0.7.0-dev.18

- see e.g. 3NIR

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.7",
+  "version": "0.7.0-dev.18",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.7",
+  "version": "0.7.0-dev.18",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -34,12 +34,12 @@
     "model-server-watch": "nodemon --watch lib lib/servers/servers/model/server.js",
     "volume-server-test": "node lib/servers/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
     "plugin-state": "node lib/servers/servers/plugin-state/index.js",
-    "preversion": "npm run test",
-    "postversion": "git push && git push --tags",
-    "prepublishOnly": "npm run test && npm run build"
+    "preversion": "npm run test && npm run build",
+    "postversion": "git push && git push --tags"
   },
   "files": [
-    "lib/"
+    "lib/",
+    "build/viewer/"
   ],
   "bin": {
     "cif2bcif": "lib/apps/cif2bcif/index.js",

src/apps/structure-info/model.ts

@@ -117,7 +117,7 @@ export function printSequence(model: Model) {
     for (const key of Object.keys(byEntityKey)) {
         const { sequence, entityId } = byEntityKey[+key];
         const { seqId, compId } = sequence;
-        console.log(`${entityId} (${sequence.kind} ${seqId.value(0)} (offset ${sequence.offset}), ${seqId.value(seqId.rowCount - 1)}) (${compId.value(0)}, ${compId.value(compId.rowCount - 1)})`);
+        console.log(`${entityId} (${sequence.kind} ${seqId.value(0)}, ${seqId.value(seqId.rowCount - 1)}) (${compId.value(0)}, ${compId.value(compId.rowCount - 1)})`);
         console.log(`${Sequence.getSequenceString(sequence)}`);
     }
     console.log();

src/apps/structure-info/volume.ts

@@ -8,38 +8,36 @@ import * as fs from 'fs';
 import * as argparse from 'argparse';
 import * as util from 'util';
 
-import { VolumeData, VolumeIsoValue } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
 import { downloadCif } from './helpers';
 import { CIF } from '../../mol-io/reader/cif';
-import { DensityServer_Data_Database } from '../../mol-io/reader/cif/schema/density-server';
 import { Table } from '../../mol-data/db';
 import { StringBuilder } from '../../mol-util';
 import { Task } from '../../mol-task';
 import { createVolumeIsosurfaceMesh } from '../../mol-repr/volume/isosurface';
 import { Theme } from '../../mol-theme/theme';
-import { volumeFromDensityServerData } from '../../mol-model-formats/volume/density-server';
+import { volumeFromDensityServerData, DscifFormat } from '../../mol-model-formats/volume/density-server';
 
 require('util.promisify').shim();
 const writeFileAsync = util.promisify(fs.writeFile);
 
-type Volume = { source: DensityServer_Data_Database, volume: VolumeData }
-
 async function getVolume(url: string): Promise<Volume> {
     const cif = await downloadCif(url, true);
     const data = CIF.schema.densityServer(cif.blocks[1]);
-    return { source: data, volume: await volumeFromDensityServerData(data).run() };
+    return await volumeFromDensityServerData(data).run();
 }
 
-function print(data: Volume) {
-    const { volume_data_3d_info } = data.source;
+function print(volume: Volume) {
+    if (!DscifFormat.is(volume.sourceData)) return;
+    const { volume_data_3d_info } = volume.sourceData.data;
     const row = Table.getRow(volume_data_3d_info, 0);
     console.log(row);
-    if (data.volume.transform) console.log(data.volume.transform);
-    console.log(data.volume.dataStats);
+    console.log(volume.grid.transform);
+    console.log(volume.grid.stats);
 }
 
-async function doMesh(data: Volume, filename: string) {
-    const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, data.volume, Theme.createEmpty(), { isoValue: VolumeIsoValue.absolute(1.5) } )).run();
+async function doMesh(volume: Volume, filename: string) {
+    const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, volume, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) } )).run();
     console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });
 
     // Export the mesh in OBJ format.

src/apps/viewer/embedded.html

@@ -0,0 +1,63 @@
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Embedded Mol* Viewer</title>
+        <style>
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            var viewer = new molstar.Viewer('app', {
+                layoutIsExpanded: false,
+                layoutShowControls: false,
+                layoutShowRemoteState: false,
+                layoutShowSequence: true,
+                layoutShowLog: false,
+                layoutShowLeftPanel: true,
+
+                viewportShowExpand: true,
+                viewportShowSelectionMode: false,
+                viewportShowAnimation: false,
+
+                pdbProvider: 'rcsb',
+                emdbProvider: 'rcsb',
+            });
+            viewer.loadPdb('7bv2');
+            viewer.loadEmdb('EMD-30210');
+
+            // TODO add Volume.customProperty and load suggested isoValue via custom property
+            var sub = viewer.plugin.managers.volume.hierarchy.behaviors.selection.subscribe(function (value) {
+                if (value.volume?.representations[0]) {
+                    var ref = value.volume.representations[0].cell;
+                    var tree = viewer.plugin.state.data.build().to(ref).update({
+                        type: {
+                            name: 'isosurface',
+                            params: {
+                                isoValue: {
+                                    kind: 'relative',
+                                    relativeValue: 6
+                                }
+                            }
+                        },
+                        colorTheme: ref.transform.params?.colorTheme
+                    });
+                    viewer.plugin.runTask(viewer.plugin.state.data.updateTree(tree));
+                    if (typeof sub !== 'undefined') sub.unsubscribe();
+                }
+            });
+        </script>
+    </body>
+</html>

src/apps/viewer/index.html

@@ -34,10 +34,43 @@
                 height: 600px;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="app.css" />
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
     </head>
     <body>
         <div id="app"></div>
-        <script type="text/javascript" src="./index.js"></script>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            function getParam(name, regex) {
+                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
+                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+            }
+
+            var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
+            var viewer = new molstar.Viewer('app', {
+                layoutShowControls: !hideControls,
+                viewportShowExpand: false,
+            });
+
+            var snapshotId = getParam('snapshot-id', '[^&]+').trim();
+            if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
+
+            var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
+            var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim();
+            if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
+
+            var structureUrl = getParam('structure-url', '[^&]+').trim();
+            var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
+            var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
+            if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
+
+            var pdb = getParam('pdb', '[^&]+').trim();
+            if (pdb) viewer.loadPdb(pdb);
+
+            var pdbDev = getParam('pdb-dev', '[^&]+').trim();
+            if (pdbDev) viewer.loadPdbDev(pdbDev);
+
+            var emdb = getParam('emdb', '[^&]+').trim();
+            if (emdb) viewer.loadEmdb(emdb);
+        </script>
     </body>
 </html>

src/apps/viewer/index.ts

@@ -8,84 +8,110 @@
 import '../../mol-util/polyfill';
 import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
 import './index.html';
+import './embedded.html';
 import './favicon.ico';
 import { PluginContext } from '../../mol-plugin/context';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginSpec } from '../../mol-plugin/spec';
-import { DownloadStructure } from '../../mol-plugin-state/actions/structure';
+import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
 import { PluginConfig } from '../../mol-plugin/config';
 import { CellPack } from '../../extensions/cellpack';
 import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { Asset } from '../../mol-util/assets';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+import { PluginState } from '../../mol-plugin/state';
+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
 require('mol-plugin-ui/skin/light.scss');
 
-function getParam(name: string, regex: string): string {
-    let r = new RegExp(`${name}=(${regex})[&]?`, 'i');
-    return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
-}
+const Extensions = {
+    'cellpack': PluginSpec.Behavior(CellPack),
+    'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
+    'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
+    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport)
+};
 
-const hideControls = getParam('hide-controls', `[^&]+`) === '1';
+const DefaultViewerOptions = {
+    extensions: ObjectKeys(Extensions),
+    layoutIsExpanded: true,
+    layoutShowControls: true,
+    layoutShowRemoteState: true,
+    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
+    layoutShowSequence: true,
+    layoutShowLog: true,
+    layoutShowLeftPanel: true,
 
-function init() {
-    const spec: PluginSpec = {
-        actions: [...DefaultPluginSpec.actions],
-        behaviors: [
-            ...DefaultPluginSpec.behaviors,
-            PluginSpec.Behavior(CellPack),
-            PluginSpec.Behavior(PDBeStructureQualityReport),
-            PluginSpec.Behavior(RCSBAssemblySymmetry),
-            PluginSpec.Behavior(RCSBValidationReport),
-        ],
-        animations: [...DefaultPluginSpec.animations || []],
-        customParamEditors: DefaultPluginSpec.customParamEditors,
-        layout: {
-            initial: {
-                isExpanded: true,
-                showControls: !hideControls
+    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
+    viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
+    viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
+    pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
+    volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
+    pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
+    emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
+};
+type ViewerOptions = typeof DefaultViewerOptions;
+
+export class Viewer {
+    plugin: PluginContext
+
+    constructor(elementId: string, options: Partial<ViewerOptions> = {}) {
+        const o = { ...DefaultViewerOptions, ...options };
+
+        const spec: PluginSpec = {
+            actions: [...DefaultPluginSpec.actions],
+            behaviors: [
+                ...DefaultPluginSpec.behaviors,
+                ...o.extensions.map(e => Extensions[e]),
+            ],
+            animations: [...DefaultPluginSpec.animations || []],
+            customParamEditors: DefaultPluginSpec.customParamEditors,
+            layout: {
+                initial: {
+                    isExpanded: o.layoutIsExpanded,
+                    showControls: o.layoutShowControls,
+                    controlsDisplay: o.layoutControlsDisplay,
+                },
+                controls: {
+                    ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls,
+                    top: o.layoutShowSequence ? undefined : 'none',
+                    bottom: o.layoutShowLog ? undefined : 'none',
+                    left: o.layoutShowLeftPanel ? undefined : 'none',
+                }
             },
-            controls: {
-                ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls
-            }
-        },
-        config: DefaultPluginSpec.config
-    };
-    spec.config?.set(PluginConfig.Viewport.ShowExpand, false);
-    const plugin = createPlugin(document.getElementById('app')!, spec);
-    trySetSnapshot(plugin);
-    tryLoadFromUrl(plugin);
-}
+            components: {
+                ...DefaultPluginSpec.components,
+                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
+            },
+            config: DefaultPluginSpec.config
+        };
 
-async function trySetSnapshot(ctx: PluginContext) {
-    try {
-        const snapshotUrl = getParam('snapshot-url', `[^&]+`);
-        const snapshotId = getParam('snapshot-id', `[^&]+`);
-        if (!snapshotUrl && !snapshotId) return;
-        // TODO parametrize the server
-        const url = snapshotId
-            ? `https://webchem.ncbr.muni.cz/molstar-state/get/${snapshotId}`
-            : snapshotUrl;
-        await PluginCommands.State.Snapshots.Fetch(ctx, { url });
-    } catch (e) {
-        ctx.log.error('Failed to load snapshot.');
-        console.warn('Failed to load snapshot', e);
+        spec.config?.set(PluginConfig.Viewport.ShowExpand, o.viewportShowExpand);
+        spec.config?.set(PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode);
+        spec.config?.set(PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation);
+        spec.config?.set(PluginConfig.State.DefaultServer, o.pluginStateServer);
+        spec.config?.set(PluginConfig.State.CurrentServer, o.pluginStateServer);
+        spec.config?.set(PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer);
+        spec.config?.set(PluginConfig.Download.DefaultPdbProvider, o.pdbProvider);
+        spec.config?.set(PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider);
+
+        const element = document.getElementById(elementId);
+        if (!element) throw new Error(`Could not get element with id '${elementId}'`);
+        this.plugin = createPlugin(element, spec);
     }
-}
 
-async function tryLoadFromUrl(ctx: PluginContext) {
-    const url = getParam('loadFromURL', '[^&]+').trim();
-    try {
-        if (!url) return;
+    async setRemoteSnapshot(id: string) {
+        const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
+        await PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
+    }
 
-        let format = 'cif', isBinary = false;
-        switch (getParam('loadFromURLFormat', '[a-z]+').toLocaleLowerCase().trim()) {
-            case 'pdb': format = 'pdb'; break;
-            case 'mmbcif': isBinary = true; break;
-        }
+    async loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
+        await PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
+    }
 
-        const params = DownloadStructure.createDefaultParams(void 0 as any, ctx);
-
-        return ctx.runTask(ctx.state.data.applyAction(DownloadStructure, {
+    async loadStructureFromUrl(url: string, format = 'cif', isBinary = false) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
             source: {
                 name: 'url',
                 params: {
@@ -96,10 +122,54 @@ async function tryLoadFromUrl(ctx: PluginContext) {
                 }
             }
         }));
-    } catch (e) {
-        ctx.log.error(`Failed to load from URL (${url})`);
-        console.warn(`Failed to load from URL (${url})`, e);
     }
-}
 
-init();
+    async loadPdb(pdb: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb' as const,
+                params: {
+                    provider: {
+                        id: pdb,
+                        server: {
+                            name: provider,
+                            params: PdbDownloadProvider[provider].defaultValue as any
+                        }
+                    },
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    async loadPdbDev(pdbDev: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb-dev' as const,
+                params: {
+                    id: pdbDev,
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    async loadEmdb(emdb: string) {
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
+            source: {
+                name: 'pdb-emd-ds' as const,
+                params: {
+                    provider: {
+                        id: emdb,
+                        server: provider,
+                    },
+                    detail: 3,
+                }
+            }
+        }));
+    }
+}

src/examples/basic-wrapper/index.html

@@ -41,7 +41,7 @@
                 display: block;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="app.css" />
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
         <script type="text/javascript" src="./index.js"></script>
     </head>
     <body>
@@ -55,13 +55,13 @@
             </select>
         </div>
         <div id="app"></div>
-        <script>      
+        <script>
             function $(id) { return document.getElementById(id); }
-        
+
             var pdbId = '1grm', assemblyId= '1';
             var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
             var format = 'mmcif';
-            
+
             $('url').value = url;
             $('url').onchange = function (e) { url = e.target.value; }
             $('assemblyId').value = assemblyId;
@@ -86,7 +86,7 @@
 
             addHeader('Camera');
             addControl('Toggle Spin', () => BasicMolStarWrapper.toggleSpin());
-            
+
             addSeparator();
 
             addHeader('Animation');
@@ -115,7 +115,7 @@
             addControl('Static Superposition', () => BasicMolStarWrapper.tests.staticSuperposition());
             addControl('Dynamic Superposition', () => BasicMolStarWrapper.tests.dynamicSuperposition());
             addControl('Validation Tooltip', () => BasicMolStarWrapper.tests.toggleValidationTooltip());
-            
+
             addControl('Show Toasts', () => BasicMolStarWrapper.tests.showToasts());
             addControl('Hide Toasts', () => BasicMolStarWrapper.tests.hideToasts());
 

src/examples/lighting/index.html

@@ -38,16 +38,16 @@
                 display: block;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="app.css" />
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
         <script type="text/javascript" src="./index.js"></script>
     </head>
     <body>
         <div id='controls'></div>
         <div id="app"></div>
-        <script>      
+        <script>
             LightingDemo.init('app')
             LightingDemo.load({ url: 'https://files.rcsb.org/download/1M07.cif', assemblyId: '1' })
-            
+
             addHeader('Example PDB IDs');
             addControl('1M07', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/1M07.cif', assemblyId: '1' }));
             addControl('6HY0', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/6HY0.cif', assemblyId: '1' }));

src/examples/proteopedia-wrapper/index.html

@@ -48,7 +48,7 @@
                 width: 300px;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="app.css" />
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
         <script type="text/javascript" src="./index.js"></script>
     </head>
     <body>
@@ -65,7 +65,7 @@
         <div id="app"></div>
         <div id="volume-streaming-wrapper"></div>
         <script>
-            // it might be a good idea to define these colors in a separate script file 
+            // it might be a good idea to define these colors in a separate script file
             var CustomColors = [0x00ff00, 0x0000ff];
 
             // create an instance of the plugin
@@ -74,11 +74,11 @@
             console.log('Wrapper version', MolStarProteopediaWrapper.VERSION_MAJOR, MolStarProteopediaWrapper.VERSION_MINOR);
 
             function $(id) { return document.getElementById(id); }
-        
+
             var pdbId = '1cbs', assemblyId= 'preferred', isBinary = true;
             var url = 'https://www.ebi.ac.uk/pdbe/entry-files/download/' + pdbId + '.bcif'
             var format = 'cif';
-            
+
             $('url').value = url;
             $('url').onchange = function (e) { url = e.target.value; }
             $('assemblyId').value = assemblyId;
@@ -92,6 +92,12 @@
             // var format = 'pdb';
             // var assemblyId = 'deposited';
 
+            function loadAndSnapshot(params) {
+                PluginWrapper.load(params).then(() => {
+                    setTimeout(() => snapshot = PluginWrapper.plugin.state.getSnapshot({ canvas3d: false /* do not save spinning state */ }), 500);
+                });
+            }
+
             var representationStyle = {
                 // sequence: { coloring: 'proteopedia-custom' }, // or just { }
                 hetGroups: { kind: 'ball-and-stick' }, // or 'spacefill
@@ -103,7 +109,7 @@
                 customColorList: CustomColors
             });
             PluginWrapper.setBackground(0xffffff);
-            PluginWrapper.load({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
+            loadAndSnapshot({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
             PluginWrapper.toggleSpin();
 
             PluginWrapper.events.modelInfo.subscribe(function (info) {
@@ -111,8 +117,8 @@
                 listHetGroups(info);
             });
 
-            addControl('Load Asym Unit', () => PluginWrapper.load({ url: url, format: format, isBinary }));
-            addControl('Load Assembly', () => PluginWrapper.load({ url: url, format: format, isBinary, assemblyId: assemblyId }));
+            addControl('Load Asym Unit', () => loadAndSnapshot({ url: url, format: format, isBinary }));
+            addControl('Load Assembly', () => loadAndSnapshot({ url: url, format: format, isBinary, assemblyId: assemblyId }));
 
             addSeparator();
 
@@ -138,7 +144,7 @@
             // Same as "wheel icon" and Viewport options
             // addControl('Clip', () => PluginWrapper.viewport.setSettings({ clip: [33, 66] }));
             // addControl('Reset Clip', () => PluginWrapper.viewport.setSettings({ clip: [1, 100] }));
-            
+
             addSeparator();
 
             addHeader('Animation');
@@ -171,7 +177,7 @@
             addControl('Init', () => PluginWrapper.experimentalData.init($('volume-streaming-wrapper')));
             addControl('Remove', () => PluginWrapper.experimentalData.remove());
 
-            addSeparator(); 
+            addSeparator();
             addHeader('State');
 
             var snapshot;
@@ -185,10 +191,10 @@
                 PluginWrapper.snapshot.set(snapshot);
             });
             addControl('Download State', () => {
-                snapshot = PluginWrapper.snapshot.download('molj');
+                PluginWrapper.snapshot.download('molj');
             });
             addControl('Download Session', () => {
-                snapshot = PluginWrapper.snapshot.download('molx');
+                PluginWrapper.snapshot.download('molx');
             });
 
             ////////////////////////////////////////////////////////

src/examples/proteopedia-wrapper/index.ts

@@ -5,35 +5,34 @@
  */
 
 import * as ReactDOM from 'react-dom';
+import { Canvas3DProps, DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
 import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import './index.html';
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { Color } from '../../mol-util/color';
-import { PluginStateObject as PSO, PluginStateObject } from '../../mol-plugin-state/objects';
 import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
-import { StateBuilder, StateObject, StateSelection } from '../../mol-state';
-import { EvolutionaryConservation } from './annotation';
-import { LoadParams, SupportedFormats, RepresentationStyle, ModelInfo, StateElements } from './helpers';
-import { RxEventHelper } from '../../mol-util/rx-event-helper';
-import { volumeStreamingControls } from './ui/controls';
-import { PluginState } from '../../mol-plugin/state';
-import { Scheduler } from '../../mol-task';
-import { createProteopediaCustomTheme } from './coloring';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import { ColorNames } from '../../mol-util/color/names';
-import { InitVolumeStreaming, CreateVolumeStreamingInfo } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
-import { DefaultCanvas3DParams, Canvas3DProps } from '../../mol-canvas3d/canvas3d';
 import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
-import { download } from '../../mol-util/download';
-import { getFormattedTime } from '../../mol-util/date';
+import { PluginStateObject, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { CreateVolumeStreamingInfo, InitVolumeStreaming } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
+import { PluginState } from '../../mol-plugin/state';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import { StateBuilder, StateObject, StateSelection } from '../../mol-state';
 import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
+import { ColorNames } from '../../mol-util/color/names';
+import { getFormattedTime } from '../../mol-util/date';
+import { download } from '../../mol-util/download';
+import { RxEventHelper } from '../../mol-util/rx-event-helper';
+import { EvolutionaryConservation } from './annotation';
+import { createProteopediaCustomTheme } from './coloring';
+import { LoadParams, ModelInfo, RepresentationStyle, StateElements, SupportedFormats } from './helpers';
+import './index.html';
+import { volumeStreamingControls } from './ui/controls';
 require('../../mol-plugin-ui/skin/light.scss');
 
 class MolStarProteopediaWrapper {
     static VERSION_MAJOR = 5;
-    static VERSION_MINOR = 4;
+    static VERSION_MINOR = 5;
 
     private _ev = RxEventHelper.create();
 
@@ -233,7 +232,6 @@ class MolStarProteopediaWrapper {
         await this.updateStyle(representationStyle);
 
         this.loadedParams = { url, format, assemblyId };
-        Scheduler.setImmediate(() => PluginCommands.Camera.Reset(this.plugin, { }));
     }
 
     async updateStyle(style?: RepresentationStyle, partial?: boolean) {
@@ -407,7 +405,7 @@ class MolStarProteopediaWrapper {
             try {
                 const data = await this.plugin.runTask(this.plugin.fetch({ url, type: 'binary' }));
                 this.loadedParams = { ...this.emptyLoadedParams };
-                await this.plugin.managers.snapshot.open(new File([data], `state.${type}`));
+                return await this.plugin.managers.snapshot.open(new File([data], `state.${type}`));
             } catch (e) {
                 console.log(e);
             }

src/extensions/cellpack/model.ts

@@ -27,61 +27,75 @@ import { Column } from '../../mol-data/db';
 import { createModels } from '../../mol-model-formats/structure/basic/parser';
 import { CellpackPackingPreset, CellpackMembranePreset } from './preset';
 import { Asset } from '../../mol-util/assets';
+import { readFromFile } from '../../mol-util/data-source';
+import { objectForEach } from '../../mol-util/object';
 
 function getCellPackModelUrl(fileName: string, baseUrl: string) {
     return `${baseUrl}/results/${fileName}`;
 }
 
-async function getModel(plugin: PluginContext, id: string, ingredient: Ingredient, baseUrl: string, file?: Asset.File) {
+class TrajectoryCache {
+    private map = new Map<string, Model.Trajectory>();
+    set(id: string, trajectory: Model.Trajectory) { this.map.set(id, trajectory); }
+    get(id: string) { return this.map.get(id); }
+}
+
+async function getModel(plugin: PluginContext, id: string, ingredient: Ingredient, baseUrl: string, trajCache: TrajectoryCache, file?: Asset.File) {
     const assetManager = plugin.managers.asset;
-    const model_id = (ingredient.source.model) ? parseInt(ingredient.source.model) : 0;
+    const modelIndex = (ingredient.source.model) ? parseInt(ingredient.source.model) : 0;
     const surface = (ingredient.ingtype) ? (ingredient.ingtype === 'transmembrane') : false;
-    let model: Model;
+    let trajectory = trajCache.get(id);
     let assets: Asset.Wrapper[] = [];
-    if (file) {
-        if (file.name.endsWith('.cif')) {
-            const text = await plugin.runTask(assetManager.resolve(file, 'string'));
-            assets.push(text);
-            const cif = (await parseCif(plugin, text.data)).blocks[0];
-            model = (await plugin.runTask(trajectoryFromMmCIF(cif)))[model_id];
-        } else if (file.name.endsWith('.bcif')) {
-            const binary = await plugin.runTask(assetManager.resolve(file, 'binary'));
-            assets.push(binary);
-            const cif = (await parseCif(plugin, binary.data)).blocks[0];
-            model = (await plugin.runTask(trajectoryFromMmCIF(cif)))[model_id];
-        } else if (file.name.endsWith('.pdb')) {
-            const text = await plugin.runTask(assetManager.resolve(file, 'string'));
-            assets.push(text);
-            const pdb = await parsePDBfile(plugin, text.data, id);
-            model = (await plugin.runTask(trajectoryFromPDB(pdb)))[model_id];
-        } else {
-            throw new Error(`unsupported file type '${file.name}'`);
-        }
-    } else if (id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) {
-        if (surface){
-            const data = await getFromOPM(plugin, id, assetManager);
-            if (data.asset){
-                assets.push(data.asset);
-                model = (await plugin.runTask(trajectoryFromPDB(data.pdb)))[model_id];
+    if (!trajectory) {
+        if (file) {
+            if (file.name.endsWith('.cif')) {
+                const text = await plugin.runTask(assetManager.resolve(file, 'string'));
+                assets.push(text);
+                const cif = (await parseCif(plugin, text.data)).blocks[0];
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(cif));
+            } else if (file.name.endsWith('.bcif')) {
+                const binary = await plugin.runTask(assetManager.resolve(file, 'binary'));
+                assets.push(binary);
+                const cif = (await parseCif(plugin, binary.data)).blocks[0];
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(cif));
+            } else if (file.name.endsWith('.pdb')) {
+                const text = await plugin.runTask(assetManager.resolve(file, 'string'));
+                assets.push(text);
+                const pdb = await parsePDBfile(plugin, text.data, id);
+                trajectory = await plugin.runTask(trajectoryFromPDB(pdb));
+            } else {
+                throw new Error(`unsupported file type '${file.name}'`);
+            }
+        } else if (id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) {
+            if (surface){
+                try {
+                    const data = await getFromOPM(plugin, id, assetManager);
+                    assets.push(data.asset);
+                    trajectory = await plugin.runTask(trajectoryFromPDB(data.pdb));
+                } catch (e) {
+                    // fallback to getFromPdb
+                    // console.error(e);
+                    const { mmcif, asset } = await getFromPdb(plugin, id, assetManager);
+                    assets.push(asset);
+                    trajectory = await plugin.runTask(trajectoryFromMmCIF(mmcif));
+                }
             } else {
                 const { mmcif, asset } = await getFromPdb(plugin, id, assetManager);
                 assets.push(asset);
-                model = (await plugin.runTask(trajectoryFromMmCIF(mmcif)))[model_id];
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(mmcif));
             }
         } else {
-            const { mmcif, asset } = await getFromPdb(plugin, id, assetManager);
-            assets.push(asset);
-            model = (await plugin.runTask(trajectoryFromMmCIF(mmcif)))[model_id];
-        }
-    } else {
-        const data = await getFromCellPackDB(plugin, id, baseUrl, assetManager);
-        assets.push(data.asset);
-        if ('pdb' in data) {
-            model = (await plugin.runTask(trajectoryFromPDB(data.pdb)))[model_id];
-        } else {
-            model = (await plugin.runTask(trajectoryFromMmCIF(data.mmcif)))[model_id];
+            const data = await getFromCellPackDB(plugin, id, baseUrl, assetManager);
+            assets.push(data.asset);
+            if ('pdb' in data) {
+                trajectory = await plugin.runTask(trajectoryFromPDB(data.pdb));
+            } else {
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(data.mmcif));
+            }
         }
+        trajCache.set(id, trajectory);
     }
+    const model = trajectory[modelIndex];
     return { model, assets };
 }
 
@@ -133,7 +147,6 @@ function getTransform(trans: Vec3, rot: Quat) {
     return m;
 }
 
-
 function getResultTransforms(results: Ingredient['results'], legacy: boolean) {
     if (legacy) return results.map((r: Ingredient['results'][0]) => getTransformLegacy(r[0], r[1]));
     else return results.map((r: Ingredient['results'][0]) => getTransform(r[0], r[1]));
@@ -288,7 +301,7 @@ async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredi
     return getStructure(plugin, curveModel, ingredient.source);
 }
 
-async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles) {
+async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles, trajCache: TrajectoryCache) {
     const { name, source, results, nbCurve } = ingredient;
     if (source.pdb === 'None') return;
 
@@ -303,7 +316,7 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
     }
 
     // model id in case structure is NMR
-    const { model, assets } = await getModel(plugin, source.pdb || name, ingredient, baseUrl, file);
+    const { model, assets } = await getModel(plugin, source.pdb || name, ingredient, baseUrl, trajCache, file);
     if (!model) return;
 
     let structure: Structure;
@@ -354,10 +367,11 @@ export function createStructureFromCellPack(plugin: PluginContext, packing: Cell
     return Task.create('Create Packing Structure', async ctx => {
         const { ingredients, name } = packing;
         const assets: Asset.Wrapper[] = [];
+        const trajCache = new TrajectoryCache();
         const structures: Structure[] = [];
         for (const iName in ingredients) {
             if (ctx.shouldUpdate) await ctx.update(iName);
-            const ingredientStructure = await getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles);
+            const ingredientStructure = await getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles, trajCache);
             if (ingredientStructure) {
                 structures.push(ingredientStructure.structure);
                 assets.push(...ingredientStructure.assets);
@@ -444,6 +458,8 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
 }
 
 async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, state: State, params: LoadCellPackModelParams) {
+    const ingredientFiles = params.ingredients.files || [];
+
     let cellPackJson: StateBuilder.To<PSO.Format.Json, StateTransformer<PSO.Data.String, PSO.Format.Json>>;
     if (params.source.name === 'id') {
         const url = Asset.getUrlAsset(plugin.managers.asset, getCellPackModelUrl(params.source.params, params.baseUrl));
@@ -451,12 +467,25 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
             .apply(StateTransforms.Data.Download, { url, isBinary: false, label: params.source.params }, { state: { isGhost: true } });
     } else {
         const file = params.source.params;
-        if (file === null) {
+        if (!file?.file) {
             plugin.log.error('No file selected');
             return;
         }
+
+        let jsonFile: Asset.File;
+        if (file.name.toLowerCase().endsWith('.zip')) {
+            const data = await readFromFile(file.file, 'zip').runInContext(runtime);
+            jsonFile = Asset.File(new File([data['model.json']], 'model.json'));
+            objectForEach(data, (v, k) => {
+                if (k === 'model.json') return;
+                ingredientFiles.push(Asset.File(new File([v], k)));
+            });
+        } else {
+            jsonFile = file;
+        }
+
         cellPackJson = state.build().toRoot()
-            .apply(StateTransforms.Data.ReadFile, { file, isBinary: false, label: file.name }, { state: { isGhost: true } });
+            .apply(StateTransforms.Data.ReadFile, { file: jsonFile, isBinary: false, label: jsonFile.name }, { state: { isGhost: true } });
     }
 
     const cellPackBuilder = cellPackJson
@@ -469,7 +498,7 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
     await handleHivRna(plugin, packings, params.baseUrl);
 
     for (let i = 0, il = packings.length; i < il; ++i) {
-        const p = { packing: i, baseUrl: params.baseUrl, ingredientFiles: params.ingredients.files };
+        const p = { packing: i, baseUrl: params.baseUrl, ingredientFiles };
 
         const packing = await state.build()
             .to(cellPackBuilder.ref)
@@ -497,8 +526,8 @@ const LoadCellPackModelParams = {
             ['influenza_model1.json', 'influenza_model1'],
             ['ExosomeModel.json', 'ExosomeModel'],
             ['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma1.5_mixed_pdb_fixed'],
-        ] as const),
-        'file': PD.File({ accept: 'id' }),
+        ] as const, { description: 'Download the model definition with `id` from the server at `baseUrl.`' }),
+        'file': PD.File({ accept: '.json,.cpr,.zip', description: 'Open model definition from .json/.cpr file or open .zip file containing model definition plus ingredients.' }),
     }, { options: [['id', 'Id'], ['file', 'File']] }),
     baseUrl: PD.Text(DefaultCellPackBaseUrl),
     ingredients : PD.Group({

src/extensions/cellpack/property.ts

@@ -5,9 +5,10 @@
  */
 
 import { CustomStructureProperty } from '../../mol-model-props/common/custom-structure-property';
-import { Structure, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
 import { CustomProperty } from '../../mol-model-props/common/custom-property';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export type CellPackInfoValue = {
     packingsCount: number

src/extensions/pdbe/preferred-assembly.ts

@@ -7,9 +7,10 @@
 import { Column, Table } from '../../mol-data/db';
 import { toTable } from '../../mol-io/reader/cif/schema';
 import { CifWriter } from '../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { Model } from '../../mol-model/structure';
 import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
 import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export namespace PDBePreferredAssembly {
     export type Property = string

src/extensions/pdbe/struct-ref-domain.ts

@@ -7,9 +7,10 @@
 import { Column, Table } from '../../mol-data/db';
 import { toTable } from '../../mol-io/reader/cif/schema';
 import { CifWriter } from '../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { Model } from '../../mol-model/structure';
 import { PropertyWrapper } from '../../mol-model-props/common/wrapper';
 import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export namespace PDBeStructRefDomain {
     export type Property = PropertyWrapper<Table<Schema['pdbe_struct_ref_domain']> | undefined>

src/extensions/pdbe/structure-quality-report/prop.ts

@@ -9,7 +9,7 @@ import { Column, Table } from '../../../mol-data/db';
 import { toTable } from '../../../mol-io/reader/cif/schema';
 import { mmCIF_residueId_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
 import { CifWriter } from '../../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor, ResidueIndex, Unit, IndexedCustomProperty } from '../../../mol-model/structure';
+import { Model, ResidueIndex, Unit, IndexedCustomProperty } from '../../../mol-model/structure';
 import { residueIdFields } from '../../../mol-model/structure/export/categories/atom_site';
 import { StructureElement, CifExportContext, Structure } from '../../../mol-model/structure/structure';
 import { CustomPropSymbol } from '../../../mol-script/language/symbol';
@@ -22,6 +22,7 @@ import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
 import { CustomProperty } from '../../../mol-model-props/common/custom-property';
 import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
 import { Asset } from '../../../mol-util/assets';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 export { StructureQualityReport };
 

src/extensions/rcsb/assembly-symmetry/prop.ts

@@ -8,7 +8,7 @@ import { AssemblySymmetryQuery, AssemblySymmetryQueryVariables } from '../graphq
 import query from '../graphql/symmetry.gql';
 
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { CustomPropertyDescriptor, Structure, Model, StructureSelection, QueryContext } from '../../../mol-model/structure';
+import { Structure, Model, StructureSelection, QueryContext } from '../../../mol-model/structure';
 import { Database as _Database, Column } from '../../../mol-data/db';
 import { GraphQLClient } from '../../../mol-util/graphql-client';
 import { CustomProperty } from '../../../mol-model-props/common/custom-property';
@@ -19,6 +19,7 @@ import { ReadonlyVec3 } from '../../../mol-math/linear-algebra/3d/vec3';
 import { SetUtils } from '../../../mol-util/set';
 import { MolScriptBuilder as MS } from '../../../mol-script/language/builder';
 import { compile } from '../../../mol-script/runtime/query/compiler';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 const BiologicalAssemblyNames = new Set([
     'author_and_software_defined_assembly',

src/extensions/rcsb/validation-report/prop.ts

@@ -5,7 +5,7 @@
  */
 
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { CustomPropertyDescriptor, Structure, Unit } from '../../../mol-model/structure';
+import { Structure, Unit } from '../../../mol-model/structure';
 import { CustomProperty } from '../../../mol-model-props/common/custom-property';
 import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
 import { Model, ElementIndex, ResidueIndex } from '../../../mol-model/structure/model';
@@ -21,6 +21,7 @@ import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
 import { CustomPropSymbol } from '../../../mol-script/language/symbol';
 import Type from '../../../mol-script/language/type';
 import { Asset } from '../../../mol-util/assets';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 export { ValidationReport };
 

src/mol-canvas3d/passes/postprocessing.ts

@@ -59,7 +59,7 @@ export const PostprocessingParams = {
     outline: PD.MappedStatic('off', {
         on: PD.Group({
             scale: PD.Numeric(1, { min: 0, max: 10, step: 1 }),
-            threshold: PD.Numeric(0.8, { min: 0, max: 1, step: 0.01 }),
+            threshold: PD.Numeric(0.8, { min: 0, max: 5, step: 0.01 }),
         }),
         off: PD.Group({})
     }, { cycle: true, description: 'Draw outline around 3D objects' })

src/mol-gl/renderable.ts

@@ -44,9 +44,6 @@ export function createRenderable<T extends Values<RenderableSchema>>(renderItem:
             if (values.uAlpha && values.alpha) {
                 ValueCell.updateIfChanged(values.uAlpha, clamp(values.alpha.ref.value * state.alphaFactor, 0, 1));
             }
-            if (values.uPickable) {
-                ValueCell.updateIfChanged(values.uPickable, state.pickable ? 1 : 0);
-            }
             renderItem.render(variant);
         },
         getProgram: (variant: GraphicsRenderVariant) => renderItem.getProgram(variant),

src/mol-gl/renderable/direct-volume.ts

@@ -73,7 +73,6 @@ export function DirectVolumeRenderable(ctx: WebGLContext, id: number, values: Di
     const schema = { ...GlobalUniformSchema, ...InternalSchema, ...DirectVolumeSchema };
     const internalValues: InternalValues = {
         uObjectId: ValueCell.create(id),
-        uPickable: ValueCell.create(state.pickable ? 1 : 0),
     };
     const shaderCode = DirectVolumeShaderCode;
     const renderItem = createGraphicsRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId);

src/mol-gl/renderable/image.ts

@@ -33,7 +33,6 @@ export function ImageRenderable(ctx: WebGLContext, id: number, values: ImageValu
     const schema = { ...GlobalUniformSchema, ...InternalSchema, ...ImageSchema };
     const internalValues: InternalValues = {
         uObjectId: ValueCell.create(id),
-        uPickable: ValueCell.create(state.pickable ? 1 : 0),
     };
     const shaderCode = ImageShaderCode;
     const renderItem = createGraphicsRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId);

src/mol-gl/renderable/lines.ts

@@ -29,7 +29,6 @@ export function LinesRenderable(ctx: WebGLContext, id: number, values: LinesValu
     const schema = { ...GlobalUniformSchema, ...InternalSchema, ...LinesSchema };
     const internalValues: InternalValues = {
         uObjectId: ValueCell.create(id),
-        uPickable: ValueCell.create(state.pickable ? 1 : 0)
     };
     const shaderCode = LinesShaderCode;
     const renderItem = createGraphicsRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId);

src/mol-gl/renderable/mesh.ts

@@ -28,7 +28,6 @@ export function MeshRenderable(ctx: WebGLContext, id: number, values: MeshValues
     const schema = { ...GlobalUniformSchema, ...InternalSchema, ...MeshSchema };
     const internalValues: InternalValues = {
         uObjectId: ValueCell.create(id),
-        uPickable: ValueCell.create(state.pickable ? 1 : 0)
     };
     const shaderCode = MeshShaderCode;
     const renderItem = createGraphicsRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId);

src/mol-gl/renderable/points.ts

@@ -26,7 +26,6 @@ export function PointsRenderable(ctx: WebGLContext, id: number, values: PointsVa
     const schema = { ...GlobalUniformSchema, ...InternalSchema, ...PointsSchema };
     const internalValues: InternalValues = {
         uObjectId: ValueCell.create(id),
-        uPickable: ValueCell.create(state.pickable ? 1 : 0)
     };
     const shaderCode = PointsShaderCode;
     const renderItem = createGraphicsRenderItem(ctx, 'points', shaderCode, schema, { ...values, ...internalValues }, materialId);

src/mol-gl/renderable/schema.ts

@@ -187,7 +187,6 @@ export type GlobalUniformValues = Values<GlobalUniformSchema> // { [k in keyof G
 
 export const InternalSchema = {
     uObjectId: UniformSpec('i'),
-    uPickable: UniformSpec('i', true),
 } as const;
 export type InternalSchema = typeof InternalSchema
 export type InternalValues = { [k in keyof InternalSchema]: ValueCell<any> }

src/mol-gl/renderable/spheres.ts

@@ -29,7 +29,6 @@ export function SpheresRenderable(ctx: WebGLContext, id: number, values: Spheres
     const schema = { ...GlobalUniformSchema, ...InternalSchema, ...SpheresSchema };
     const internalValues: InternalValues = {
         uObjectId: ValueCell.create(id),
-        uPickable: ValueCell.create(state.pickable ? 1 : 0)
     };
     const shaderCode = SpheresShaderCode;
     const renderItem = createGraphicsRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId);

src/mol-gl/renderable/text.ts

@@ -38,7 +38,6 @@ export function TextRenderable(ctx: WebGLContext, id: number, values: TextValues
     const schema = { ...GlobalUniformSchema, ...InternalSchema, ...TextSchema };
     const internalValues: InternalValues = {
         uObjectId: ValueCell.create(id),
-        uPickable: ValueCell.create(state.pickable ? 1 : 0)
     };
     const shaderCode = TextShaderCode;
     const renderItem = createGraphicsRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId);

src/mol-gl/renderable/texture-mesh.ts

@@ -31,7 +31,6 @@ export function TextureMeshRenderable(ctx: WebGLContext, id: number, values: Tex
     const schema = { ...GlobalUniformSchema, ...InternalSchema, ...TextureMeshSchema };
     const internalValues: InternalValues = {
         uObjectId: ValueCell.create(id),
-        uPickable: ValueCell.create(state.pickable ? 1 : 0)
     };
     const shaderCode = MeshShaderCode;
     const renderItem = createGraphicsRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId);

src/mol-gl/renderer.ts

@@ -173,51 +173,53 @@ namespace Renderer {
         let globalUniformsNeedUpdate = true;
 
         const renderObject = (r: Renderable<RenderableValues & BaseValues>, variant: GraphicsRenderVariant) => {
+            if (!r.state.visible || (!r.state.pickable && variant[0] === 'p')) {
+                return;
+            }
+
             const program = r.getProgram(variant);
-            if (r.state.visible) {
-                if (state.currentProgramId !== program.id) {
-                    // console.log('new program')
-                    globalUniformsNeedUpdate = true;
-                    program.use();
-                }
+            if (state.currentProgramId !== program.id) {
+                // console.log('new program')
+                globalUniformsNeedUpdate = true;
+                program.use();
+            }
 
-                if (globalUniformsNeedUpdate) {
-                    // console.log('globalUniformsNeedUpdate')
-                    program.setUniforms(globalUniformList);
-                    globalUniformsNeedUpdate = false;
-                }
+            if (globalUniformsNeedUpdate) {
+                // console.log('globalUniformsNeedUpdate')
+                program.setUniforms(globalUniformList);
+                globalUniformsNeedUpdate = false;
+            }
 
-                if (r.values.dDoubleSided) {
-                    if (r.values.dDoubleSided.ref.value) {
-                        state.disable(gl.CULL_FACE);
-                    } else {
-                        state.enable(gl.CULL_FACE);
-                    }
-                } else {
-                    // webgl default
+            if (r.values.dDoubleSided) {
+                if (r.values.dDoubleSided.ref.value) {
                     state.disable(gl.CULL_FACE);
-                }
-
-                if (r.values.dFlipSided) {
-                    if (r.values.dFlipSided.ref.value) {
-                        state.frontFace(gl.CW);
-                        state.cullFace(gl.FRONT);
-                    } else {
-                        state.frontFace(gl.CCW);
-                        state.cullFace(gl.BACK);
-                    }
                 } else {
-                    // webgl default
+                    state.enable(gl.CULL_FACE);
+                }
+            } else {
+                // webgl default
+                state.disable(gl.CULL_FACE);
+            }
+
+            if (r.values.dFlipSided) {
+                if (r.values.dFlipSided.ref.value) {
+                    state.frontFace(gl.CW);
+                    state.cullFace(gl.FRONT);
+                } else {
                     state.frontFace(gl.CCW);
                     state.cullFace(gl.BACK);
                 }
-
-                if (variant === 'color') {
-                    state.depthMask(r.state.writeDepth);
-                }
-
-                r.render(variant);
+            } else {
+                // webgl default
+                state.frontFace(gl.CCW);
+                state.cullFace(gl.BACK);
             }
+
+            if (variant === 'color') {
+                state.depthMask(r.state.writeDepth);
+            }
+
+            r.render(variant);
         };
 
         const render = (scene: Scene, camera: Camera, variant: GraphicsRenderVariant, clear: boolean, transparentBackground: boolean) => {

src/mol-gl/shader/chunks/assign-material-color.glsl.ts

@@ -34,7 +34,7 @@ export default `
         if (ta < 0.99 && (ta < 0.01 || ta < at)) discard;
     #endif
 #elif defined(dRenderVariant_pick)
-    vec4 material = uPickable == 1 ? vColor : vec4(0.0, 0.0, 0.0, 1.0); // set to empty picking id
+    vec4 material = vColor;
 #elif defined(dRenderVariant_depth)
     #ifdef enabledFragDepth
         vec4 material = packDepthToRGBA(gl_FragDepthEXT);

src/mol-gl/shader/chunks/common-frag-params.glsl.ts

@@ -21,7 +21,6 @@ uniform vec3 uFogColor;
 
 uniform float uAlpha;
 uniform float uPickingAlphaThreshold;
-uniform int uPickable;
 uniform int uTransparentBackground;
 
 uniform float uInteriorDarkening;

src/mol-gl/shader/direct-volume.frag.ts

@@ -28,7 +28,6 @@ uniform sampler2D tMarker;
 
 uniform float uAlpha;
 uniform float uPickingAlphaThreshold;
-uniform int uPickable;
 
 #if defined(dGridTexType_2d)
     precision highp sampler2D;
@@ -117,8 +116,6 @@ vec4 raymarch(vec3 startLoc, vec3 step, vec3 viewDir) {
                 #if defined(dRenderVariant_pick)
                     if (uAlpha < uPickingAlphaThreshold)
                         discard; // ignore so the element below can be picked
-                    if (uPickable == 0)
-                        return vec4(0.0, 0.0, 0.0, 1.0); // set to empty picking id
                 #endif
 
                 #if defined(dRenderVariant_pickObject)

src/mol-gl/shader/image.frag.ts

@@ -99,18 +99,14 @@ void main() {
         if (imageData.a < 0.3)
             discard;
 
-        if (uPickable == 1) {
-            #if defined(dRenderVariant_pickObject)
-                gl_FragColor = vec4(encodeFloatRGB(float(uObjectId)), 1.0);
-            #elif defined(dRenderVariant_pickInstance)
-                gl_FragColor = vec4(encodeFloatRGB(vInstance), 1.0);
-            #elif defined(dRenderVariant_pickGroup)
-                float group = texture2D(tGroupTex, vUv).r;
-                gl_FragColor = vec4(encodeFloatRGB(group), 1.0);
-            #endif
-        } else {
-            gl_FragColor = vec4(0.0, 0.0, 0.0, 1.0); // set to empty picking id
-        }
+        #if defined(dRenderVariant_pickObject)
+            gl_FragColor = vec4(encodeFloatRGB(float(uObjectId)), 1.0);
+        #elif defined(dRenderVariant_pickInstance)
+            gl_FragColor = vec4(encodeFloatRGB(vInstance), 1.0);
+        #elif defined(dRenderVariant_pickGroup)
+            float group = texture2D(tGroupTex, vUv).r;
+            gl_FragColor = vec4(encodeFloatRGB(group), 1.0);
+        #endif
     #elif defined(dRenderVariant_depth)
         if (imageData.a < 0.05)
             discard;

src/mol-io/reader/_spec/mol2.spec.ts

@@ -1,5 +1,5 @@
 
-import Mol2 from '../mol2/parser';
+import { parseMol2 } from '../mol2/parser';
 
 const Mol2String = `@<TRIPOS>MOLECULE
 5816
@@ -246,7 +246,7 @@ GASTEIGER
 
 describe('mol2 reader', () => {
     it('basic', async () => {
-        const parsed =  await Mol2(Mol2String).run();
+        const parsed =  await parseMol2(Mol2String, '').run();
         if (parsed.isError) {
             throw new Error(parsed.message);
         }
@@ -297,7 +297,7 @@ describe('mol2 reader', () => {
     });
 
     it('multiblocks', async () => {
-        const parsed =  await Mol2(Mol2StringMultiBlocks).run();
+        const parsed =  await parseMol2(Mol2StringMultiBlocks, '').run();
         if (parsed.isError) {
             throw new Error(parsed.message);
         }
@@ -348,7 +348,7 @@ describe('mol2 reader', () => {
     });
 
     it('minimal', async () => {
-        const parsed =  await Mol2(Mol2StringMinimal).run();
+        const parsed =  await parseMol2(Mol2StringMinimal, '').run();
         if (parsed.isError) {
             throw new Error(parsed.message);
         }

src/mol-io/reader/mol2/parser.ts

@@ -54,7 +54,7 @@ const reWhitespace = /\s+/g;
 function handleMolecule(state: State) {
     const { tokenizer, molecule } = state;
 
-    while (getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE') {
+    while (getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE' && tokenizer.position < tokenizer.data.length) {
         markLine(tokenizer);
     }
 
@@ -101,7 +101,7 @@ async function handleAtoms(state: State): Promise<Schema.Mol2Atoms> {
     let hasStatus_bit = false;
 
     // skip empty lines and '@<TRIPOS>ATOM'
-    while (getTokenString(tokenizer) !== '@<TRIPOS>ATOM') {
+    while (getTokenString(tokenizer) !== '@<TRIPOS>ATOM' && tokenizer.position < tokenizer.data.length) {
         markLine(tokenizer);
     }
 
@@ -243,7 +243,7 @@ async function handleBonds(state: State): Promise<Schema.Mol2Bonds> {
     const { tokenizer, molecule } = state;
     let hasStatus_bit = false;
 
-    while (getTokenString(tokenizer) !== '@<TRIPOS>BOND') {
+    while (getTokenString(tokenizer) !== '@<TRIPOS>BOND' && tokenizer.position < tokenizer.data.length) {
         markLine(tokenizer);
     }
 
@@ -324,7 +324,7 @@ async function handleBonds(state: State): Promise<Schema.Mol2Bonds> {
     return ret;
 }
 
-async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<Schema.Mol2File>> {
+async function parseInternal(ctx: RuntimeContext, data: string, name: string): Promise<Result<Schema.Mol2File>> {
     const tokenizer = Tokenizer(data);
 
     ctx.update({ message: 'Parsing...', current: 0, max: data.length });
@@ -335,16 +335,15 @@ async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<
         const atoms = await handleAtoms(state);
         const bonds = await handleBonds(state);
         structures.push({ molecule: state.molecule, atoms, bonds });
+        skipWhitespace(tokenizer);
     }
 
-    const result: Schema.Mol2File = { structures };
+    const result: Schema.Mol2File = { name, structures };
     return Result.success(result);
 }
 
-export function parse(data: string) {
+export function parseMol2(data: string, name: string) {
     return Task.create<Result<Schema.Mol2File>>('Parse MOL2', async ctx => {
-        return await parseInternal(data, ctx);
+        return await parseInternal(ctx, data, name);
     });
-}
-
-export default parse;
+}

src/mol-io/reader/mol2/schema.d.ts

@@ -63,5 +63,6 @@ export interface Mol2Structure {
 }
 
 export interface Mol2File {
+    name: string
     structures: Mol2Structure[]
 }

src/mol-model-formats/structure/3dg.ts

@@ -6,7 +6,7 @@
 
 import { Model } from '../../mol-model/structure/model';
 import { Task } from '../../mol-task';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
 import { Column, Table } from '../../mol-data/db';
 import { EntityBuilder } from './common/entity';
 import { File3DG } from '../../mol-io/reader/3dg/parser';

src/mol-model-formats/structure/basic/atomic.ts

@@ -16,7 +16,7 @@ import { ElementSymbol } from '../../../mol-model/structure/model/types';
 import { Entities } from '../../../mol-model/structure/model/properties/common';
 import { getAtomicDerivedData } from '../../../mol-model/structure/model/properties/utils/atomic-derived';
 import { AtomSite } from './schema';
-import { ModelFormat } from '../format';
+import { ModelFormat } from '../../format';
 import { SymmetryOperator } from '../../../mol-math/geometry';
 import { MmcifFormat } from '../mmcif';
 import { AtomSiteOperatorMappingSchema } from '../../../mol-model/structure/export/categories/atom_site_operator_mapping';

src/mol-model-formats/structure/basic/parser.ts

@@ -10,12 +10,12 @@ import { RuntimeContext } from '../../../mol-task';
 import UUID from '../../../mol-util/uuid';
 import { Model } from '../../../mol-model/structure/model/model';
 import { Entities } from '../../../mol-model/structure/model/properties/common';
-import { CustomProperties } from '../../../mol-model/structure';
+import { CustomProperties } from '../../../mol-model/custom-property';
 import { getAtomicHierarchyAndConformation } from './atomic';
 import { getCoarse, EmptyCoarse, CoarseData } from './coarse';
 import { getSequence } from './sequence';
 import { sortAtomSite } from './sort';
-import { ModelFormat } from '../format';
+import { ModelFormat } from '../../format';
 import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
 import { AtomSite, BasicData } from './schema';
 import { getProperties } from './properties';

src/mol-model-formats/structure/cif-core.ts

@@ -12,7 +12,7 @@ import { createModels } from './basic/parser';
 import { BasicSchema, createBasic } from './basic/schema';
 import { ComponentBuilder } from './common/component';
 import { EntityBuilder } from './common/entity';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
 import { CifCore_Database } from '../../mol-io/reader/cif/schema/cif-core';
 import { CifFrame, CIF } from '../../mol-io/reader/cif';
 import { Spacegroup, SpacegroupCell } from '../../mol-math/geometry';

src/mol-model-formats/structure/common/property.ts

@@ -4,8 +4,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor, Model } from '../../../mol-model/structure';
-import { ModelFormat } from '../format';
+import { Model } from '../../../mol-model/structure';
+import { ModelFormat } from '../../format';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 class FormatRegistry<T> {
     private map = new Map<ModelFormat['kind'], (model: Model) => T | undefined>()

src/mol-model-formats/structure/cube.ts

@@ -12,7 +12,7 @@ import { createModels } from './basic/parser';
 import { BasicSchema, createBasic } from './basic/schema';
 import { ComponentBuilder } from './common/component';
 import { EntityBuilder } from './common/entity';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
 import { CubeFile } from '../../mol-io/reader/cube/parser';
 
 async function getModels(cube: CubeFile, ctx: RuntimeContext): Promise<Model[]> {

src/mol-model-formats/structure/gro.ts

@@ -6,7 +6,7 @@
 
 import { Model } from '../../mol-model/structure/model';
 import { Task } from '../../mol-task';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
 import { GroFile, GroAtoms } from '../../mol-io/reader/gro/schema';
 import { Column, Table } from '../../mol-data/db';
 import { guessElementSymbolString } from './util';

src/mol-model-formats/structure/mmcif.ts

@@ -7,7 +7,7 @@
 
 import { Model } from '../../mol-model/structure/model/model';
 import { Task } from '../../mol-task';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
 import { CifFrame, CIF } from '../../mol-io/reader/cif';
 import { mmCIF_Database } from '../../mol-io/reader/cif/schema/mmcif';
 import { createModels } from './basic/parser';

src/mol-model-formats/structure/mol.ts

@@ -14,7 +14,7 @@ import { createModels } from './basic/parser';
 import { BasicSchema, createBasic } from './basic/schema';
 import { ComponentBuilder } from './common/component';
 import { EntityBuilder } from './common/entity';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
 import { IndexPairBonds } from './property/bonds/index-pair';
 
 async function getModels(mol: MolFile, ctx: RuntimeContext): Promise<Model[]> {

src/mol-model-formats/structure/mol2.ts

@@ -0,0 +1,98 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Column, Table } from '../../mol-data/db';
+import { Model } from '../../mol-model/structure/model';
+import { MoleculeType } from '../../mol-model/structure/model/types';
+import { RuntimeContext, Task } from '../../mol-task';
+import { createModels } from './basic/parser';
+import { BasicSchema, createBasic } from './basic/schema';
+import { ComponentBuilder } from './common/component';
+import { EntityBuilder } from './common/entity';
+import { ModelFormat } from '../format';
+import { IndexPairBonds } from './property/bonds/index-pair';
+import { Mol2File } from '../../mol-io/reader/mol2/schema';
+
+async function getModels(mol2: Mol2File, ctx: RuntimeContext): Promise<Model[]> {
+    const models: Model[] = [];
+
+    for (let i = 0, il = mol2.structures.length; i < il; ++i) {
+        const { atoms, bonds } = mol2.structures[i];
+
+        const A = Column.ofConst('A', atoms.count, Column.Schema.str);
+
+        const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
+            auth_asym_id: A,
+            auth_atom_id: Column.asArrayColumn(atoms.atom_type),
+            auth_comp_id: atoms.subst_name,
+            auth_seq_id: atoms.subst_id,
+            Cartn_x: Column.asArrayColumn(atoms.x, Float32Array),
+            Cartn_y: Column.asArrayColumn(atoms.y, Float32Array),
+            Cartn_z: Column.asArrayColumn(atoms.z, Float32Array),
+            id: Column.asArrayColumn(atoms.atom_id),
+
+            label_asym_id: A,
+            label_atom_id: Column.asArrayColumn(atoms.atom_type),
+            label_comp_id: atoms.subst_name,
+            label_seq_id: atoms.subst_id,
+            label_entity_id: Column.ofConst('1', atoms.count, Column.Schema.str),
+
+            occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
+            type_symbol: Column.asArrayColumn(atoms.atom_name),
+
+            pdbx_PDB_model_num: Column.ofConst(i, atoms.count, Column.Schema.int),
+        }, atoms.count);
+
+        const entityBuilder = new EntityBuilder();
+        entityBuilder.setNames([['MOL', 'Unknown Entity']]);
+        entityBuilder.getEntityId('MOL', MoleculeType.Unknown, 'A');
+
+        const componentBuilder = new ComponentBuilder(atoms.subst_id, atoms.atom_name);
+        for (let i = 0, il = atoms.subst_name.rowCount; i < il; ++i) {
+            componentBuilder.add(atoms.subst_name.value(i), i);
+        }
+
+        const basics = createBasic({
+            entity: entityBuilder.getEntityTable(),
+            chem_comp: componentBuilder.getChemCompTable(),
+            atom_site
+        });
+
+        const _models = await createModels(basics, Mol2Format.create(mol2), ctx);
+
+        if (_models.length > 0) {
+            const indexA = Column.ofIntArray(Column.mapToArray(bonds.origin_atom_id, x => x - 1, Int32Array));
+            const indexB = Column.ofIntArray(Column.mapToArray(bonds.target_atom_id, x => x - 1, Int32Array));
+            const order = Column.ofIntArray(Column.mapToArray(bonds.bond_type, x => x === 'ar' ? 1 : parseInt(x), Int8Array));
+            const pairBonds = IndexPairBonds.fromData({ pairs: { indexA, indexB, order }, count: bonds.count });
+            IndexPairBonds.Provider.set(_models[0], pairBonds);
+
+            models.push(_models[0]);
+        }
+    }
+
+    return models;
+}
+
+//
+
+export { Mol2Format };
+
+type Mol2Format = ModelFormat<Mol2File>
+
+namespace Mol2Format {
+    export function is(x: ModelFormat): x is Mol2Format {
+        return x.kind === 'mol2';
+    }
+
+    export function create(mol2: Mol2File): Mol2Format {
+        return { kind: 'mol2', name: mol2.name, data: mol2 };
+    }
+}
+
+export function trajectoryFromMol2(mol2: Mol2File): Task<Model.Trajectory> {
+    return Task.create('Parse MOL2', ctx => getModels(mol2, ctx));
+}

src/mol-model-formats/structure/property/anisotropic.ts

@@ -5,7 +5,7 @@
  */
 
 import { Table, Column } from '../../../mol-data/db';
-import { CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
 import { CifWriter } from '../../../mol-io/writer/cif';
 import { FormatPropertyProvider } from '../common/property';

src/mol-model-formats/structure/property/bonds/comp.ts

@@ -7,7 +7,7 @@
 
 import { Model } from '../../../../mol-model/structure/model/model';
 import { BondType } from '../../../../mol-model/structure/model/types';
-import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
 import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
 import { CifWriter } from '../../../../mol-io/writer/cif';
 import { Table } from '../../../../mol-data/db';

src/mol-model-formats/structure/property/bonds/index-pair.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
 import { IntAdjacencyGraph } from '../../../../mol-math/graph';
 import { Column } from '../../../../mol-data/db';
 import { FormatPropertyProvider } from '../../common/property';

src/mol-model-formats/structure/property/bonds/struct_conn.ts

@@ -9,7 +9,7 @@ import { Model } from '../../../../mol-model/structure/model/model';
 import { Structure } from '../../../../mol-model/structure';
 import { BondType } from '../../../../mol-model/structure/model/types';
 import { Column, Table } from '../../../../mol-data/db';
-import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
 import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
 import { SortedArray } from '../../../../mol-data/int';
 import { CifWriter } from '../../../../mol-io/writer/cif';

src/mol-model-formats/structure/property/secondary-structure.ts

@@ -13,7 +13,7 @@ import { SecondaryStructure } from '../../../mol-model/structure/model/propertie
 import { Column, Table } from '../../../mol-data/db';
 import { ChainIndex, ResidueIndex } from '../../../mol-model/structure/model/indexing';
 import { FormatPropertyProvider } from '../common/property';
-import { CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 export { ModelSecondaryStructure };
 

src/mol-model-formats/structure/property/symmetry.ts

@@ -10,7 +10,7 @@ import { Spacegroup, SpacegroupCell, SymmetryOperator } from '../../../mol-math/
 import { Tensor, Vec3, Mat3 } from '../../../mol-math/linear-algebra';
 import { Symmetry } from '../../../mol-model/structure/model/properties/symmetry';
 import { createAssemblies } from './assembly';
-import { CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 import { FormatPropertyProvider } from '../common/property';
 import { Table } from '../../../mol-data/db';
 

src/mol-model-formats/structure/psf.ts

@@ -12,7 +12,7 @@ import { guessElementSymbolString } from './util';
 import { MoleculeType, getMoleculeType } from '../../mol-model/structure/model/types';
 import { getChainId } from './common/util';
 import { Task } from '../../mol-task';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
 import { Topology } from '../../mol-model/structure/topology/topology';
 import { createBasic, BasicSchema } from './basic/schema';
 

src/mol-model-formats/volume/ccp4.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
 import { Task } from '../../mol-task';
 import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
 import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
@@ -13,6 +13,8 @@ import { degToRad } from '../../mol-math/misc';
 import { getCcp4ValueType } from '../../mol-io/reader/ccp4/parser';
 import { TypedArrayValueType } from '../../mol-io/common/typed-array';
 import { arrayMin, arrayRms, arrayMean, arrayMax } from '../../mol-util/array';
+import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
 
 /** When available (e.g. in MRC files) use ORIGIN records instead of N[CRS]START */
 export function getCcp4Origin(header: Ccp4Header): Vec3 {
@@ -38,8 +40,8 @@ function getTypedArrayCtor(header: Ccp4Header) {
     throw Error(`${valueType} is not a supported value format.`);
 }
 
-export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, offset?: Vec3, label?: string }): Task<VolumeData> {
-    return Task.create<VolumeData>('Create Volume Data', async ctx => {
+export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, offset?: Vec3, label?: string }): Task<Volume> {
+    return Task.create<Volume>('Create Volume', async ctx => {
         const { header, values } = source;
         const size = Vec3.create(header.xLength, header.yLength, header.zLength);
         if (params && params.voxelSize) Vec3.mul(size, size, params.voxelSize);
@@ -68,14 +70,35 @@ export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, of
 
         return {
             label: params?.label,
-            transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
-            data,
-            dataStats: {
-                min: isNaN(header.AMIN) ? arrayMin(values) : header.AMIN,
-                max: isNaN(header.AMAX) ? arrayMax(values) : header.AMAX,
-                mean: isNaN(header.AMEAN) ? arrayMean(values) : header.AMEAN,
-                sigma: (isNaN(header.ARMS) || header.ARMS === 0) ? arrayRms(values) : header.ARMS
-            }
+            grid: {
+                transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
+                cells: data,
+                stats: {
+                    min: isNaN(header.AMIN) ? arrayMin(values) : header.AMIN,
+                    max: isNaN(header.AMAX) ? arrayMax(values) : header.AMAX,
+                    mean: isNaN(header.AMEAN) ? arrayMean(values) : header.AMEAN,
+                    sigma: (isNaN(header.ARMS) || header.ARMS === 0) ? arrayRms(values) : header.ARMS
+                },
+            },
+            sourceData: Ccp4Format.create(source),
+            customProperties: new CustomProperties(),
+            _propertyData: Object.create(null),
         };
     });
+}
+
+//
+
+export { Ccp4Format };
+
+type Ccp4Format = ModelFormat<Ccp4File>
+
+namespace Ccp4Format {
+    export function is(x: ModelFormat): x is Ccp4Format {
+        return x.kind === 'ccp4';
+    }
+
+    export function create(ccp4: Ccp4File): Ccp4Format {
+        return { kind: 'ccp4', name: ccp4.name, data: ccp4 };
+    }
 }

src/mol-model-formats/volume/cube.ts

@@ -6,12 +6,14 @@
 
 import { CubeFile } from '../../mol-io/reader/cube/parser';
 import { Mat4, Tensor } from '../../mol-math/linear-algebra';
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
 import { Task } from '../../mol-task';
 import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
+import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
 
-export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string }): Task<VolumeData> {
-    return Task.create<VolumeData>('Create Volume Data', async () => {
+export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string }): Task<Volume> {
+    return Task.create<Volume>('Create Volume', async () => {
         const { header, values: sourceValues } = source;
         const space = Tensor.Space(header.dim, [0, 1, 2], Float64Array);
 
@@ -44,14 +46,35 @@ export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number,
 
         return {
             label: params?.label,
-            transform: { kind: 'matrix', matrix },
-            data,
-            dataStats: {
-                min: arrayMin(values),
-                max: arrayMax(values),
-                mean: arrayMean(values),
-                sigma: arrayRms(values)
-            }
+            grid: {
+                transform: { kind: 'matrix', matrix },
+                cells: data,
+                stats: {
+                    min: arrayMin(values),
+                    max: arrayMax(values),
+                    mean: arrayMean(values),
+                    sigma: arrayRms(values)
+                },
+            },
+            sourceData: CubeFormat.create(source),
+            customProperties: new CustomProperties(),
+            _propertyData: Object.create(null),
         };
     });
+}
+
+//
+
+export { CubeFormat };
+
+type CubeFormat = ModelFormat<CubeFile>
+
+namespace CubeFormat {
+    export function is(x: ModelFormat): x is CubeFormat {
+        return x.kind === 'cube';
+    }
+
+    export function create(cube: CubeFile): CubeFormat {
+        return { kind: 'cube', name: cube.name, data: cube };
+    }
 }

src/mol-model-formats/volume/density-server.ts

@@ -5,13 +5,15 @@
  */
 
 import { DensityServer_Data_Database } from '../../mol-io/reader/cif/schema/density-server';
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
 import { Task } from '../../mol-task';
 import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
 import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
+import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
 
-function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<VolumeData> {
-    return Task.create<VolumeData>('Create Volume Data', async ctx => {
+export function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<Volume> {
+    return Task.create<Volume>('Create Volume', async ctx => {
         const { volume_data_3d_info: info, volume_data_3d: values } = source;
         const cell = SpacegroupCell.create(
             info.spacegroup_number.value(0),
@@ -34,16 +36,35 @@ function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<
         const dimensions = Vec3.ofArray(normalizeOrder(info.dimensions.value(0)));
 
         return {
-            transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin, Vec3.add(Vec3.zero(), origin, dimensions)) },
-            data,
-            dataStats: {
-                min: info.min_sampled.value(0),
-                max: info.max_sampled.value(0),
-                mean: info.mean_sampled.value(0),
-                sigma: info.sigma_sampled.value(0)
-            }
+            grid: {
+                transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin, Vec3.add(Vec3.zero(), origin, dimensions)) },
+                cells: data,
+                stats: {
+                    min: info.min_sampled.value(0),
+                    max: info.max_sampled.value(0),
+                    mean: info.mean_sampled.value(0),
+                    sigma: info.sigma_sampled.value(0)
+                },
+            },
+            sourceData: DscifFormat.create(source),
+            customProperties: new CustomProperties(),
+            _propertyData: Object.create(null),
         };
     });
 }
 
-export { volumeFromDensityServerData };
+//
+
+export { DscifFormat };
+
+type DscifFormat = ModelFormat<DensityServer_Data_Database>
+
+namespace DscifFormat {
+    export function is(x: ModelFormat): x is DscifFormat {
+        return x.kind === 'dscif';
+    }
+
+    export function create(dscif: DensityServer_Data_Database): DscifFormat {
+        return { kind: 'dscif', name: dscif._name, data: dscif };
+    }
+}

src/mol-model-formats/volume/dsn6.ts

@@ -4,16 +4,18 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
 import { Task } from '../../mol-task';
 import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
 import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
 import { degToRad } from '../../mol-math/misc';
 import { Dsn6File } from '../../mol-io/reader/dsn6/schema';
 import { arrayMin, arrayMax, arrayMean, arrayRms } from '../../mol-util/array';
+import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
 
-function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, label?: string }): Task<VolumeData> {
-    return Task.create<VolumeData>('Create Volume Data', async ctx => {
+export function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, label?: string }): Task<Volume> {
+    return Task.create<Volume>('Create Volume', async ctx => {
         const { header, values } = source;
         const size = Vec3.create(header.xlen, header.ylen, header.zlen);
         if (params && params.voxelSize) Vec3.mul(size, size, params.voxelSize);
@@ -33,16 +35,35 @@ function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, label?: s
 
         return {
             label: params?.label,
-            transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
-            data,
-            dataStats: {
-                min: arrayMin(values),
-                max: arrayMax(values),
-                mean: arrayMean(values),
-                sigma: header.sigma !== undefined ? header.sigma : arrayRms(values)
-            }
+            grid: {
+                transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
+                cells: data,
+                stats: {
+                    min: arrayMin(values),
+                    max: arrayMax(values),
+                    mean: arrayMean(values),
+                    sigma: header.sigma !== undefined ? header.sigma : arrayRms(values)
+                },
+            },
+            sourceData: Dsn6Format.create(source),
+            customProperties: new CustomProperties(),
+            _propertyData: Object.create(null),
         };
     });
 }
 
-export { volumeFromDsn6 };
+//
+
+export { Dsn6Format };
+
+type Dsn6Format = ModelFormat<Dsn6File>
+
+namespace Dsn6Format {
+    export function is(x: ModelFormat): x is Dsn6Format {
+        return x.kind === 'dsn6';
+    }
+
+    export function create(dsn6: Dsn6File): Dsn6Format {
+        return { kind: 'dsn6', name: dsn6.name, data: dsn6 };
+    }
+}

src/mol-model-formats/volume/dx.ts

@@ -6,12 +6,14 @@
 
 import { DxFile } from '../../mol-io/reader/dx/parser';
 import { Mat4, Tensor } from '../../mol-math/linear-algebra';
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
 import { Task } from '../../mol-task';
 import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
+import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
 
-export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<VolumeData> {
-    return Task.create<VolumeData>('Create Volume Data', async () => {
+export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<Volume> {
+    return Task.create<Volume>('Create Volume', async () => {
         const { header, values } = source;
         const space = Tensor.Space(header.dim, [0, 1, 2], Float64Array);
         const data = Tensor.create(space, Tensor.Data1(values));
@@ -21,14 +23,35 @@ export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<
 
         return {
             label: params?.label,
-            transform: { kind: 'matrix', matrix },
-            data,
-            dataStats: {
-                min: arrayMin(values),
-                max: arrayMax(values),
-                mean: arrayMean(values),
-                sigma: arrayRms(values)
-            }
+            grid: {
+                transform: { kind: 'matrix', matrix },
+                cells: data,
+                stats: {
+                    min: arrayMin(values),
+                    max: arrayMax(values),
+                    mean: arrayMean(values),
+                    sigma: arrayRms(values)
+                },
+            },
+            sourceData: DxFormat.create(source),
+            customProperties: new CustomProperties(),
+            _propertyData: Object.create(null),
         };
     });
+}
+
+//
+
+export { DxFormat };
+
+type DxFormat = ModelFormat<DxFile>
+
+namespace DxFormat {
+    export function is(x: ModelFormat): x is DxFormat {
+        return x.kind === 'dx';
+    }
+
+    export function create(dx: DxFile): DxFormat {
+        return { kind: 'dx', name: dx.name, data: dx };
+    }
 }

src/mol-model-props/common/custom-element-property.ts

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { ElementIndex, Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { ElementIndex, Model } from '../../mol-model/structure';
 import { StructureElement } from '../../mol-model/structure/structure';
 import { Location } from '../../mol-model/location';
 import { ThemeDataContext } from '../../mol-theme/theme';
@@ -16,6 +16,7 @@ import { OrderedSet } from '../../mol-data/int';
 import { CustomModelProperty } from './custom-model-property';
 import { CustomProperty } from './custom-property';
 import { LociLabelProvider } from '../../mol-plugin-state/manager/loci-label';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export { CustomElementProperty };
 

src/mol-model-props/common/custom-model-property.ts

@@ -4,10 +4,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor, Model } from '../../mol-model/structure';
+import { Model } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ValueBox } from '../../mol-util';
 import { CustomProperty } from './custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export { CustomModelProperty };
 

src/mol-model-props/common/custom-property.ts

@@ -5,7 +5,7 @@
  */
 
 import { RuntimeContext } from '../../mol-task';
-import { CustomPropertyDescriptor } from '../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ValueBox } from '../../mol-util';
 import { OrderedMap } from 'immutable';

src/mol-model-props/common/custom-structure-property.ts

@@ -4,10 +4,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor, Structure } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ValueBox } from '../../mol-util';
 import { CustomProperty } from './custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export { CustomStructureProperty };
 

src/mol-model-props/computed/accessible-surface-area.ts

@@ -7,12 +7,13 @@
 
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ShrakeRupleyComputationParams, AccessibleSurfaceArea } from './accessible-surface-area/shrake-rupley';
-import { Structure, CustomPropertyDescriptor, Unit } from '../../mol-model/structure';
+import { Structure, Unit } from '../../mol-model/structure';
 import { CustomStructureProperty } from '../common/custom-structure-property';
 import { CustomProperty } from '../common/custom-property';
 import { QuerySymbolRuntime } from '../../mol-script/runtime/query/compiler';
 import { CustomPropSymbol } from '../../mol-script/language/symbol';
 import Type from '../../mol-script/language/type';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export const AccessibleSurfaceAreaParams = {
     ...ShrakeRupleyComputationParams

src/mol-model-props/computed/interactions.ts

@@ -4,11 +4,12 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor, Structure } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { computeInteractions, Interactions, InteractionsParams as _InteractionsParams } from './interactions/interactions';
 import { CustomStructureProperty } from '../common/custom-structure-property';
 import { CustomProperty } from '../common/custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export const InteractionsParams = {
     ..._InteractionsParams

src/mol-model-props/computed/secondary-structure.ts

@@ -12,7 +12,7 @@ import { Unit } from '../../mol-model/structure/structure';
 import { CustomStructureProperty } from '../common/custom-structure-property';
 import { CustomProperty } from '../common/custom-property';
 import { ModelSecondaryStructure } from '../../mol-model-formats/structure/property/secondary-structure';
-import { CustomPropertyDescriptor } from '../../mol-model/structure/common/custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 import { Model } from '../../mol-model/structure/model';
 
 function getSecondaryStructureParams(data?: Structure) {

src/mol-model-props/computed/valence-model.ts

@@ -4,11 +4,12 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor, Structure } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { calcValenceModel, ValenceModel, ValenceModelParams as _ValenceModelParams } from './chemistry/valence-model';
 import { CustomStructureProperty } from '../common/custom-structure-property';
 import { CustomProperty } from '../common/custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export const ValenceModelParams = {
     ..._ValenceModelParams

src/mol-model-props/integrative/cross-link-restraint/format.ts

@@ -7,9 +7,10 @@
 import { Model } from '../../../mol-model/structure/model/model';
 import { Table } from '../../../mol-data/db';
 import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
-import { Unit, CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { Unit } from '../../../mol-model/structure';
 import { ElementIndex } from '../../../mol-model/structure/model/indexing';
 import { FormatPropertyProvider } from '../../../mol-model-formats/structure/common/property';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 export { ModelCrossLinkRestraint };
 

src/mol-model-props/integrative/cross-link-restraint/property.ts

@@ -5,7 +5,7 @@
  */
 
 import { ModelCrossLinkRestraint } from './format';
-import { Unit, StructureElement, Structure, CustomPropertyDescriptor, Bond} from '../../../mol-model/structure';
+import { Unit, StructureElement, Structure, Bond} from '../../../mol-model/structure';
 import { PairRestraints, PairRestraint } from '../pair-restraints';
 import { CustomStructureProperty } from '../../common/custom-structure-property';
 import { CustomProperty } from '../../common/custom-property';
@@ -15,6 +15,7 @@ import { Sphere3D } from '../../../mol-math/geometry';
 import { CentroidHelper } from '../../../mol-math/geometry/centroid-helper';
 import { bondLabel } from '../../../mol-theme/label';
 import { Vec3 } from '../../../mol-math/linear-algebra';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 export type CrossLinkRestraintValue = PairRestraints<CrossLinkRestraint>
 

src/mol-model/custom-property.ts

@@ -5,11 +5,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CifWriter } from '../../../mol-io/writer/cif';
-import { CifExportContext } from '../export/mmcif';
-import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
-import { UUID } from '../../../mol-util';
-import { Asset } from '../../../mol-util/assets';
+import { CifWriter } from '../mol-io/writer/cif';
+import { CifExportContext } from './structure/export/mmcif';
+import { QuerySymbolRuntime } from '../mol-script/runtime/query/compiler';
+import { UUID } from '../mol-util';
+import { Asset } from '../mol-util/assets';
 
 export { CustomPropertyDescriptor, CustomProperties };
 

src/mol-model/sequence/sequence.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -24,14 +24,18 @@ namespace Sequence {
     export interface Base<K extends Kind, Alphabet extends string> {
         readonly kind: K,
         readonly length: number,
-        readonly offset: number,
 
+        /** One letter code */
         readonly code: Column<Alphabet>
         readonly label: Column<string>
 
         readonly seqId: Column<number>
+        /** Component id */
         readonly compId: Column<string>
 
+        /** returns index for given seqId */
+        readonly index: (seqId: number) => number
+
         /** maps seqId to list of compIds */
         readonly microHet: ReadonlyMap<number, string[]>
     }
@@ -41,11 +45,6 @@ namespace Sequence {
     export interface DNA extends Base<Kind.DNA, NuclecicAlphabet> { }
     export interface Generic extends Base<Kind.Generic, 'X' | '-'> { }
 
-    export function create<K extends Kind, Alphabet extends string>(kind: K, code: Column<Alphabet>, label: Column<string>, seqId: Column<number>, compId: Column<string>, microHet: Map<number, string[]>, offset: number = 0): Base<K, Alphabet> {
-        const length = code.rowCount;
-        return { kind, code, label, seqId, compId, microHet, offset, length };
-    }
-
     export function getSequenceString(seq: Sequence) {
         const array = seq.code.toArray();
         return (array instanceof Array ? array : Array.from(array)).join('');
@@ -88,100 +87,60 @@ namespace Sequence {
     }
 
     class ResidueNamesImpl<K extends Kind, Alphabet extends string> implements Base<K, Alphabet> {
-        private _offset = 0;
-        private _length = 0;
-        private _microHet: ReadonlyMap<number, string[]> | undefined = void 0;
-        private _code: Column<Alphabet> | undefined = undefined
-        private _label: Column<string> | undefined = undefined
+        public length: number
+        public code: Column<Alphabet>
+        public label: Column<string>
+        public seqId: Column<number>
+        public compId: Column<string>
+        public microHet: ReadonlyMap<number, string[]> = new Map()
 
-        private codeFromName: (name: string) => string
-
-        get code(): Column<Alphabet> {
-            if (this._code !== void 0) return this._code;
-            this.create();
-            return this._code!;
+        private indexMap: Map<number, number>
+        index(seqId: number) {
+            return this.indexMap.get(seqId)!;
         }
 
-        get label(): Column<string> {
-            if (this._label !== void 0) return this._label;
-            this.create();
-            return this._label!;
-        }
+        constructor(public kind: K, compId: Column<string>, seqId: Column<number>) {
+            const codeFromName = codeProvider(kind);
+            const codes: string[] = [];
+            const compIds: string[] = [];
+            const seqIds: number[] = [];
+            const microHet = new Map<number, string[]>();
 
-        get offset() {
-            if (this._code !== void 0) return this._offset;
-            this.create();
-            return this._offset;
-        }
+            let idx = 0;
+            const indexMap = new Map<number, number>();
+            for (let i = 0, il = seqId.rowCount; i < il; ++i) {
+                const seq_id = seqId.value(i);
 
-        get length() {
-            if (this._code !== void 0) return this._length;
-            this.create();
-            return this._length;
-        }
-
-        get microHet(): ReadonlyMap<number, string[]> {
-            if (this._microHet !== void 0) return this._microHet;
-            this.create();
-            return this._microHet!;
-        }
-
-        private create() {
-            let maxSeqId = 0, minSeqId = Number.MAX_SAFE_INTEGER;
-            for (let i = 0, _i = this.seqId.rowCount; i < _i; i++) {
-                const id = this.seqId.value(i);
-                if (maxSeqId < id) maxSeqId = id;
-                if (id < minSeqId) minSeqId = id;
-            }
-
-            const count = maxSeqId - minSeqId + 1;
-            const sequenceArray = new Array<string>(maxSeqId + 1);
-            const labels = new Array<string[]>(maxSeqId + 1);
-            for (let i = 0; i < count; i++) {
-                sequenceArray[i] = '-';
-                labels[i] = [];
-            }
-
-            const compIds = new Array<string[]>(maxSeqId + 1);
-            for (let i = minSeqId; i <= maxSeqId; ++i) {
-                compIds[i] = [];
-            }
-
-            for (let i = 0, _i = this.seqId.rowCount; i < _i; i++) {
-                const seqId = this.seqId.value(i);
-                const idx = seqId - minSeqId;
-                const name = this.compId.value(i);
-                const code = this.codeFromName(name);
-                // in case of MICROHETEROGENEITY `sequenceArray[idx]` may already be set
-                if (!sequenceArray[idx] || sequenceArray[idx] === '-') {
-                    sequenceArray[idx] = code;
+                if (!indexMap.has(seq_id)) {
+                    indexMap.set(seq_id, idx);
+                    const comp_id = compId.value(i);
+                    compIds[idx] = comp_id;
+                    seqIds[idx] = seq_id;
+                    codes[idx] = codeFromName(comp_id);
+                    idx += 1;
+                } else {
+                    // micro-heterogeneity
+                    if (!microHet.has(seq_id)) {
+                        microHet.set(seq_id, [compIds[indexMap.get(seq_id)!], compId.value(i)]);
+                    } else {
+                        microHet.get(seq_id)!.push(compId.value(i));
+                    }
                 }
-                labels[idx].push(code === 'X' ? name : code);
-                compIds[seqId].push(name);
             }
 
-            const microHet = new Map();
-            for (let i = minSeqId; i <= maxSeqId; ++i) {
-                if (compIds[i].length > 1) microHet.set(i, compIds[i]);
+            const labels: string[] = [];
+            for (let i = 0, il = idx; i < il; ++i) {
+                const mh = microHet.get(seqIds[i]);
+                labels[i] = mh ? `(${mh.join('|')})` : codes[i];
             }
 
-            this._code = Column.ofStringArray(sequenceArray) as Column<Alphabet>;
-            this._label = Column.ofLambda({
-                value: i => {
-                    const l = labels[i];
-                    return l.length > 1 ? `(${l.join('|')})` : l.join('');
-                },
-                rowCount: labels.length,
-                schema: Column.Schema.str
-            });
-            this._microHet = microHet;
-            this._offset = minSeqId - 1;
-            this._length = count;
-        }
-
-        constructor(public kind: K, public compId: Column<string>, public seqId: Column<number>) {
-
-            this.codeFromName = codeProvider(kind);
+            this.length = idx;
+            this.code = Column.ofStringArray(codes) as Column<Alphabet>;
+            this.compId = Column.ofStringArray(compIds);
+            this.seqId = Column.ofIntArray(seqIds);
+            this.label = Column.ofStringArray(labels);
+            this.microHet = microHet;
+            this.indexMap = indexMap;
         }
     }
 
@@ -192,13 +151,17 @@ namespace Sequence {
     }
 
     class SequenceRangesImpl<K extends Kind, Alphabet extends string> implements Base<K, Alphabet> {
-        public offset: number
         public length: number
         public code: Column<Alphabet>
         public label: Column<string>
         public seqId: Column<number>
         public compId: Column<string>
-        public microHet: ReadonlyMap<number, string[]>
+        public microHet: ReadonlyMap<number, string[]> = new Map()
+
+        private minSeqId: number
+        index(seqId: number) {
+            return seqId - this.minSeqId;
+        }
 
         constructor(public kind: K, private seqIdStart: Column<number>, private seqIdEnd: Column<number>) {
             let maxSeqId = 0, minSeqId = Number.MAX_SAFE_INTEGER;
@@ -220,8 +183,8 @@ namespace Sequence {
             });
             this.compId = Column.ofConst('', count, Column.Schema.str);
 
-            this.offset = minSeqId - 1;
             this.length = count;
+            this.minSeqId = minSeqId;
         }
     }
 }

src/mol-model/structure.ts

@@ -9,5 +9,4 @@ export * from './structure/coordinates';
 export * from './structure/topology';
 export * from './structure/model';
 export * from './structure/structure';
-export * from './structure/query';
-export * from './structure/common/custom-property';
+export * from './structure/query';

src/mol-model/structure/export/mmcif.ts

@@ -15,7 +15,7 @@ import { _chem_comp, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './
 import { Model } from '../model';
 import { getUniqueEntityIndicesFromStructures, copy_mmCif_category, copy_source_mmCifCategory } from './categories/utils';
 import { _struct_asym, _entity_poly, _entity_poly_seq } from './categories/sequence';
-import { CustomPropertyDescriptor } from '../common/custom-property';
+import { CustomPropertyDescriptor } from '../../custom-property';
 import { atom_site_operator_mapping } from './categories/atom_site_operator_mapping';
 import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
 

src/mol-model/structure/model/model.ts

@@ -10,9 +10,9 @@ import StructureSequence from './properties/sequence';
 import { AtomicHierarchy, AtomicConformation, AtomicRanges } from './properties/atomic';
 import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
 import { Entities, ChemicalComponentMap, MissingResidues, StructAsymMap } from './properties/common';
-import { CustomProperties } from '../common/custom-property';
+import { CustomProperties } from '../../custom-property';
 import { SaccharideComponentMap } from '../structure/carbohydrates/constants';
-import { ModelFormat } from '../../../mol-model-formats/structure/format';
+import { ModelFormat } from '../../../mol-model-formats/format';
 import { calcModelCenter } from './util';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { Mutable } from '../../../mol-util/type-helpers';

src/mol-model/structure/structure/structure.ts

@@ -25,7 +25,7 @@ import { Vec3, Mat4 } from '../../../mol-math/linear-algebra';
 import { idFactory } from '../../../mol-util/id-factory';
 import { GridLookup3D } from '../../../mol-math/geometry';
 import { UUID } from '../../../mol-util';
-import { CustomProperties } from '../common/custom-property';
+import { CustomProperties } from '../../custom-property';
 import { AtomicHierarchy } from '../model/properties/atomic';
 import { StructureSelection } from '../query/selection';
 import { getBoundary } from '../../../mol-math/geometry/boundary';

src/mol-model/structure/structure/unit/bonds/intra-compute.ts

@@ -37,9 +37,11 @@ function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUni
 
     const { x, y, z } = unit.model.atomicConformation;
     const atomCount = unit.elements.length;
-    const { elements: atoms, residueIndex } = unit;
+    const { elements: atoms, residueIndex, chainIndex } = unit;
     const { type_symbol, label_atom_id, label_alt_id } = unit.model.atomicHierarchy.atoms;
-    const { label_comp_id } = unit.model.atomicHierarchy.residues;
+    const { label_comp_id, label_seq_id } = unit.model.atomicHierarchy.residues;
+    const { index } = unit.model.atomicHierarchy;
+    const { byEntityKey } = unit.model.sequence;
     const query3d = unit.lookup3d;
 
     const structConn = StructConn.Provider.get(unit.model);
@@ -101,7 +103,13 @@ function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUni
 
         if (!props.forceCompute && raI !== lastResidue) {
             if (!!component && component.entries.has(compId)) {
-                componentMap = component.entries.get(compId)!.map;
+                const entitySeq = byEntityKey[index.getEntityFromChain(chainIndex[aI])];
+                if (entitySeq && entitySeq.sequence.microHet.has(label_seq_id.value(raI))) {
+                    // compute for sequence positions with micro-heterogeneity
+                    componentMap = void 0;
+                } else {
+                    componentMap = component.entries.get(compId)!.map;
+                }
             } else {
                 componentMap = void 0;
             }

src/mol-model/structure/topology/topology.ts

@@ -7,7 +7,7 @@
 import { UUID } from '../../../mol-util';
 import { Column } from '../../../mol-data/db';
 import { BasicData } from '../../../mol-model-formats/structure/basic/schema';
-import { ModelFormat } from '../../../mol-model-formats/structure/format';
+import { ModelFormat } from '../../../mol-model-formats/format';
 
 export { Topology };
 

src/mol-model/volume.ts

@@ -1,7 +1,9 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-export * from './volume/data';
+export * from './volume/volume';
+export * from './volume/grid';

src/mol-model/volume/data.ts

@@ -1,93 +0,0 @@
-/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
-import { Tensor, Mat4, Vec3 } from '../../mol-math/linear-algebra';
-import { equalEps } from '../../mol-math/linear-algebra/3d/common';
-
-/** The basic unit cell that contains the data. */
-interface VolumeDataBase {
-    readonly label?: string,
-    readonly transform: { kind: 'spacegroup', cell: SpacegroupCell, fractionalBox: Box3D } | { kind: 'matrix', matrix: Mat4 },
-    readonly data: Tensor,
-    readonly dataStats: Readonly<{
-        min: number,
-        max: number,
-        mean: number,
-        sigma: number
-    }>
-}
-
-interface VolumeData extends VolumeDataBase {
-    readonly colorVolume?: VolumeDataBase
-}
-
-namespace VolumeData {
-    export const One: VolumeData = {
-        transform: { kind: 'matrix', matrix: Mat4.identity() },
-        data: Tensor.create(Tensor.Space([1, 1, 1], [0, 1, 2]), Tensor.Data1([0])),
-        dataStats: { min: 0, max: 0, mean: 0, sigma: 0 }
-    };
-
-    const _scale = Mat4.zero(), _translate = Mat4.zero();
-    export function getGridToCartesianTransform(volume: VolumeData) {
-        if (volume.transform.kind === 'matrix') {
-            return Mat4.copy(Mat4(), volume.transform.matrix);
-        }
-
-        if (volume.transform.kind === 'spacegroup') {
-            const { data: { space } } = volume;
-            const scale = Mat4.fromScaling(_scale, Vec3.div(Vec3.zero(), Box3D.size(Vec3.zero(), volume.transform.fractionalBox), Vec3.ofArray(space.dimensions)));
-            const translate = Mat4.fromTranslation(_translate, volume.transform.fractionalBox.min);
-            return Mat4.mul3(Mat4.zero(), volume.transform.cell.fromFractional, translate, scale);
-        }
-
-        return Mat4.identity();
-    }
-
-    export function areEquivalent(volA: VolumeData, volB: VolumeData) {
-        return volA === volB;
-    }
-}
-
-type VolumeIsoValue = VolumeIsoValue.Absolute | VolumeIsoValue.Relative
-
-namespace VolumeIsoValue {
-    export type Relative = Readonly<{ kind: 'relative', relativeValue: number }>
-    export type Absolute = Readonly<{ kind: 'absolute', absoluteValue: number }>
-
-    export function areSame(a: VolumeIsoValue, b: VolumeIsoValue, stats: VolumeData['dataStats']) {
-        return equalEps(toAbsolute(a, stats).absoluteValue, toAbsolute(b, stats).absoluteValue, stats.sigma / 100);
-    }
-
-    export function absolute(value: number): Absolute { return { kind: 'absolute', absoluteValue: value }; }
-    export function relative(value: number): Relative { return { kind: 'relative', relativeValue: value }; }
-
-    export function calcAbsolute(stats: VolumeData['dataStats'], relativeValue: number): number {
-        return relativeValue * stats.sigma + stats.mean;
-    }
-
-    export function calcRelative(stats: VolumeData['dataStats'], absoluteValue: number): number {
-        return stats.sigma === 0 ? 0 : ((absoluteValue - stats.mean) / stats.sigma);
-    }
-
-    export function toAbsolute(value: VolumeIsoValue, stats: VolumeData['dataStats']): Absolute {
-        return value.kind === 'absolute' ? value : { kind: 'absolute', absoluteValue: VolumeIsoValue.calcAbsolute(stats, value.relativeValue) };
-    }
-
-    export function toRelative(value: VolumeIsoValue, stats: VolumeData['dataStats']): Relative {
-        return value.kind === 'relative' ? value : { kind: 'relative', relativeValue: VolumeIsoValue.calcRelative(stats, value.absoluteValue) };
-    }
-
-    export function toString(value: VolumeIsoValue) {
-        return value.kind === 'relative'
-            ? `${value.relativeValue.toFixed(2)} σ`
-            : `${value.absoluteValue.toPrecision(4)}`;
-    }
-}
-
-export { VolumeData, VolumeIsoValue };

src/mol-model/volume/grid.ts

@@ -0,0 +1,57 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
+import { Tensor, Mat4, Vec3 } from '../../mol-math/linear-algebra';
+
+/** The basic unit cell that contains the grid data. */
+interface Grid {
+    readonly transform: Grid.Transform,
+    readonly cells: Tensor,
+    readonly stats: Readonly<{
+        min: number,
+        max: number,
+        mean: number,
+        sigma: number
+    }>
+}
+
+namespace Grid {
+    export const One: Grid = {
+        transform: { kind: 'matrix', matrix: Mat4.identity() },
+        cells: Tensor.create(Tensor.Space([1, 1, 1], [0, 1, 2]), Tensor.Data1([0])),
+        stats: { min: 0, max: 0, mean: 0, sigma: 0 },
+    };
+
+    export type Transform = { kind: 'spacegroup', cell: SpacegroupCell, fractionalBox: Box3D } | { kind: 'matrix', matrix: Mat4 }
+
+    const _scale = Mat4.zero(), _translate = Mat4.zero();
+    export function getGridToCartesianTransform(grid: Grid) {
+        if (grid.transform.kind === 'matrix') {
+            return Mat4.copy(Mat4(), grid.transform.matrix);
+        }
+
+        if (grid.transform.kind === 'spacegroup') {
+            const { cells: { space } } = grid;
+            const scale = Mat4.fromScaling(_scale, Vec3.div(Vec3.zero(), Box3D.size(Vec3.zero(), grid.transform.fractionalBox), Vec3.ofArray(space.dimensions)));
+            const translate = Mat4.fromTranslation(_translate, grid.transform.fractionalBox.min);
+            return Mat4.mul3(Mat4.zero(), grid.transform.cell.fromFractional, translate, scale);
+        }
+
+        return Mat4.identity();
+    }
+
+    export function areEquivalent(gridA: Grid, gridB: Grid) {
+        return gridA === gridB;
+    }
+
+    export function isEmpty(grid: Grid) {
+        return grid.cells.data.length === 0;
+    }
+}
+
+export { Grid };

src/mol-model/volume/volume.ts

@@ -4,26 +4,105 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { VolumeData, VolumeIsoValue } from './data';
+import { Grid } from './grid';
 import { OrderedSet } from '../../mol-data/int';
 import { Sphere3D } from '../../mol-math/geometry';
-import { Vec3 } from '../../mol-math/linear-algebra';
+import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
 import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
+import { CubeFormat } from '../../mol-model-formats/volume/cube';
+import { equalEps } from '../../mol-math/linear-algebra/3d/common';
+import { ModelFormat } from '../../mol-model-formats/format';
+import { CustomProperties } from '../custom-property';
+
+export interface Volume {
+    readonly label?: string
+    readonly grid: Grid
+    readonly sourceData: ModelFormat
+
+    // TODO use...
+    customProperties: CustomProperties
+
+    /**
+     * Not to be accessed directly, each custom property descriptor
+     * defines property accessors that use this field to store the data.
+     */
+    _propertyData: { [name: string]: any }
+
+    // TODO add as customProperty?
+    readonly colorVolume?: Volume
+}
 
 export namespace Volume {
     export type CellIndex = { readonly '@type': 'cell-index' } & number
 
-    export interface Loci { readonly kind: 'volume-loci', readonly volume: VolumeData }
-    export function Loci(volume: VolumeData): Loci { return { kind: 'volume-loci', volume }; }
+    export type IsoValue = IsoValue.Absolute | IsoValue.Relative
+
+    export namespace IsoValue {
+        export type Relative = Readonly<{ kind: 'relative', relativeValue: number }>
+        export type Absolute = Readonly<{ kind: 'absolute', absoluteValue: number }>
+
+        export function areSame(a: IsoValue, b: IsoValue, stats: Grid['stats']) {
+            return equalEps(toAbsolute(a, stats).absoluteValue, toAbsolute(b, stats).absoluteValue, stats.sigma / 100);
+        }
+
+        export function absolute(value: number): Absolute { return { kind: 'absolute', absoluteValue: value }; }
+        export function relative(value: number): Relative { return { kind: 'relative', relativeValue: value }; }
+
+        export function calcAbsolute(stats: Grid['stats'], relativeValue: number): number {
+            return relativeValue * stats.sigma + stats.mean;
+        }
+
+        export function calcRelative(stats: Grid['stats'], absoluteValue: number): number {
+            return stats.sigma === 0 ? 0 : ((absoluteValue - stats.mean) / stats.sigma);
+        }
+
+        export function toAbsolute(value: IsoValue, stats: Grid['stats']): Absolute {
+            return value.kind === 'absolute' ? value : { kind: 'absolute', absoluteValue: IsoValue.calcAbsolute(stats, value.relativeValue) };
+        }
+
+        export function toRelative(value: IsoValue, stats: Grid['stats']): Relative {
+            return value.kind === 'relative' ? value : { kind: 'relative', relativeValue: IsoValue.calcRelative(stats, value.absoluteValue) };
+        }
+
+        export function toString(value: IsoValue) {
+            return value.kind === 'relative'
+                ? `${value.relativeValue.toFixed(2)} σ`
+                : `${value.absoluteValue.toPrecision(4)}`;
+        }
+    }
+
+    export const One: Volume = {
+        label: '',
+        grid: Grid.One,
+        sourceData: { kind: '', name: '', data: {} },
+        customProperties: new CustomProperties(),
+        _propertyData: Object.create(null),
+    };
+
+    export function areEquivalent(volA: Volume, volB: Volume) {
+        return Grid.areEquivalent(volA.grid, volB.grid);
+    }
+
+    export function isEmpty(vol: Volume) {
+        return Grid.isEmpty(vol.grid);
+    }
+
+    export function isOrbitals(volume: Volume) {
+        if (!CubeFormat.is(volume.sourceData)) return false;
+        return volume.sourceData.data.header.orbitals;
+    }
+
+    export interface Loci { readonly kind: 'volume-loci', readonly volume: Volume }
+    export function Loci(volume: Volume): Loci { return { kind: 'volume-loci', volume }; }
     export function isLoci(x: any): x is Loci { return !!x && x.kind === 'volume-loci'; }
     export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume; }
-    export function isLociEmpty(loci: Loci) { return loci.volume.data.data.length === 0; }
+    export function isLociEmpty(loci: Loci) { return Grid.isEmpty(loci.volume.grid); }
 
-    export function getBoundingSphere(volume: VolumeData, boundingSphere?: Sphere3D) {
+    export function getBoundingSphere(volume: Volume, boundingSphere?: Sphere3D) {
         if (!boundingSphere) boundingSphere = Sphere3D();
 
-        const transform = VolumeData.getGridToCartesianTransform(volume);
-        const [x, y, z] = volume.data.space.dimensions;
+        const transform = Grid.getGridToCartesianTransform(volume.grid);
+        const [x, y, z] = volume.grid.cells.space.dimensions;
 
         const cpA = Vec3.create(0, 0, 0); Vec3.transformMat4(cpA, cpA, transform);
         const cpB = Vec3.create(x, y, z); Vec3.transformMat4(cpB, cpB, transform);
@@ -46,31 +125,31 @@ export namespace Volume {
     }
 
     export namespace Isosurface {
-        export interface Loci { readonly kind: 'isosurface-loci', readonly volume: VolumeData, readonly isoValue: VolumeIsoValue }
-        export function Loci(volume: VolumeData, isoValue: VolumeIsoValue): Loci { return { kind: 'isosurface-loci', volume, isoValue }; }
+        export interface Loci { readonly kind: 'isosurface-loci', readonly volume: Volume, readonly isoValue: Volume.IsoValue }
+        export function Loci(volume: Volume, isoValue: Volume.IsoValue): Loci { return { kind: 'isosurface-loci', volume, isoValue }; }
         export function isLoci(x: any): x is Loci { return !!x && x.kind === 'isosurface-loci'; }
-        export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume && VolumeIsoValue.areSame(a.isoValue, b.isoValue, a.volume.dataStats); }
-        export function isLociEmpty(loci: Loci) { return loci.volume.data.data.length === 0; }
+        export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume && Volume.IsoValue.areSame(a.isoValue, b.isoValue, a.volume.grid.stats); }
+        export function isLociEmpty(loci: Loci) { return loci.volume.grid.cells.data.length === 0; }
 
-        export function getBoundingSphere(volume: VolumeData, isoValue: VolumeIsoValue, boundingSphere?: Sphere3D) {
+        export function getBoundingSphere(volume: Volume, isoValue: Volume.IsoValue, boundingSphere?: Sphere3D) {
             // TODO get bounding sphere for subgrid with values >= isoValue
             return Volume.getBoundingSphere(volume, boundingSphere);
         }
     }
 
     export namespace Cell {
-        export interface Loci { readonly kind: 'cell-loci', readonly volume: VolumeData, readonly indices: OrderedSet<CellIndex> }
-        export function Loci(volume: VolumeData, indices: OrderedSet<CellIndex>): Loci { return { kind: 'cell-loci', volume, indices }; }
+        export interface Loci { readonly kind: 'cell-loci', readonly volume: Volume, readonly indices: OrderedSet<CellIndex> }
+        export function Loci(volume: Volume, indices: OrderedSet<CellIndex>): Loci { return { kind: 'cell-loci', volume, indices }; }
         export function isLoci(x: any): x is Loci { return !!x && x.kind === 'cell-loci'; }
         export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume && OrderedSet.areEqual(a.indices, b.indices); }
         export function isLociEmpty(loci: Loci) { return OrderedSet.size(loci.indices) === 0; }
 
         const boundaryHelper = new BoundaryHelper('98');
         const tmpBoundaryPos = Vec3();
-        export function getBoundingSphere(volume: VolumeData, indices: OrderedSet<CellIndex>, boundingSphere?: Sphere3D) {
+        export function getBoundingSphere(volume: Volume, indices: OrderedSet<CellIndex>, boundingSphere?: Sphere3D) {
             boundaryHelper.reset();
-            const transform = VolumeData.getGridToCartesianTransform(volume);
-            const { getCoords } = volume.data.space;
+            const transform = Grid.getGridToCartesianTransform(volume.grid);
+            const { getCoords } = volume.grid.cells.space;
 
             for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
                 const o = OrderedSet.getAt(indices, i);
@@ -86,7 +165,8 @@ export namespace Volume {
                 boundaryHelper.radiusPosition(tmpBoundaryPos);
             }
 
-            return boundaryHelper.getSphere(boundingSphere);
+            const bs = boundaryHelper.getSphere(boundingSphere);
+            return Sphere3D.expand(bs, bs, Mat4.getMaxScaleOnAxis(transform) * 10);
         }
     }
 }

src/mol-plugin-state/actions/structure.ts

@@ -17,6 +17,7 @@ import { StateTransforms } from '../transforms';
 import { Download } from '../transforms/data';
 import { CustomModelProperties, CustomStructureProperties, TrajectoryFromModelAndCoordinates } from '../transforms/model';
 import { Asset } from '../../mol-util/assets';
+import { PluginConfig } from '../../mol-plugin/config';
 
 const DownloadModelRepresentationOptions = (plugin: PluginContext) => PD.Group({
     type: RootStructureDefinition.getParams(void 0, 'auto').type,
@@ -26,6 +27,16 @@ const DownloadModelRepresentationOptions = (plugin: PluginContext) => PD.Group({
     asTrajectory: PD.Optional(PD.Boolean(false, { description: 'Load all entries into a single trajectory.' }))
 }, { isExpanded: false });
 
+export const PdbDownloadProvider = {
+    'rcsb': PD.Group({
+        encoding: PD.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']] as ['cif' | 'bcif', string][]),
+    }, { label: 'RCSB PDB', isFlat: true }),
+    'pdbe': PD.Group({
+        variant: PD.Select('updated-bcif', [['updated-bcif', 'Updated (bcif)'], ['updated', 'Updated'], ['archival', 'Archival']] as ['updated' | 'archival', string][]),
+    }, { label: 'PDBe', isFlat: true }),
+};
+export type PdbDownloadProvider = keyof typeof PdbDownloadProvider;
+
 export { DownloadStructure };
 type DownloadStructure = typeof DownloadStructure
 const DownloadStructure = StateAction.build({
@@ -33,19 +44,13 @@ const DownloadStructure = StateAction.build({
     display: { name: 'Download Structure', description: 'Load a structure from the provided source and create its representation.' },
     params: (_, plugin: PluginContext) => {
         const options = DownloadModelRepresentationOptions(plugin);
+        const defaultPdbProvider = plugin.config.get(PluginConfig.Download.DefaultPdbProvider) || 'pdbe';
         return {
             source: PD.MappedStatic('pdb', {
                 'pdb': PD.Group({
                     provider: PD.Group({
                         id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma/space separated PDB ids.' }),
-                        server: PD.MappedStatic('pdbe', {
-                            'rcsb': PD.Group({
-                                encoding: PD.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']] as ['cif' | 'bcif', string][]),
-                            }, { label: 'RCSB PDB', isFlat: true }),
-                            'pdbe': PD.Group({
-                                variant: PD.Select('updated-bcif', [['updated-bcif', 'Updated (bcif)'], ['updated', 'Updated'], ['archival', 'Archival']] as ['updated' | 'archival', string][]),
-                            }, { label: 'PDBe', isFlat: true }),
-                        }),
+                        server: PD.MappedStatic(defaultPdbProvider, PdbDownloadProvider),
                     }, { pivot: 'id' }),
                     options
                 }, { isFlat: true, label: 'PDB' }),

src/mol-plugin-state/actions/volume.ts

@@ -16,6 +16,8 @@ import { DataFormatProvider } from '../formats/provider';
 import { Asset } from '../../mol-util/assets';
 import { StateTransforms } from '../transforms';
 
+export type EmdbDownloadProvider = 'pdbe' | 'rcsb'
+
 export { DownloadDensity };
 type DownloadDensity = typeof DownloadDensity
 const DownloadDensity = StateAction.build({
@@ -42,7 +44,7 @@ const DownloadDensity = StateAction.build({
                 'pdb-emd-ds': PD.Group({
                     provider: PD.Group({
                         id: PD.Text('emd-8004', { label: 'Id' }),
-                        server: PD.Select('pdbe', [['pdbe', 'PDBe'], ['rcsb', 'RCSB PDB']]),
+                        server: PD.Select<EmdbDownloadProvider>('pdbe', [['pdbe', 'PDBe'], ['rcsb', 'RCSB PDB']]),
                     }, { pivot: 'id' }),
                     detail: PD.Numeric(3, { min: 0, max: 10, step: 1 }, { label: 'Detail' }),
                 }, { isFlat: true }),

src/mol-plugin-state/builder/structure/representation-preset.ts

@@ -237,7 +237,13 @@ const atomicDetail = StructureRepresentationPresetProvider({
 
         const components = {
             all: await presetStaticComponent(plugin, structureCell, 'all'),
+            branched: undefined
         };
+        if (params.showCarbohydrateSymbol) {
+            Object.assign(components, {
+                branched: await presetStaticComponent(plugin, structureCell, 'branched', { label: 'Carbohydrate' }),
+            });
+        }
 
         const { update, builder, typeParams, color } = reprBuilder(plugin, params);
         const representations = {
@@ -245,7 +251,7 @@ const atomicDetail = StructureRepresentationPresetProvider({
         };
         if (params.showCarbohydrateSymbol) {
             Object.assign(representations, {
-                snfg3d: builder.buildRepresentation(update, components.all, { type: 'carbohydrate', typeParams: { ...typeParams, alpha: 0.4, visuals: ['carbohydrate-symbol'] }, color }, { tag: 'snfg-3d' }),
+                snfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams: { ...typeParams, alpha: 0.4, visuals: ['carbohydrate-symbol'] }, color }, { tag: 'snfg-3d' }),
             });
         }
 

src/mol-plugin-state/component.ts

@@ -7,6 +7,7 @@
 import { shallowMergeArray } from '../mol-util/object';
 import { RxEventHelper } from '../mol-util/rx-event-helper';
 import { Subscription, Observable } from 'rxjs';
+import { arraySetRemove } from '../mol-util/array';
 
 export class PluginComponent {
     private _ev: RxEventHelper | undefined;
@@ -14,7 +15,18 @@ export class PluginComponent {
 
     protected subscribe<T>(obs: Observable<T>, action: (v: T) => void) {
         if (typeof this.subs === 'undefined') this.subs = [];
-        this.subs.push(obs.subscribe(action));
+
+        let sub: Subscription | undefined = obs.subscribe(action);
+        this.subs.push(sub);
+
+        return {
+            unsubscribe: () => {
+                if (sub && this.subs && arraySetRemove(this.subs, sub)) {
+                    sub.unsubscribe();
+                    sub = void 0;
+                }
+            }
+        };
     }
 
     protected get ev() {

src/mol-plugin-state/formats/trajectory.ts

@@ -114,14 +114,22 @@ export const Provider3dg: TrajectoryFormatProvider = {
 };
 
 export const MolProvider: TrajectoryFormatProvider = {
-    label: 'MOL',
-    description: 'MOL',
+    label: 'MOL/SDF',
+    description: 'MOL/SDF',
     category: Category,
-    stringExtensions: ['mol', 'sdf'],
+    stringExtensions: ['mol', 'sdf', 'sd'],
     parse: directTrajectory(StateTransforms.Model.TrajectoryFromMOL),
     visuals: defaultVisuals
 };
 
+export const Mol2Provider: TrajectoryFormatProvider = {
+    label: 'MOL2',
+    description: 'MOL2',
+    category: Category,
+    stringExtensions: ['mol2'],
+    parse: directTrajectory(StateTransforms.Model.TrajectoryFromMOL2),
+    visuals: defaultVisuals
+};
 
 export const BuiltInTrajectoryFormats = [
     ['mmcif', MmcifProvider] as const,
@@ -129,7 +137,8 @@ export const BuiltInTrajectoryFormats = [
     ['pdb', PdbProvider] as const,
     ['gro', GroProvider] as const,
     ['3dg', Provider3dg] as const,
-    ['mol', MolProvider] as const
+    ['mol', MolProvider] as const,
+    ['mol2', Mol2Provider] as const,
 ] as const;
 
 export type BuiltInTrajectoryFormat = (typeof BuiltInTrajectoryFormats)[number][0]

src/mol-plugin-state/formats/volume.ts

@@ -12,7 +12,7 @@ import { StateObjectSelector } from '../../mol-state';
 import { PluginStateObject } from '../objects';
 import { VolumeRepresentation3DHelpers } from '../transforms/representation';
 import { ColorNames } from '../../mol-util/color/names';
-import { VolumeIsoValue } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
 import { createVolumeRepresentationParams } from '../helpers/volume-representation-params';
 import { objectForEach } from '../../mol-util/object';
 
@@ -104,30 +104,41 @@ export const CubeProvider = DataFormatProvider({
     visuals: async (plugin: PluginContext, data: { volume: StateObjectSelector<PluginStateObject.Volume.Data>, structure: StateObjectSelector<PluginStateObject.Molecule.Structure> }) => {
         const surfaces = plugin.build();
 
+        const volumeReprs: StateObjectSelector<PluginStateObject.Volume.Representation3D>[] = [];
         const volumeData = data.volume.cell?.obj?.data;
-        const volumePos = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
-            type: 'isosurface',
-            typeParams: { isoValue: VolumeIsoValue.relative(1), alpha: 0.4 },
-            color: 'uniform',
-            colorParams: { value: ColorNames.blue }
-        }));
-        const volumeNeg = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
-            type: 'isosurface',
-            typeParams: { isoValue: VolumeIsoValue.relative(-1), alpha: 0.4 },
-            color: 'uniform',
-            colorParams: { value: ColorNames.red }
-        }));
+        if (volumeData && Volume.isOrbitals(volumeData)) {
+            const volumePos = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
+                type: 'isosurface',
+                typeParams: { isoValue: Volume.IsoValue.relative(1), alpha: 0.4 },
+                color: 'uniform',
+                colorParams: { value: ColorNames.blue }
+            }));
+            const volumeNeg = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
+                type: 'isosurface',
+                typeParams: { isoValue: Volume.IsoValue.relative(-1), alpha: 0.4 },
+                color: 'uniform',
+                colorParams: { value: ColorNames.red }
+            }));
+            volumeReprs.push(volumePos.selector, volumeNeg.selector);
+        } else {
+            const volume = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
+                type: 'isosurface',
+                typeParams: { isoValue: Volume.IsoValue.relative(2), alpha: 0.4 },
+                color: 'uniform',
+                colorParams: { value: ColorNames.grey }
+            }));
+            volumeReprs.push(volume.selector);
+        }
 
         const structure = await plugin.builders.structure.representation.applyPreset(data.structure, 'auto');
         await surfaces.commit();
 
         const structureReprs: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D>[] = [];
-
         objectForEach(structure?.representations as any, (r: any) => {
             if (r) structureReprs.push(r);
         });
 
-        return [volumePos.selector, volumeNeg.selector, ...structureReprs];
+        return [...volumeReprs, ...structureReprs];
     }
 });
 
@@ -164,13 +175,13 @@ export const DscifProvider = DataFormatProvider({
         if (volumes.length > 0) {
             visuals[0] = tree
                 .to(volumes[0])
-                .apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 0.3 }, 'uniform', { value: ColorNames.teal }))
+                .apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: Volume.IsoValue.relative(1.5), alpha: 1 }, 'uniform', { value: ColorNames.teal }))
                 .selector;
         }
 
         if (volumes.length > 1) {
-            const posParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(3), alpha: 0.3 }, 'uniform', { value: ColorNames.green });
-            const negParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(-3), alpha: 0.3 }, 'uniform', { value: ColorNames.red });
+            const posParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: Volume.IsoValue.relative(3), alpha: 0.3 }, 'uniform', { value: ColorNames.green });
+            const negParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: Volume.IsoValue.relative(-3), alpha: 0.3 }, 'uniform', { value: ColorNames.red });
             visuals[visuals.length] = tree.to(volumes[1]).apply(StateTransforms.Representation.VolumeRepresentation3D, posParams).selector;
             visuals[visuals.length] = tree.to(volumes[1]).apply(StateTransforms.Representation.VolumeRepresentation3D, negParams).selector;
         }

src/mol-plugin-state/helpers/structure-selection-query.ts

@@ -394,63 +394,68 @@ const wholeResidues = StructureSelectionQuery('Whole Residues of Selection', MS.
 });
 
 const StandardAminoAcids = [
-    [['HIS'], 'HISTIDINE'],
-    [['ARG'], 'ARGININE'],
-    [['LYS'], 'LYSINE'],
-    [['ILE'], 'ISOLEUCINE'],
-    [['PHE'], 'PHENYLALANINE'],
-    [['LEU'], 'LEUCINE'],
-    [['TRP'], 'TRYPTOPHAN'],
-    [['ALA'], 'ALANINE'],
-    [['MET'], 'METHIONINE'],
-    [['PRO'], 'PROLINE'],
-    [['CYS'], 'CYSTEINE'],
-    [['ASN'], 'ASPARAGINE'],
-    [['VAL'], 'VALINE'],
-    [['GLY'], 'GLYCINE'],
-    [['SER'], 'SERINE'],
-    [['GLN'], 'GLUTAMINE'],
-    [['TYR'], 'TYROSINE'],
-    [['ASP'], 'ASPARTIC ACID'],
-    [['GLU'], 'GLUTAMIC ACID'],
-    [['THR'], 'THREONINE'],
-    [['SEC'], 'SELENOCYSTEINE'],
-    [['PYL'], 'PYRROLYSINE'],
-    [['UNK'], 'UNKNOWN'],
+    [['HIS'], 'Histidine'],
+    [['ARG'], 'Arginine'],
+    [['LYS'], 'Lysine'],
+    [['ILE'], 'Isoleucine'],
+    [['PHE'], 'Phenylalanine'],
+    [['LEU'], 'Leucine'],
+    [['TRP'], 'Tryptophan'],
+    [['ALA'], 'Alanine'],
+    [['MET'], 'Methionine'],
+    [['PRO'], 'Proline'],
+    [['CYS'], 'Cysteine'],
+    [['ASN'], 'Asparagine'],
+    [['VAL'], 'Valine'],
+    [['GLY'], 'Glycine'],
+    [['SER'], 'Serine'],
+    [['GLN'], 'Glutamine'],
+    [['TYR'], 'Tyrosine'],
+    [['ASP'], 'Aspartic Acid'],
+    [['GLU'], 'Glutamic Acid'],
+    [['THR'], 'Threonine'],
+    [['SEC'], 'Selenocysteine'],
+    [['PYL'], 'Pyrrolysine'],
+    [['UNK'], 'Unknown'],
 ].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0) as [string[], string][];
 
 const StandardNucleicBases = [
-    [['A', 'DA'], 'ADENOSINE'],
-    [['C', 'DC'], 'CYTIDINE'],
-    [['T', 'DT'], 'THYMIDINE'],
-    [['G', 'DG'], 'GUANOSINE'],
-    [['I', 'DI'], 'INOSINE'],
-    [['U', 'DU'], 'URIDINE'],
-    [['N', 'DN'], 'UNKNOWN'],
+    [['A', 'DA'], 'Adenosine'],
+    [['C', 'DC'], 'Cytidine'],
+    [['T', 'DT'], 'Thymidine'],
+    [['G', 'DG'], 'Guanosine'],
+    [['I', 'DI'], 'Inosine'],
+    [['U', 'DU'], 'Uridine'],
+    [['N', 'DN'], 'Unknown'],
 ].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0) as [string[], string][];
 
 export function ResidueQuery([names, label]: [string[], string], category: string, priority = 0) {
-    return StructureSelectionQuery(`${label} (${names.join(', ')})`, MS.struct.modifier.union([
+    const description = names.length === 1 && !StandardResidues.has(names[0])
+        ? `[${names[0]}] ${label}`
+        : `${label} (${names.join(', ')})`;
+    return StructureSelectionQuery(description, MS.struct.modifier.union([
         MS.struct.generator.atomGroups({
             'residue-test': MS.core.set.has([MS.set(...names), MS.ammp('auth_comp_id')])
         })
-    ]), { category, priority, description: label });
+    ]), { category, priority, description });
 }
 
 export function ElementSymbolQuery([names, label]: [string[], string], category: string, priority: number) {
-    return StructureSelectionQuery(`${label} (${names.join(', ')})`, MS.struct.modifier.union([
+    const description = `${label} (${names.join(', ')})`;
+    return StructureSelectionQuery(description, MS.struct.modifier.union([
         MS.struct.generator.atomGroups({
             'atom-test': MS.core.set.has([MS.set(...names), MS.acp('elementSymbol')])
         })
-    ]), { category, priority });
+    ]), { category, priority, description });
 }
 
-export function EntityDescriptionQuery([description, label]: [string[], string], category: string, priority: number) {
+export function EntityDescriptionQuery([names, label]: [string[], string], category: string, priority: number) {
+    const description = `${label}`;
     return StructureSelectionQuery(`${label}`, MS.struct.modifier.union([
         MS.struct.generator.atomGroups({
-            'entity-test': MS.core.list.equal([MS.list(...description), MS.ammp('entityDescription')])
+            'entity-test': MS.core.list.equal([MS.list(...names), MS.ammp('entityDescription')])
         })
-    ]), { category, priority, description: description.join(', ') });
+    ]), { category, priority, description });
 }
 
 const StandardResidues = SetUtils.unionMany(

src/mol-plugin-state/helpers/volume-representation-params.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { VolumeData } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
 import { PluginContext } from '../../mol-plugin/context';
 import { RepresentationProvider } from '../../mol-repr/representation';
 import { VolumeRepresentationRegistry } from '../../mol-repr/volume/registry';
@@ -30,7 +30,7 @@ export interface VolumeRepresentationBuiltInProps<
 }
 
 export interface VolumeRepresentationProps<
-    R extends RepresentationProvider<VolumeData> = RepresentationProvider<VolumeData>,
+    R extends RepresentationProvider<Volume> = RepresentationProvider<Volume>,
     C extends ColorTheme.Provider = ColorTheme.Provider,
     S extends SizeTheme.Provider = SizeTheme.Provider> {
     type?: R,
@@ -41,43 +41,43 @@ export interface VolumeRepresentationProps<
     sizeParams?: Partial<SizeTheme.ParamValues<S>>
 }
 
-export function createVolumeRepresentationParams<R extends VolumeRepresentationRegistry.BuiltIn, C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(ctx: PluginContext, volume?: VolumeData, props?: VolumeRepresentationBuiltInProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
-export function createVolumeRepresentationParams<R extends RepresentationProvider<VolumeData>, C extends ColorTheme.Provider, S extends SizeTheme.Provider>(ctx: PluginContext, volume?: VolumeData, props?: VolumeRepresentationProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
-export function createVolumeRepresentationParams(ctx: PluginContext, volume?: VolumeData, props: any = {}): StateTransformer.Params<VolumeRepresentation3D>  {
+export function createVolumeRepresentationParams<R extends VolumeRepresentationRegistry.BuiltIn, C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(ctx: PluginContext, volume?: Volume, props?: VolumeRepresentationBuiltInProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
+export function createVolumeRepresentationParams<R extends RepresentationProvider<Volume>, C extends ColorTheme.Provider, S extends SizeTheme.Provider>(ctx: PluginContext, volume?: Volume, props?: VolumeRepresentationProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
+export function createVolumeRepresentationParams(ctx: PluginContext, volume?: Volume, props: any = {}): StateTransformer.Params<VolumeRepresentation3D>  {
     const p = props as VolumeRepresentationBuiltInProps;
-    if (typeof p.type === 'string' || typeof p.color === 'string' || typeof p.size === 'string') return createParamsByName(ctx, volume || VolumeData.One, props);
-    return createParamsProvider(ctx, volume || VolumeData.One, props);
+    if (typeof p.type === 'string' || typeof p.color === 'string' || typeof p.size === 'string') return createParamsByName(ctx, volume || Volume.One, props);
+    return createParamsProvider(ctx, volume || Volume.One, props);
 }
 
-export function getVolumeThemeTypes(ctx: PluginContext, volume?: VolumeData) {
+export function getVolumeThemeTypes(ctx: PluginContext, volume?: Volume) {
     const { themes: themeCtx } = ctx.representation.volume;
     if (!volume) return themeCtx.colorThemeRegistry.types;
     return themeCtx.colorThemeRegistry.getApplicableTypes({ volume });
 }
 
-export function createVolumeColorThemeParams<T extends ColorTheme.BuiltIn>(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName: T, params?: ColorTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
-export function createVolumeColorThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
-export function createVolumeColorThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme'] {
+export function createVolumeColorThemeParams<T extends ColorTheme.BuiltIn>(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName: T, params?: ColorTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
+export function createVolumeColorThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
+export function createVolumeColorThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme'] {
     const { registry, themes } = ctx.representation.volume;
     const repr = registry.get(typeName || registry.default.name);
     const color = themes.colorThemeRegistry.get(themeName || repr.defaultColorTheme.name);
-    const colorDefaultParams = PD.getDefaultValues(color.getParams({ volume: volume || VolumeData.One }));
+    const colorDefaultParams = PD.getDefaultValues(color.getParams({ volume: volume || Volume.One }));
     if (color.name === repr.defaultColorTheme.name) Object.assign(colorDefaultParams, repr.defaultColorTheme.props);
     return { name: color.name, params: Object.assign(colorDefaultParams, params) };
 }
 
-export function createVolumeSizeThemeParams<T extends SizeTheme.BuiltIn>(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName: T, params?: SizeTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
-export function createVolumeSizeThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
-export function createVolumeSizeThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme'] {
+export function createVolumeSizeThemeParams<T extends SizeTheme.BuiltIn>(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName: T, params?: SizeTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
+export function createVolumeSizeThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
+export function createVolumeSizeThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme'] {
     const { registry, themes } = ctx.representation.volume;
     const repr = registry.get(typeName || registry.default.name);
     const size = themes.sizeThemeRegistry.get(themeName || repr.defaultSizeTheme.name);
-    const sizeDefaultParams = PD.getDefaultValues(size.getParams({ volume: volume || VolumeData.One }));
+    const sizeDefaultParams = PD.getDefaultValues(size.getParams({ volume: volume || Volume.One }));
     if (size.name === repr.defaultSizeTheme.name) Object.assign(sizeDefaultParams, repr.defaultSizeTheme.props);
     return { name: size.name, params: Object.assign(sizeDefaultParams, params) };
 }
 
-function createParamsByName(ctx: PluginContext, volume: VolumeData, props: VolumeRepresentationBuiltInProps): StateTransformer.Params<VolumeRepresentation3D> {
+function createParamsByName(ctx: PluginContext, volume: Volume, props: VolumeRepresentationBuiltInProps): StateTransformer.Params<VolumeRepresentation3D> {
     const typeProvider = (props.type && ctx.representation.volume.registry.get(props.type))
         || ctx.representation.volume.registry.default.provider;
     const colorProvider = (props.color && ctx.representation.volume.themes.colorThemeRegistry.get(props.color))
@@ -95,7 +95,7 @@ function createParamsByName(ctx: PluginContext, volume: VolumeData, props: Volum
     });
 }
 
-function createParamsProvider(ctx: PluginContext, volume: VolumeData, props: VolumeRepresentationProps = {}): StateTransformer.Params<VolumeRepresentation3D> {
+function createParamsProvider(ctx: PluginContext, volume: Volume, props: VolumeRepresentationProps = {}): StateTransformer.Params<VolumeRepresentation3D> {
     const { themes: themeCtx } = ctx.representation.volume;
     const themeDataCtx = { volume };
 

src/mol-plugin-state/manager/animation.ts

@@ -44,6 +44,7 @@ class PluginAnimationManager extends StatefulPluginComponent<PluginAnimationMana
     }
 
     updateParams(newParams: Partial<PluginAnimationManager.State['params']>) {
+        if (this.isEmpty) return;
         this.updateState({ params: { ...this.state.params, ...newParams } });
         const anim = this.map.get(this.state.params.current)!;
         const params = anim.params(this.context) as PD.Params;
@@ -59,6 +60,7 @@ class PluginAnimationManager extends StatefulPluginComponent<PluginAnimationMana
     }
 
     updateCurrentParams(values: any) {
+        if (this.isEmpty) return;
         this._current.paramValues = { ...this._current.paramValues, ...values };
         this.triggerUpdate();
     }
@@ -163,6 +165,7 @@ class PluginAnimationManager extends StatefulPluginComponent<PluginAnimationMana
     }
 
     setSnapshot(snapshot: PluginAnimationManager.Snapshot) {
+        if (this.isEmpty) return;
         this.updateState({ animationState: snapshot.state.animationState });
         this.updateParams(snapshot.state.params);
 

src/mol-plugin-state/manager/snapshots.ts

@@ -132,7 +132,7 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
     async setStateSnapshot(snapshot: PluginStateSnapshotManager.StateSnapshot): Promise<PluginState.Snapshot | undefined> {
         if (snapshot.version !== PLUGIN_VERSION) {
             // TODO
-            console.warn('state snapshot version mismatch');
+            // console.warn('state snapshot version mismatch');
         }
 
         this.clear();

src/mol-plugin-state/manager/structure/measurement.ts

@@ -37,6 +37,12 @@ export interface StructureMeasurementManagerState {
     options: StructureMeasurementOptions
 }
 
+type StructureMeasurementManagerAddOptions = {
+    customText?: string,
+    selectionTags?: string | string[],
+    reprTags?: string | string[]
+}
+
 class StructureMeasurementManager extends StatefulPluginComponent<StructureMeasurementManagerState>  {
     readonly behaviors = {
         state: this.ev.behavior(this.state)
@@ -80,7 +86,7 @@ class StructureMeasurementManager extends StatefulPluginComponent<StructureMeasu
         await PluginCommands.State.Update(this.plugin, { state: this.plugin.state.data, tree: update, options: { doNotLogTiming: true } });
     }
 
-    async addDistance(a: StructureElement.Loci, b: StructureElement.Loci) {
+    async addDistance(a: StructureElement.Loci, b: StructureElement.Loci, options?: StructureMeasurementManagerAddOptions) {
         const cellA = this.plugin.helpers.substructureParent.get(a.structure);
         const cellB = this.plugin.helpers.substructureParent.get(b.structure);
 
@@ -98,17 +104,18 @@ class StructureMeasurementManager extends StatefulPluginComponent<StructureMeasu
                 ],
                 isTransitive: true,
                 label: 'Distance'
-            }, { dependsOn })
+            }, { dependsOn, tags: options?.selectionTags })
             .apply(StateTransforms.Representation.StructureSelectionsDistance3D, {
+                customText: options?.customText || '',
                 unitLabel: this.state.options.distanceUnitLabel,
                 textColor: this.state.options.textColor
-            });
+            }, { tags: options?.reprTags });
 
         const state = this.plugin.state.data;
         await PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotLogTiming: true } });
     }
 
-    async addAngle(a: StructureElement.Loci, b: StructureElement.Loci, c: StructureElement.Loci) {
+    async addAngle(a: StructureElement.Loci, b: StructureElement.Loci, c: StructureElement.Loci, options?: StructureMeasurementManagerAddOptions) {
         const cellA = this.plugin.helpers.substructureParent.get(a.structure);
         const cellB = this.plugin.helpers.substructureParent.get(b.structure);
         const cellC = this.plugin.helpers.substructureParent.get(c.structure);
@@ -129,16 +136,17 @@ class StructureMeasurementManager extends StatefulPluginComponent<StructureMeasu
                 ],
                 isTransitive: true,
                 label: 'Angle'
-            }, { dependsOn })
+            }, { dependsOn, tags: options?.selectionTags })
             .apply(StateTransforms.Representation.StructureSelectionsAngle3D, {
+                customText: options?.customText || '',
                 textColor: this.state.options.textColor
-            });
+            }, { tags: options?.reprTags });
 
         const state = this.plugin.state.data;
         await PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotLogTiming: true } });
     }
 
-    async addDihedral(a: StructureElement.Loci, b: StructureElement.Loci, c: StructureElement.Loci, d: StructureElement.Loci) {
+    async addDihedral(a: StructureElement.Loci, b: StructureElement.Loci, c: StructureElement.Loci, d: StructureElement.Loci, options?: StructureMeasurementManagerAddOptions) {
         const cellA = this.plugin.helpers.substructureParent.get(a.structure);
         const cellB = this.plugin.helpers.substructureParent.get(b.structure);
         const cellC = this.plugin.helpers.substructureParent.get(c.structure);
@@ -162,16 +170,17 @@ class StructureMeasurementManager extends StatefulPluginComponent<StructureMeasu
                 ],
                 isTransitive: true,
                 label: 'Dihedral'
-            }, { dependsOn })
+            }, { dependsOn, tags: options?.selectionTags })
             .apply(StateTransforms.Representation.StructureSelectionsDihedral3D, {
+                customText: options?.customText || '',
                 textColor: this.state.options.textColor
-            });
+            }, { tags: options?.reprTags });
 
         const state = this.plugin.state.data;
         await PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotLogTiming: true } });
     }
 
-    async addLabel(a: StructureElement.Loci) {
+    async addLabel(a: StructureElement.Loci, options?: Omit<StructureMeasurementManagerAddOptions, 'customText'>) {
         const cellA = this.plugin.helpers.substructureParent.get(a.structure);
 
         if (!cellA) return;
@@ -186,10 +195,10 @@ class StructureMeasurementManager extends StatefulPluginComponent<StructureMeasu
                 ],
                 isTransitive: true,
                 label: 'Label'
-            }, { dependsOn })
+            }, { dependsOn, tags: options?.selectionTags })
             .apply(StateTransforms.Representation.StructureSelectionsLabel3D, {
                 textColor: this.state.options.textColor
-            });
+            }, { tags: options?.reprTags });
 
         const state = this.plugin.state.data;
         await PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotLogTiming: true } });

src/mol-plugin-state/objects.ts

@@ -14,7 +14,7 @@ import { PlyFile } from '../mol-io/reader/ply/schema';
 import { PsfFile } from '../mol-io/reader/psf/parser';
 import { ShapeProvider } from '../mol-model/shape/provider';
 import { Coordinates as _Coordinates, Model as _Model, Structure as _Structure, StructureElement, Topology as _Topology } from '../mol-model/structure';
-import { VolumeData } from '../mol-model/volume';
+import { Volume as _Volume } from '../mol-model/volume';
 import { PluginBehavior } from '../mol-plugin/behavior/behavior';
 import { Representation } from '../mol-repr/representation';
 import { ShapeRepresentation } from '../mol-repr/shape/representation';
@@ -121,7 +121,7 @@ export namespace PluginStateObject {
     }
 
     export namespace Volume {
-        export class Data extends Create<VolumeData>({ name: 'Volume Data', typeClass: 'Object' }) { }
+        export class Data extends Create<_Volume>({ name: 'Volume', typeClass: 'Object' }) { }
         export class Representation3D extends CreateRepresentation3D<VolumeRepresentation<any>>({ name: 'Volume 3D' }) { }
     }
 

src/mol-plugin-state/transforms/model.ts

@@ -35,6 +35,8 @@ import { parseMol } from '../../mol-io/reader/mol/parser';
 import { trajectoryFromMol } from '../../mol-model-formats/structure/mol';
 import { trajectoryFromCifCore } from '../../mol-model-formats/structure/cif-core';
 import { trajectoryFromCube } from '../../mol-model-formats/structure/cube';
+import { parseMol2 } from '../../mol-io/reader/mol2/parser';
+import { trajectoryFromMol2 } from '../../mol-model-formats/structure/mol2';
 
 export { CoordinatesFromDcd };
 export { TopologyFromPsf };
@@ -44,6 +46,7 @@ export { TrajectoryFromMmCif };
 export { TrajectoryFromPDB };
 export { TrajectoryFromGRO };
 export { TrajectoryFromMOL };
+export { TrajectoryFromMOL2 };
 export { TrajectoryFromCube };
 export { TrajectoryFromCifCore };
 export { TrajectoryFrom3DG };
@@ -235,6 +238,24 @@ const TrajectoryFromMOL = PluginStateTransform.BuiltIn({
     }
 });
 
+type TrajectoryFromMOL2 = typeof TrajectoryFromMOL
+const TrajectoryFromMOL2 = PluginStateTransform.BuiltIn({
+    name: 'trajectory-from-mol2',
+    display: { name: 'Parse MOL2', description: 'Parse MOL2 string and create trajectory.' },
+    from: [SO.Data.String],
+    to: SO.Molecule.Trajectory
+})({
+    apply({ a }) {
+        return Task.create('Parse MOL2', async ctx => {
+            const parsed = await parseMol2(a.data, a.label).runInContext(ctx);
+            if (parsed.isError) throw new Error(parsed.message);
+            const models = await trajectoryFromMol2(parsed.result).runInContext(ctx);
+            const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+            return new SO.Molecule.Trajectory(models, props);
+        });
+    }
+});
+
 type TrajectoryFromCube = typeof TrajectoryFromCube
 const TrajectoryFromCube = PluginStateTransform.BuiltIn({
     name: 'trajectory-from-cube',

src/mol-plugin-state/transforms/representation.ts

@@ -6,7 +6,7 @@
  */
 
 import { Structure, StructureElement } from '../../mol-model/structure';
-import { VolumeData, VolumeIsoValue } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
 import { PluginContext } from '../../mol-plugin/context';
 import { VolumeRepresentationRegistry } from '../../mol-repr/volume/registry';
 import { VolumeParams } from '../../mol-repr/volume/representation';
@@ -441,7 +441,7 @@ const TransparencyStructureRepresentation3DFromBundle = PluginStateTransform.Bui
 //
 
 export namespace VolumeRepresentation3DHelpers {
-    export function getDefaultParams(ctx: PluginContext, name: VolumeRepresentationRegistry.BuiltIn, volume: VolumeData, volumeParams?: Partial<PD.Values<VolumeParams>>): StateTransformer.Params<VolumeRepresentation3D> {
+    export function getDefaultParams(ctx: PluginContext, name: VolumeRepresentationRegistry.BuiltIn, volume: Volume, volumeParams?: Partial<PD.Values<VolumeParams>>): StateTransformer.Params<VolumeRepresentation3D> {
         const type = ctx.representation.volume.registry.get(name);
 
         const themeDataCtx = { volume };
@@ -467,7 +467,7 @@ export namespace VolumeRepresentation3DHelpers {
     }
 
     export function getDescription(props: any) {
-        return props.isoValue && VolumeIsoValue.toString(props.isoValue);
+        return props.isoValue && Volume.IsoValue.toString(props.isoValue);
     }
 }
 type VolumeRepresentation3D = typeof VolumeRepresentation3D
@@ -485,16 +485,16 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
                 type: PD.Mapped<any>(
                     registry.default.name,
                     registry.types,
-                    name => PD.Group<any>(registry.get(name).getParams(themeCtx, VolumeData.One))),
+                    name => PD.Group<any>(registry.get(name).getParams(themeCtx, Volume.One))),
                 colorTheme: PD.Mapped<any>(
                     type.defaultColorTheme.name,
                     themeCtx.colorThemeRegistry.types,
-                    name => PD.Group<any>(themeCtx.colorThemeRegistry.get(name).getParams({ volume: VolumeData.One }))
+                    name => PD.Group<any>(themeCtx.colorThemeRegistry.get(name).getParams({ volume: Volume.One }))
                 ),
                 sizeTheme: PD.Mapped<any>(
                     type.defaultSizeTheme.name,
                     themeCtx.sizeThemeRegistry.types,
-                    name => PD.Group<any>(themeCtx.sizeThemeRegistry.get(name).getParams({ volume: VolumeData.One }))
+                    name => PD.Group<any>(themeCtx.sizeThemeRegistry.get(name).getParams({ volume: Volume.One }))
                 )
             };
         }

src/mol-plugin-state/transforms/volume.ts

@@ -15,7 +15,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject as SO, PluginStateTransform } from '../objects';
 import { volumeFromCube } from '../../mol-model-formats/volume/cube';
 import { volumeFromDx } from '../../mol-model-formats/volume/dx';
-import { VolumeData } from '../../mol-model/volume';
+import {  Volume } from '../../mol-model/volume';
 import { PluginContext } from '../../mol-plugin/context';
 import { StateSelection } from '../../mol-state';
 
@@ -160,8 +160,8 @@ const AssignColorVolume = PluginStateTransform.BuiltIn({
             if (!dependencies || !dependencies[params.ref]) {
                 throw new Error('Dependency not available.');
             }
-            const colorVolume = dependencies[params.ref].data as VolumeData;
-            const volume: VolumeData = {
+            const colorVolume = dependencies[params.ref].data as Volume;
+            const volume: Volume = {
                 ...a.data,
                 colorVolume
             };

src/mol-plugin-ui/controls.tsx

@@ -29,6 +29,7 @@ import { StructureMeasurementsControls } from './structure/measurements';
 import { StructureSelectionActionsControls } from './structure/selection';
 import { StructureSourceControls } from './structure/source';
 import { VolumeStreamingControls, VolumeSourceControls } from './structure/volume';
+import { PluginConfig } from '../mol-plugin/config';
 
 export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: boolean, label: string }> {
     state = { show: false, label: '' }
@@ -219,9 +220,8 @@ export class AnimationViewportControls extends PluginUIComponent<{}, { isEmpty:
     }
 
     render() {
-        // if (!this.state.show) return null;
         const isPlaying = this.plugin.managers.snapshot.state.isPlaying;
-        if (isPlaying || this.state.isEmpty) return null;
+        if (isPlaying || this.state.isEmpty || this.plugin.managers.animation.isEmpty || !this.plugin.config.get(PluginConfig.Viewport.ShowAnimation)) return null;
 
         const isAnimating = this.state.isAnimating;
 

src/mol-plugin-ui/custom/volume.tsx

@@ -12,7 +12,7 @@ import { ExpandableControlRow, IconButton } from '../controls/common';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ParameterControls, ParamOnChange } from '../controls/parameters';
 import { Slider } from '../controls/slider';
-import { VolumeIsoValue, VolumeData } from '../../mol-model/volume';
+import { Volume, Grid } from '../../mol-model/volume';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { ColorNames } from '../../mol-util/color/names';
 import { toPrecision } from '../../mol-util/number';
@@ -34,7 +34,7 @@ class Channel extends PluginUIComponent<{
     channels: { [k: string]: VolumeStreaming.ChannelParams },
     isRelative: boolean,
     params: StateTransformParameters.Props,
-    stats: VolumeData['dataStats'],
+    stats: Grid['stats'],
     changeIso: (name: string, value: number, isRelative: boolean) => void,
     changeParams: (name: string, param: string, value: any) => void,
     bCell: StateObjectCell,
@@ -111,7 +111,7 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
                         ...old.entry.params.channels,
                         [name]: {
                             ...(old.entry.params.channels as any)[name],
-                            isoValue: isRelative ? VolumeIsoValue.relative(value) : VolumeIsoValue.absolute(value)
+                            isoValue: isRelative ? Volume.IsoValue.relative(value) : Volume.IsoValue.absolute(value)
                         }
                     }
                 }
@@ -139,11 +139,11 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
         });
     };
 
-    convert(channel: any, stats: VolumeData['dataStats'], isRelative: boolean) {
+    convert(channel: any, stats: Grid['stats'], isRelative: boolean) {
         return {
             ...channel, isoValue: isRelative
-                ? VolumeIsoValue.toRelative(channel.isoValue, stats)
-                : VolumeIsoValue.toAbsolute(channel.isoValue, stats)
+                ? Volume.IsoValue.toRelative(channel.isoValue, stats)
+                : Volume.IsoValue.toAbsolute(channel.isoValue, stats)
         };
     }
 
@@ -215,7 +215,7 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
         const params = this.props.params as VolumeStreaming.Params;
         const detailLevel = ((this.props.info.params as VolumeStreaming.ParamDefinition)
             .entry.map(params.entry.name) as PD.Group<VolumeStreaming.EntryParamDefinition>).params.detailLevel;
-        const isRelative = ((params.entry.params.channels as any)[pivot].isoValue as VolumeIsoValue).kind === 'relative';
+        const isRelative = ((params.entry.params.channels as any)[pivot].isoValue as Volume.IsoValue).kind === 'relative';
 
         const sampling = b.info.header.sampling[0];
 

src/mol-plugin-ui/sequence/polymer.ts

@@ -44,18 +44,18 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
     mark(loci: Loci, action: MarkerAction): boolean {
         let changed = false;
         const { structure } = this.data;
+        const index = (seqId: number) => this.sequence.index(seqId);
         if (StructureElement.Loci.is(loci)) {
             if (!Structure.areRootsEquivalent(loci.structure, structure)) return false;
             loci = StructureElement.Loci.remap(loci, structure);
 
-            const { offset } = this.sequence;
             for (const e of loci.elements) {
                 if (!this.unitMap.has(e.unit.id)) continue;
 
                 if (Unit.isAtomic(e.unit)) {
-                    changed = applyMarkerAtomic(e, action, this.markerArray, offset) || changed;
+                    changed = applyMarkerAtomic(e, action, this.markerArray, index) || changed;
                 } else {
-                    changed = applyMarkerCoarse(e, action, this.markerArray, offset) || changed;
+                    changed = applyMarkerCoarse(e, action, this.markerArray, index) || changed;
                 }
             }
         } else if (Structure.isLoci(loci)) {
@@ -117,27 +117,28 @@ function createResidueQuery(chainGroupId: number, operatorName: string, label_se
     });
 }
 
-function applyMarkerAtomic(e: StructureElement.Loci.Element, action: MarkerAction, markerArray: Uint8Array, offset: number) {
+function applyMarkerAtomic(e: StructureElement.Loci.Element, action: MarkerAction, markerArray: Uint8Array, index: (seqId: number) => number) {
     const { model, elements } = e.unit;
-    const { index } = model.atomicHierarchy.residueAtomSegments;
+    const { index: residueIndex } = model.atomicHierarchy.residueAtomSegments;
     const { label_seq_id } = model.atomicHierarchy.residues;
 
     let changed = false;
-    OrderedSet.forEachSegment(e.indices, i => index[elements[i]], rI => {
+    OrderedSet.forEachSegment(e.indices, i => residueIndex[elements[i]], rI => {
         const seqId = label_seq_id.value(rI);
-        changed = applyMarkerActionAtPosition(markerArray, seqId - 1 - offset, action) || changed;
+        changed = applyMarkerActionAtPosition(markerArray, index(seqId), action) || changed;
     });
     return changed;
 }
 
-function applyMarkerCoarse(e: StructureElement.Loci.Element, action: MarkerAction, markerArray: Uint8Array, offset: number) {
+function applyMarkerCoarse(e: StructureElement.Loci.Element, action: MarkerAction, markerArray: Uint8Array, index: (seqId: number) => number) {
     const { model, elements } = e.unit;
     const begin = Unit.isSpheres(e.unit) ? model.coarseHierarchy.spheres.seq_id_begin : model.coarseHierarchy.gaussians.seq_id_begin;
     const end = Unit.isSpheres(e.unit) ? model.coarseHierarchy.spheres.seq_id_end : model.coarseHierarchy.gaussians.seq_id_end;
 
     let changed = false;
     OrderedSet.forEach(e.indices, i => {
-        for (let s = begin.value(elements[i]) - 1 - offset, e = end.value(elements[i]) - 1 - offset; s <= e; s++) {
+        const eI = elements[i];
+        for (let s = index(begin.value(eI)), e = index(end.value(eI)); s <= e; s++) {
             changed = applyMarkerActionAtPosition(markerArray, s, action) || changed;
         }
     });