0.7.0-dev.18

- see e.g. 3NIR

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.3",
+  "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",
@@ -82,52 +82,52 @@
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^1.13.2",
-    "@graphql-codegen/cli": "^1.13.2",
-    "@graphql-codegen/time": "^1.13.2",
-    "@graphql-codegen/typescript": "^1.13.2",
-    "@graphql-codegen/typescript-graphql-files-modules": "^1.13.2",
-    "@graphql-codegen/typescript-graphql-request": "^1.13.2",
-    "@graphql-codegen/typescript-operations": "^1.13.2",
+    "@graphql-codegen/add": "^1.13.3",
+    "@graphql-codegen/cli": "^1.13.3",
+    "@graphql-codegen/time": "^1.13.3",
+    "@graphql-codegen/typescript": "^1.13.3",
+    "@graphql-codegen/typescript-graphql-files-modules": "^1.13.3",
+    "@graphql-codegen/typescript-graphql-request": "^1.13.3",
+    "@graphql-codegen/typescript-operations": "^1.13.3",
     "@types/cors": "^2.8.6",
-    "@typescript-eslint/eslint-plugin": "^2.28.0",
-    "@typescript-eslint/parser": "^2.28.0",
+    "@typescript-eslint/eslint-plugin": "^2.29.0",
+    "@typescript-eslint/parser": "^2.29.0",
     "benchmark": "^2.1.4",
     "circular-dependency-plugin": "^5.2.0",
     "concurrently": "^5.1.0",
     "cpx2": "^2.0.0",
-    "css-loader": "^3.5.2",
+    "css-loader": "^3.5.3",
     "eslint": "^6.8.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.0.0",
     "fs-extra": "^9.0.0",
     "graphql": "^15.0.0",
     "http-server": "^0.12.1",
-    "jest": "^25.3.0",
+    "jest": "^25.4.0",
     "jest-raw-loader": "^1.0.1",
     "mini-css-extract-plugin": "^0.9.0",
-    "node-sass": "^4.13.1",
+    "node-sass": "^4.14.0",
     "raw-loader": "^4.0.1",
     "resolve-url-loader": "^3.1.1",
     "sass-loader": "^8.0.2",
     "simple-git": "^1.132.0",
-    "style-loader": "^1.1.4",
+    "style-loader": "^1.2.0",
     "ts-jest": "^25.4.0",
     "typescript": "^3.8.3",
-    "webpack": "^4.42.1",
+    "webpack": "^4.43.0",
     "webpack-cli": "^3.3.11",
     "webpack-version-file-plugin": "^0.4.0"
   },
   "dependencies": {
-    "@material-ui/core": "^4.9.10",
+    "@material-ui/core": "^4.9.11",
     "@material-ui/icons": "^4.9.1",
     "@types/argparse": "^1.0.38",
     "@types/benchmark": "^1.0.31",
     "@types/compression": "1.7.0",
     "@types/express": "^4.17.6",
     "@types/jest": "^25.2.1",
-    "@types/node": "^13.13.0",
-    "@types/node-fetch": "^2.5.6",
+    "@types/node": "^13.13.2",
+    "@types/node-fetch": "^2.5.7",
     "@types/react": "^16.9.34",
     "@types/react-dom": "^16.9.6",
     "@types/swagger-ui-dist": "3.0.5",

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/assembly-symmetry/representation.ts

@@ -225,6 +225,7 @@ function getSymbolScale(symbol: string) {
 function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.RotationAxes, size: number, structure: Structure) {
     const eye = Vec3();
     const target = Vec3();
+    const dir = Vec3();
     const up = Vec3();
     let pair: Mutable<AssemblySymmetry.RotationAxes> | undefined = undefined;
 
@@ -246,8 +247,8 @@ function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.Rota
         const a5dir = Vec3.sub(Vec3(), a5.end, a5.start);
         pair = [a5];
         for (const a of axes.filter(a => a.order === 3)) {
-            let d = radToDeg(Vec3.angle(Vec3.sub(up, a.end, a.start), a5dir));
-            if (equalEps(d, 100.81, 0.1) || equalEps(d, 79.19, 0.1)) {
+            const d = radToDeg(Vec3.angle(Vec3.sub(up, a.end, a.start), a5dir));
+            if (!pair[1] && (equalEps(d, 100.81, 0.1) || equalEps(d, 79.19, 0.1))) {
                 pair[1] = a;
                 break;
             }
@@ -263,8 +264,8 @@ function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.Rota
         Vec3.copy(target, aA.end);
         if (aB) {
             Vec3.sub(up, aB.end, aB.start);
-            const d = Vec3.dot(eye, up);
-            if (d < 0) Vec3.negate(up, up);
+            Vec3.sub(dir, eye, target);
+            if (Vec3.dot(dir, up) < 0) Vec3.negate(up, up);
             Mat4.targetTo(t, eye, target, up);
             Mat4.scaleUniformly(t, t, size * getSymbolScale(symbol));
         } else {

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

@@ -340,7 +340,7 @@ export const ValidationReportDensityFitPreset = StructureRepresentationPresetPro
         description: 'Color structure based on density fit. Data from wwPDB Validation Report, obtained via RCSB PDB.'
     },
     isApplicable(a) {
-        return a.data.models.length === 1 && ValidationReport.isApplicable(a.data.models[0]) && Model.hasXrayMap(a.data.models[0]);
+        return a.data.models.length === 1 && ValidationReport.isApplicable(a.data.models[0]) && Model.isFromXray(a.data.models[0]) && Model.probablyHasDensityMap(a.data.models[0]);
     },
     params: () => StructureRepresentationPresetProvider.CommonParams,
     async apply(ref, params, plugin) {

src/extensions/rcsb/validation-report/color/density-fit.ts

@@ -67,7 +67,7 @@ export const DensityFitColorThemeProvider: ColorTheme.Provider<{}, ValidationRep
     factory: DensityFitColorTheme,
     getParams: () => ({}),
     defaultValues: PD.getDefaultValues({}),
-    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.hasXrayMap(ctx.structure.models[0]),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.isFromXray(ctx.structure.models[0]) && Model.probablyHasDensityMap(ctx.structure.models[0]),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
         detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ValidationReportProvider.descriptor, false)

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/canvas3d.ts

@@ -132,12 +132,12 @@ namespace Canvas3D {
                     if (webgl.isContextLost) return;
                     if (!e.shiftKey || !e.ctrlKey || !e.altKey) return;
 
-                    console.log('lose context');
+                    if (isDebugMode) console.log('lose context');
                     loseContextExt.loseContext();
 
                     setTimeout(() => {
                         if (!webgl.isContextLost) return;
-                        console.log('restore context');
+                        if (isDebugMode) console.log('restore context');
                         loseContextExt.restoreContext();
                     }, 1000);
                 }, false);

src/mol-canvas3d/helper/bounding-sphere-helper.ts

@@ -159,5 +159,5 @@ const instanceMaterialId = getNextMaterialId();
 
 function createBoundingSphereRenderObject(mesh: Mesh, color: Color, materialId: number, transform?: TransformData) {
     const values = Mesh.Utils.createValuesSimple(mesh, { alpha: 0.1, doubleSided: false }, color, 1, transform);
-    return createRenderObject('mesh', values, { visible: true, alphaFactor: 1, pickable: false, opaque: false }, materialId);
+    return createRenderObject('mesh', values, { visible: true, alphaFactor: 1, pickable: false, opaque: false, writeDepth: false }, materialId);
 }

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-geo/geometry/base.ts

@@ -72,15 +72,18 @@ export namespace BaseGeometry {
     }
 
     export function createRenderableState(props: Partial<PD.Values<Params>> = {}): RenderableState {
+        const opaque = props.alpha === undefined ? true : props.alpha === 1;
         return {
             visible: true,
             alphaFactor: 1,
             pickable: true,
-            opaque: props.alpha === undefined ? true : props.alpha === 1
+            opaque,
+            writeDepth: opaque,
         };
     }
 
     export function updateRenderableState(state: RenderableState, props: PD.Values<Params>) {
         state.opaque = props.alpha * state.alphaFactor >= 1;
+        state.writeDepth = state.opaque;
     }
 }

src/mol-geo/geometry/image/image.ts

@@ -98,8 +98,7 @@ namespace Image {
         return image;
     }
 
-    function update(imageTexture: TextureImage<Uint8Array | Float32Array>, corners: Float32Array, groupTexture: TextureImage<Float32Array>, image: Image): Image {
-
+    function update(imageTexture: TextureImage<Float32Array>, corners: Float32Array, groupTexture: TextureImage<Float32Array>, image: Image): Image {
         const width = imageTexture.width;
         const height = imageTexture.height;
 
@@ -116,7 +115,7 @@ namespace Image {
 
     export const Params = {
         ...BaseGeometry.Params,
-        interpolation: PD.Select('bspline', PD.objectToOptions(InterpolationTypes), { isEssential: true }),
+        interpolation: PD.Select('bspline', PD.objectToOptions(InterpolationTypes)),
     };
     export type Params = typeof Params
 
@@ -176,7 +175,7 @@ namespace Image {
     }
 
     function updateValues(values: ImageValues, props: PD.Values<Params>) {
-        ValueCell.updateIfChanged(values.uAlpha, props.alpha);
+        BaseGeometry.updateValues(values, props);
         ValueCell.updateIfChanged(values.dInterpolation, props.interpolation);
     }
 

src/mol-geo/geometry/mesh/builder/tube.ts

@@ -53,7 +53,6 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe
             if (radialSegments === 2) {
                 // add2AndScale2(normalVector, u, v, w * Math.cos(t), h * Math.sin(t))
                 Vec3.copy(normalVector, v);
-                console.log(i, t);
                 Vec3.normalize(normalVector, normalVector);
                 if (t !== 0 || i % 2 === 0) Vec3.negate(normalVector, normalVector);
             } else {

src/mol-gl/_spec/renderer.spec.ts

@@ -86,7 +86,8 @@ function createPoints() {
         visible: true,
         alphaFactor: 1,
         pickable: true,
-        opaque: true
+        opaque: true,
+        writeDepth: true
     };
 
     return createRenderObject('points', values, state, -1);

src/mol-gl/renderable.ts

@@ -18,6 +18,7 @@ export type RenderableState = {
     alphaFactor: number
     pickable: boolean
     opaque: boolean
+    writeDepth: boolean,
 }
 
 export interface Renderable<T extends RenderableValues> {
@@ -43,9 +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/renderable/util.ts

@@ -20,6 +20,7 @@ export interface TextureImage<T extends Uint8Array | Float32Array> {
     readonly array: T
     readonly width: number
     readonly height: number
+    readonly flipY?: boolean
 }
 
 export interface TextureVolume<T extends Uint8Array | Float32Array> {

src/mol-gl/renderer.ts

@@ -173,47 +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);
                 }
-
-                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) => {
@@ -245,11 +251,11 @@ namespace Renderer {
 
             state.disable(gl.SCISSOR_TEST);
             state.disable(gl.BLEND);
-            state.depthMask(true);
             state.colorMask(true, true, true, true);
             state.enable(gl.DEPTH_TEST);
 
             if (clear) {
+                state.depthMask(true);
                 if (variant === 'color') {
                     state.clearColor(bgColor[0], bgColor[1], bgColor[2], transparentBackground ? 0 : 1);
                 } else {
@@ -268,10 +274,11 @@ namespace Renderer {
                 state.enable(gl.BLEND);
                 for (let i = 0, il = renderables.length; i < il; ++i) {
                     const r = renderables[i];
-                    if (!r.state.opaque) {
-                        state.depthMask(false);
-                        renderObject(r, variant);
-                    }
+                    if (!r.state.opaque && r.state.writeDepth) renderObject(r, variant);
+                }
+                for (let i = 0, il = renderables.length; i < il; ++i) {
+                    const r = renderables[i];
+                    if (!r.state.opaque && !r.state.writeDepth) renderObject(r, variant);
                 }
             } else { // picking & depth
                 for (let i = 0, il = renderables.length; i < il; ++i) {

src/mol-gl/scene.ts

@@ -50,9 +50,11 @@ function renderableSort(a: Renderable<RenderableValues & BaseValues>, b: Rendera
     const materialIdB = b.materialId;
 
     if (drawProgramIdA !== drawProgramIdB) {
-        return drawProgramIdA - drawProgramIdB; // sort by program id to minimize gl state changes
+        // sort by program id to minimize gl state changes
+        return drawProgramIdA - drawProgramIdB;
     } else if (materialIdA !== materialIdB) {
-        return materialIdA - materialIdB; // sort by material id to minimize gl state changes
+        // sort by material id to minimize gl state changes
+        return materialIdA - materialIdB;
     } else {
         return a.id - b.id;
     }

src/mol-gl/shader/chunks/apply-fog.glsl.ts

@@ -1,8 +1,11 @@
 export default `
 float depth = length(vViewPosition);
 float fogFactor = smoothstep(uFogNear, uFogFar, depth);
+float fogAlpha = (1.0 - fogFactor) * gl_FragColor.a;
 if (uTransparentBackground == 0) {
     gl_FragColor.rgb = mix(gl_FragColor.rgb, uFogColor, fogFactor);
+    if (gl_FragColor.a < 1.0)
+        gl_FragColor.a = fogAlpha;
 } else {
     float fogAlpha = (1.0 - fogFactor) * gl_FragColor.a;
     gl_FragColor.a = fogAlpha;

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

@@ -35,20 +35,20 @@ varying float vInstance;
             const float C = 0.333;
         #endif
 
-        float cubicFilter( float x ){
+        float cubicFilter(float x){
             float f = x;
-            if( f < 0.0 ){
+            if (f < 0.0) {
                 f = -f;
             }
-            if( f < 1.0 ){
-                return ( ( 12.0 - 9.0 * B - 6.0 * C ) * ( f * f * f ) +
-                    ( -18.0 + 12.0 * B + 6.0 *C ) * ( f * f ) +
-                    ( 6.0 - 2.0 * B ) ) / 6.0;
-            }else if( f >= 1.0 && f < 2.0 ){
-                return ( ( -B - 6.0 * C ) * ( f * f * f )
-                    + ( 6.0 * B + 30.0 * C ) * ( f *f ) +
-                    ( - ( 12.0 * B ) - 48.0 * C  ) * f +
-                    8.0 * B + 24.0 * C ) / 6.0;
+            if (f < 1.0) {
+                return ((12.0 - 9.0 * B - 6.0 * C) * (f * f * f) +
+                    (-18.0 + 12.0 * B + 6.0 * C) * (f * f) +
+                    (6.0 - 2.0 * B)) / 6.0;
+            }else if (f >= 1.0 && f < 2.0){
+                return ((-B - 6.0 * C) * ( f * f * f)
+                    + (6.0 * B + 30.0 * C) * (f * f) +
+                    (-(12.0 * B) - 48.0 * C) * f +
+                    8.0 * B + 24.0 * C) / 6.0;
             }else{
                 return 0.0;
             }
@@ -92,25 +92,23 @@ void main() {
     #else
         vec4 imageData = texture2D(tImageTex, vUv);
     #endif
+    imageData.a = clamp(imageData.a, 0.0, 1.0);
+    if (imageData.a > 0.9) imageData.a = 1.0;
 
     #if defined(dRenderVariant_pick)
         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 < 0.01)
+        if (imageData.a < 0.05)
             discard;
 
         #ifdef enabledFragDepth
@@ -119,7 +117,7 @@ void main() {
             gl_FragColor = packDepthToRGBA(gl_FragCoord.z);
         #endif
     #elif defined(dRenderVariant_color)
-        if (imageData.a < 0.01)
+        if (imageData.a < 0.05)
             discard;
 
         gl_FragColor = imageData;

src/mol-gl/webgl/texture.ts

@@ -118,6 +118,14 @@ export function getAttachment(gl: GLRenderingContext, extensions: WebGLExtension
     throw new Error('unknown texture attachment');
 }
 
+function isTexture2d(x: TextureImage<any> | TextureVolume<any>, target: number, gl: GLRenderingContext): x is TextureImage<any> {
+    return target === gl.TEXTURE_2D;
+}
+
+function isTexture3d(x: TextureImage<any> | TextureVolume<any>, target: number, gl: WebGL2RenderingContext): x is TextureImage<any> {
+    return target === gl.TEXTURE_3D;
+}
+
 export interface Texture {
     readonly id: number
     readonly target: number
@@ -214,14 +222,13 @@ export function createTexture(gl: GLRenderingContext, extensions: WebGLExtension
         gl.pixelStorei(gl.UNPACK_ALIGNMENT, 1);
         gl.pixelStorei(gl.UNPACK_COLORSPACE_CONVERSION_WEBGL, gl.NONE);
         gl.pixelStorei(gl.UNPACK_PREMULTIPLY_ALPHA_WEBGL, 0);
-        if (target === gl.TEXTURE_2D) {
-            const { array, width: _width, height: _height } = data as TextureImage<any>;
-            width = _width, height = _height;
-            gl.texImage2D(target, 0, internalFormat, width, height, 0, format, type, array);
-        } else if (isWebGL2(gl) && target === gl.TEXTURE_3D) {
-            const { array, width: _width, height: _height, depth: _depth } = data as TextureVolume<any>;
-            width = _width, height = _height, depth = _depth;
-            gl.texImage3D(target, 0, internalFormat, width, height, depth, 0, format, type, array);
+        if (isTexture2d(data, target, gl)) {
+            gl.pixelStorei(gl.UNPACK_FLIP_Y_WEBGL, !!data.flipY);
+            width = data.width, height = data.height;
+            gl.texImage2D(target, 0, internalFormat, width, height, 0, format, type, data.array);
+        } else if (isWebGL2(gl) && isTexture3d(data, target, gl)) {
+            width = data.width, height = data.height, depth = data.depth;
+            gl.texImage3D(target, 0, internalFormat, width, height, depth, 0, format, type, data.array);
         } else {
             throw new Error('unknown texture target');
         }

src/mol-io/common/file-handle.ts

@@ -11,6 +11,7 @@ import { SimpleBuffer } from './simple-buffer';
 const fs = typeof document === 'undefined' ? require('fs') as typeof import('fs') : void 0;
 
 export interface FileHandle {
+    name: string
     /**
      * Asynchronously reads data, returning buffer and number of bytes read
      *
@@ -44,8 +45,9 @@ export interface FileHandle {
 }
 
 export namespace FileHandle {
-    export function fromBuffer(buffer: SimpleBuffer): FileHandle {
+    export function fromBuffer(buffer: SimpleBuffer, name: string): FileHandle {
         return {
+            name,
             readBuffer: (position: number, sizeOrBuffer: SimpleBuffer | number, size?: number, byteOffset?: number) => {
                 let bytesRead: number;
                 let outBuffer: SimpleBuffer;
@@ -82,9 +84,10 @@ export namespace FileHandle {
         };
     }
 
-    export function fromDescriptor(file: number): FileHandle {
+    export function fromDescriptor(file: number, name: string): FileHandle {
         if (fs === undefined) throw new Error('fs module not available');
         return {
+            name,
             readBuffer: (position: number, sizeOrBuffer: SimpleBuffer | number, length?: number, byteOffset?: number) => {
                 return new Promise((res, rej) => {
                     let outBuffer: SimpleBuffer;

src/mol-io/reader/_spec/ccp4.spec.ts

@@ -31,7 +31,7 @@ function createCcp4Data() {
 describe('ccp4 reader', () => {
     it('basic', async () => {
         const data = createCcp4Data();
-        const parsed = await CCP4.parse(data).run();
+        const parsed = await CCP4.parse(data, 'test.ccp4').run();
 
         if (parsed.isError) {
             throw new Error(parsed.message);

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

@@ -8,10 +8,14 @@ import { parseFloat as fastParseFloat, parseInt as fastParseInt, getNumberType,
 
 describe('common', () => {
     it('number-parser fastParseFloat', () => {
+        // ignore suffix numbers in parentheses
         expect(fastParseFloat('11.0829(23)', 0, 11)).toBe(11.0829);
+        // scientific with no space between consecutive values
+        expect(fastParseFloat('-5.1E-01-6.1E-01', 0, 11)).toBe(-0.51);
     });
 
     it('number-parser fastParseInt', () => {
+        // ignore suffix numbers in parentheses
         expect(fastParseInt('11(23)', 0, 11)).toBe(11);
     });
 

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/ccp4/parser.ts

@@ -160,7 +160,7 @@ async function parseInternal(file: FileHandle, size: number, ctx: RuntimeContext
     const buffer = createTypedArrayBufferContext(count, valueType);
     readCcp4Slices(header, buffer, file, offset, byteCount, littleEndian);
 
-    const result: Ccp4File = { header, values: buffer.values };
+    const result: Ccp4File = { header, values: buffer.values, name: file.name };
     return result;
 }
 
@@ -174,6 +174,6 @@ export function parseFile(file: FileHandle, size: number) {
     });
 }
 
-export function parse(buffer: Uint8Array) {
-    return parseFile(FileHandle.fromBuffer(SimpleBuffer.fromUint8Array(buffer)), buffer.length);
+export function parse(buffer: Uint8Array, name: string) {
+    return parseFile(FileHandle.fromBuffer(SimpleBuffer.fromUint8Array(buffer), name), buffer.length);
 }

src/mol-io/reader/ccp4/schema.ts

@@ -114,6 +114,7 @@ export interface Ccp4Header {
  * CCP4 format does not use the ORIGIN header records (words 50-52)
  */
 export interface Ccp4File {
+    name: string
     header: Ccp4Header
     values: Float32Array | Int16Array | Int8Array | Uint16Array
 }

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

@@ -17,6 +17,7 @@ import { parseFloat as fastParseFloat } from '../common/text/number-parser';
 // https://h5cube-spec.readthedocs.io/en/latest/cubeformat.html
 
 export interface CubeFile {
+    name: string,
     header: CubeFile.Header,
     atoms: CubeFile.Atoms,
     values: Float64Array
@@ -24,6 +25,7 @@ export interface CubeFile {
 
 export namespace CubeFile {
     export interface Header {
+        orbitals: boolean,
         comment1: string,
         comment2: string,
         atomCount: number,
@@ -79,8 +81,7 @@ function readHeader(tokenizer: Tokenizer) {
         for (let i = 0, _i = +counts[0]; i < _i; i++) dataSetIds.push(+counts[i + 1]);
     }
 
-    const header: CubeFile.Header = { comment1, comment2, atomCount, origin, dim: Vec3.create(NVX, NVY, NVZ), basisX, basisY, basisZ, dataSetIds };
-
+    const header: CubeFile.Header = { orbitals: rawAtomCount < 0, comment1, comment2, atomCount, origin, dim: Vec3.create(NVX, NVY, NVZ), basisX, basisY, basisZ, dataSetIds };
     return { header, atoms };
 }
 
@@ -129,12 +130,12 @@ function readValues(ctx: RuntimeContext, tokenizer: Tokenizer, header: CubeFile.
     }, (ctx, _, i) => ctx.update({ current: Math.min(i, N), max: N }));
 }
 
-export function parseCube(data: string) {
+export function parseCube(data: string, name: string) {
     return Task.create<Result<CubeFile>>('Parse Cube', async taskCtx => {
         await taskCtx.update('Reading header...');
         const tokenizer = Tokenizer(data);
         const { header, atoms } = readHeader(tokenizer);
         const values = await readValues(taskCtx, tokenizer, header);
-        return Result.success({ header, atoms, values });
+        return Result.success({ header, atoms, values, name });
     });
 }

src/mol-io/reader/dsn6/parser.ts

@@ -134,7 +134,7 @@ async function parseInternal(file: FileHandle, size: number, ctx: RuntimeContext
     const values = new Float32Array(valueCount);
     await parseDsn6Values(header, buffer, values, littleEndian);
 
-    const result: Dsn6File = { header, values };
+    const result: Dsn6File = { header, values, name: file.name };
     return result;
 }
 
@@ -148,6 +148,6 @@ export function parseFile(file: FileHandle, size: number) {
     });
 }
 
-export function parse(buffer: Uint8Array) {
-    return parseFile(FileHandle.fromBuffer(SimpleBuffer.fromUint8Array(buffer)), buffer.length);
+export function parse(buffer: Uint8Array, name: string) {
+    return parseFile(FileHandle.fromBuffer(SimpleBuffer.fromUint8Array(buffer), name), buffer.length);
 }

src/mol-io/reader/dsn6/schema.ts

@@ -39,6 +39,7 @@ export interface Dsn6Header {
  * BRIX http://svn.cgl.ucsf.edu/svn/chimera/trunk/libs/VolumeData/dsn6/brix-1.html
  */
 export interface Dsn6File {
+    name: string
     header: Dsn6Header
     values: Float32Array
 }

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

@@ -17,6 +17,7 @@ import { utf8Read } from '../../common/utf8';
 // http://apbs-pdb2pqr.readthedocs.io/en/latest/formats/opendx.html
 
 export interface DxFile {
+    name: string,
     header: DxFile.Header,
     values: Float64Array
 }
@@ -88,16 +89,16 @@ function readValuesText(ctx: RuntimeContext, tokenizer: Tokenizer, header: DxFil
     }, (ctx, _, i) => ctx.update({ current: Math.min(i, N), max: N }));
 }
 
-async function parseText(taskCtx: RuntimeContext, data: string) {
+async function parseText(taskCtx: RuntimeContext, data: string, name: string) {
     await taskCtx.update('Reading header...');
     const tokenizer = Tokenizer(data as string);
     const { header } = readHeader(tokenizer);
     await taskCtx.update('Reading values...');
     const values = await readValuesText(taskCtx, tokenizer, header);
-    return Result.success({ header, values });
+    return Result.success({ header, values, name });
 }
 
-async function parseBinary(taskCtx: RuntimeContext, data: Uint8Array) {
+async function parseBinary(taskCtx: RuntimeContext, data: Uint8Array, name: string) {
     await taskCtx.update('Reading header...');
 
     const headerString = utf8Read(data, 0, 1000);
@@ -117,12 +118,12 @@ async function parseBinary(taskCtx: RuntimeContext, data: Uint8Array) {
 
     // TODO: why doesnt this work? throw "attempting to construct out-of-bounds TypedArray"
     // const values = new Float64Array(data.buffer, data.byteOffset + headerByteCount, header.dim[0] * header.dim[1] * header.dim[2]);
-    return Result.success({ header, values });
+    return Result.success({ header, values, name });
 }
 
-export function parseDx(data: string | Uint8Array) {
+export function parseDx(data: string | Uint8Array, name: string) {
     return Task.create<Result<DxFile>>('Parse Cube', taskCtx => {
-        if (typeof data === 'string') return parseText(taskCtx, data);
-        return parseBinary(taskCtx, data);
+        if (typeof data === 'string') return parseText(taskCtx, data, name);
+        return parseBinary(taskCtx, data, name);
     });
 }

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-math/linear-algebra/_spec/tensor.spec.ts

@@ -263,4 +263,59 @@ describe('tensor', () => {
 
         expect(data).toEqual(exp);
     });
+
+    it('indexing', () => {
+        function permutations<T>(inputArr: T[]): T[][] {
+            let result: T[][] = [];
+            function permute(arr: any, m: any = []) {
+                if (arr.length === 0) {
+                    result.push(m);
+                } else {
+                    for (let i = 0; i < arr.length; i++) {
+                        let curr = arr.slice();
+                        let next = curr.splice(i, 1);
+                        permute(curr.slice(), m.concat(next));
+                    }
+                }
+            }
+            permute(inputArr);
+
+            return result;
+        }
+
+        for (let dim = 1; dim <= 5; dim++) {
+            const axes = [], dims: number[] = [];
+            const u: number[] = [], v: number[] = [];
+
+            for (let i = 0; i < dim; i++) {
+                axes.push(i);
+                dims.push(3);
+                u.push(0);
+                v.push(0);
+            }
+
+            const forEachDim = (space: T.Space, d: number): boolean => {
+                if (d === dim) {
+                    const o = space.dataOffset(...u);
+                    space.getCoords(o, v);
+
+                    for (let e = 0; e < dims.length; e++) {
+                        expect(u[e]).toEqual(v[e]);
+                        return false;
+                    }
+                } else {
+                    for (let i = 0; i < dims[d]; i++) {
+                        u[d] = i;
+                        if (!forEachDim(space, d + 1)) return false;
+                    }
+                }
+                return true;
+            };
+
+            for (const ao of permutations(axes)) {
+                const space = T.Space(dims, ao);
+                if (!forEachDim(space, 0)) break;
+            }
+        }
+    });
 });

src/mol-math/linear-algebra/tensor.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 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 { Mat4, Vec3, Vec4, Mat3 } from './3d';
@@ -21,6 +22,8 @@ export namespace Tensor {
         get(data: Tensor.Data, ...coords: number[]): number
         set(data: Tensor.Data, ...coordsAndValue: number[]): number
         add(data: Tensor.Data, ...coordsAndValue: number[]): number
+        dataOffset(...coords: number[]): number,
+        getCoords(dataOffset: number, coords: { [i: number]: number }): number[]
     }
 
     interface Layout {
@@ -46,8 +49,8 @@ export namespace Tensor {
 
     export function Space(dimensions: number[], axisOrderSlowToFast: number[], ctor?: ArrayCtor): Space {
         const layout = Layout(dimensions, axisOrderSlowToFast, ctor);
-        const { get, set, add } = accessors(layout);
-        return { rank: dimensions.length, dimensions, axisOrderSlowToFast, create: creator(layout), get, set, add };
+        const { get, set, add, dataOffset, getCoords } = accessors(layout);
+        return { rank: dimensions.length, dimensions, axisOrderSlowToFast, create: creator(layout), get, set, add, dataOffset, getCoords };
     }
 
     export function Data1(values: ArrayLike<number>): Data { return values as Data; }
@@ -95,13 +98,15 @@ export namespace Tensor {
         return true;
     }
 
-    function accessors(layout: Layout): { get: Space['get'], set: Space['set'], add: Space['add'] } {
+    function accessors(layout: Layout): { get: Space['get'], set: Space['set'], add: Space['add'], dataOffset: Space['dataOffset'], getCoords: Space['getCoords'] } {
         const { dimensions, axisOrderFastToSlow: ao } = layout;
         switch (dimensions.length) {
             case 1: return {
                 get: (t, d) => t[d],
                 set: (t, d, x) => t[d] = x,
-                add: (t, d, x) => t[d] += x
+                add: (t, d, x) => t[d] += x,
+                dataOffset: (d) => d,
+                getCoords: (o, c) => { c[0] = o; return c as number[]; }
             };
             case 2: {
                 // column major
@@ -110,7 +115,9 @@ export namespace Tensor {
                     return {
                         get: (t, i, j) => t[j * rows + i],
                         set: (t, i, j, x) => t[j * rows + i] = x,
-                        add: (t, i, j, x) => t[j * rows + i] += x
+                        add: (t, i, j, x) => t[j * rows + i] += x,
+                        dataOffset: (i, j) => j * rows + i,
+                        getCoords: (o, c) => { c[0] = o % rows; c[1] = Math.floor(o / rows) ; return c as number[]; }
                     };
                 }
                 if (ao[0] === 1 && ao[1] === 0) {
@@ -118,7 +125,9 @@ export namespace Tensor {
                     return {
                         get: (t, i, j) => t[i * cols + j],
                         set: (t, i, j, x) => t[i * cols + j] = x,
-                        add: (t, i, j, x) => t[i * cols + j] += x
+                        add: (t, i, j, x) => t[i * cols + j] += x,
+                        dataOffset: (i, j) => i * cols + j,
+                        getCoords: (o, c) => { c[0] = Math.floor(o / cols); c[1] = o % cols; return c as number[]; }
                     };
                 }
                 throw new Error('bad axis order');
@@ -129,7 +138,15 @@ export namespace Tensor {
                     return {
                         get: (t, i, j, k) => t[i + j * u + k * uv],
                         set: (t, i, j, k, x ) => t[i + j * u + k * uv] = x,
-                        add: (t, i, j, k, x ) => t[i + j * u + k * uv] += x
+                        add: (t, i, j, k, x ) => t[i + j * u + k * uv] += x,
+                        dataOffset: (i, j, k) => i + j * u + k * uv,
+                        getCoords: (o, c) => {
+                            const p = Math.floor(o / u);
+                            c[0] = o % u;
+                            c[1] = p % v;
+                            c[2] = Math.floor(p / v);
+                            return c as number[];
+                        }
                     };
                 }
                 if (ao[0] === 0 && ao[1] === 2 && ao[2] === 1) { // 021 ikj
@@ -137,7 +154,15 @@ export namespace Tensor {
                     return {
                         get: (t, i, j, k) => t[i + k * u + j * uv],
                         set: (t, i, j, k, x ) => t[i + k * u + j * uv] = x,
-                        add: (t, i, j, k, x ) => t[i + k * u + j * uv] += x
+                        add: (t, i, j, k, x ) => t[i + k * u + j * uv] += x,
+                        dataOffset: (i, j, k) => i + k * u + j * uv,
+                        getCoords: (o, c) => {
+                            const p = Math.floor(o / u);
+                            c[0] = o % u;
+                            c[1] = Math.floor(p / v);
+                            c[2] = p % v;
+                            return c as number[];
+                        }
                     };
                 }
                 if (ao[0] === 1 && ao[1] === 0 && ao[2] === 2) { // 102 jik
@@ -145,7 +170,15 @@ export namespace Tensor {
                     return {
                         get: (t, i, j, k) => t[j + i * u + k * uv],
                         set: (t, i, j, k, x ) => t[j + i * u + k * uv] = x,
-                        add: (t, i, j, k, x ) => t[j + i * u + k * uv] += x
+                        add: (t, i, j, k, x ) => t[j + i * u + k * uv] += x,
+                        dataOffset: (i, j, k) => j + i * u + k * uv,
+                        getCoords: (o, c) => {
+                            const p = Math.floor(o / u);
+                            c[0] = p % v;
+                            c[1] = o % u;
+                            c[2] = Math.floor(p / v);
+                            return c as number[];
+                        }
                     };
                 }
                 if (ao[0] === 1 && ao[1] === 2 && ao[2] === 0) { // 120 jki
@@ -153,7 +186,15 @@ export namespace Tensor {
                     return {
                         get: (t, i, j, k) => t[j + k * u + i * uv],
                         set: (t, i, j, k, x ) => t[j + k * u + i * uv] = x,
-                        add: (t, i, j, k, x ) => t[j + k * u + i * uv] += x
+                        add: (t, i, j, k, x ) => t[j + k * u + i * uv] += x,
+                        dataOffset: (i, j, k) => j + k * u + i * uv,
+                        getCoords: (o, c) => {
+                            const p = Math.floor(o / u);
+                            c[0] = Math.floor(p / v);
+                            c[1] = o % u;
+                            c[2] = p % v;
+                            return c as number[];
+                        }
                     };
                 }
                 if (ao[0] === 2 && ao[1] === 0 && ao[2] === 1) { // 201 kij
@@ -161,7 +202,15 @@ export namespace Tensor {
                     return {
                         get: (t, i, j, k) => t[k + i * u + j * uv],
                         set: (t, i, j, k, x ) => t[k + i * u + j * uv] = x,
-                        add: (t, i, j, k, x ) => t[k + i * u + j * uv] += x
+                        add: (t, i, j, k, x ) => t[k + i * u + j * uv] += x,
+                        dataOffset: (i, j, k) => k + i * u + j * uv,
+                        getCoords: (o, c) => {
+                            const p = Math.floor(o / u);
+                            c[0] = p % v;
+                            c[1] = Math.floor(p / v);
+                            c[2] = o % u;
+                            return c as number[];
+                        }
                     };
                 }
                 if (ao[0] === 2 && ao[1] === 1 && ao[2] === 0) { // 210 kji
@@ -169,7 +218,15 @@ export namespace Tensor {
                     return {
                         get: (t, i, j, k) => t[k + j * u + i * uv],
                         set: (t, i, j, k, x ) => t[k + j * u + i * uv] = x,
-                        add: (t, i, j, k, x ) => t[k + j * u + i * uv] += x
+                        add: (t, i, j, k, x ) => t[k + j * u + i * uv] += x,
+                        dataOffset: (i, j, k) => k + j * u + i * uv,
+                        getCoords: (o, c) => {
+                            const p = Math.floor(o / u);
+                            c[0] = Math.floor(p / v);
+                            c[1] = p % v;
+                            c[2] = o % u;
+                            return c as number[];
+                        }
                     };
                 }
                 throw new Error('bad axis order');
@@ -177,7 +234,9 @@ export namespace Tensor {
             default: return {
                 get: (t, ...c) => t[dataOffset(layout, c)],
                 set: (t, ...c) => t[dataOffset(layout, c)] = c[c.length - 1],
-                add: (t, ...c) => t[dataOffset(layout, c)] += c[c.length - 1]
+                add: (t, ...c) => t[dataOffset(layout, c)] += c[c.length - 1],
+                dataOffset: (...c) => dataOffset(layout, c),
+                getCoords: (o, c) => getCoords(layout, o, c as number[]),
             };
         }
     }
@@ -199,6 +258,21 @@ export namespace Tensor {
         return o;
     }
 
+    function getCoords(layout: Layout, o: number, coords: number[]) {
+        const { dimensions: dim, axisOrderFastToSlow: ao } = layout;
+        const d = dim.length;
+
+        let c = o;
+        for (let i = 0; i < d; i++) {
+            const d = dim[ao[i]];
+            coords[ao[i]] = c % d;
+            c = Math.floor(c / d);
+        }
+        coords[ao[d + 1]] = c;
+
+        return coords;
+    }
+
     // Convers "slow to fast" axis order to "fast to slow" and vice versa.
     export function invertAxisOrder(v: number[]) {
         const ret: number[] = [];

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/loci.ts

@@ -17,7 +17,6 @@ import { FiniteArray } from '../mol-util/type-helpers';
 import { BoundaryHelper } from '../mol-math/geometry/boundary-helper';
 import { stringToWords } from '../mol-util/string';
 import { Volume } from './volume/volume';
-import { VolumeData } from './volume';
 
 /** A Loci that includes every loci */
 export const EveryLoci = { kind: 'every-loci' as 'every-loci' };
@@ -162,12 +161,11 @@ namespace Loci {
         } else if (loci.kind === 'data-loci') {
             return loci.getBoundingSphere(boundingSphere);
         } else if (loci.kind === 'volume-loci') {
-            return VolumeData.getBoundingSphere(loci.volume, boundingSphere);
+            return Volume.getBoundingSphere(loci.volume, boundingSphere);
         } else if (loci.kind === 'isosurface-loci') {
-            return VolumeData.getBoundingSphere(loci.volume, boundingSphere);
+            return Volume.Isosurface.getBoundingSphere(loci.volume, loci.isoValue, boundingSphere);
         } else if (loci.kind === 'cell-loci') {
-            // TODO
-            return VolumeData.getBoundingSphere(loci.volume, boundingSphere);
+            return Volume.Cell.getBoundingSphere(loci.volume, loci.indices, boundingSphere);
         }
     }
 

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';
 
@@ -146,7 +146,6 @@ export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures:
     if (params?.copyAllCategories && MmcifFormat.is(models[0].sourceData)) {
         encode_mmCIF_categories_copyAll(encoder, ctx);
     } else {
-        console.log('default');
         encode_mmCIF_categories_default(encoder, ctx, params);
     }
 }

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';