 @@ async function createMmcifHierarchy(plugin, trajectory) {
             const color = colorIdx !== undefined ? baseEntColors[colorIdx] : names_1.ColorNames.white;
             const group = await state.build()
                 .to(entRoot)
-                .applyOrUpdateTagged(`group:ent:${t}`, state_1.MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `ent:${t}`, label: t, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                .applyOrUpdateTagged(`group:ent:${t}`, state_1.MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `ent:${t}`, label: t, color: { type: 'generate', illustrative: false, value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
                 .commit({ revertOnError: true });
             entGroups.set(t, group);
         }
@@ -154,6 +154,9 @@ async function createMmcifHierarchy(plugin, trajectory) {
                     .apply(representation_1.StructureRepresentation3D, getSpacefillParams(color, scaleFactor, graphicsMode, clipVariant), { tags: [`ent:${t}`] });
             }
             await build.commit();
+            const values = { type: 'group-generate', value: names_1.ColorNames.white, lightness: 0, alpha: 1 };
+            const options = { ignoreLight: true, materialStyle: { metalness: 0, roughness: 1.0, bumpiness: 0 }, celShaded: true, };
+            await (0, state_1.updateColors)(plugin, values, options);
         }
         catch (e) {
             console.error(e);
@@ -164,4 +167,3 @@ async function createMmcifHierarchy(plugin, trajectory) {
         }
     }).run();
 }
-exports.createMmcifHierarchy = createMmcifHierarchy;