0.7.0-dev.7

- moved out of selection.tsx
- added queries for entities (based on entity description)

.eslintrc.json

@@ -5,7 +5,7 @@
     },
     "parser": "@typescript-eslint/parser",
     "parserOptions": {
-        "project": ["tsconfig.json", "src/servers/tsconfig.json"],
+        "project": ["tsconfig.json", "tsconfig.servers.json"],
         "sourceType": "module"
     },
     "plugins": [

.npmignore

@@ -0,0 +1 @@
+tsconfig.servers.buildinfo

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.0",
+  "version": "0.7.0-dev.7",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -16,7 +16,7 @@
     "test": "npm run lint && jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
     "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
-    "build-tsc": "tsc --incremental && tsc --build src/servers --incremental",
+    "build-tsc": "tsc --incremental && tsc --build tsconfig.servers.json --incremental",
     "build-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/",
     "build-webpack": "webpack --mode production --config ./webpack.config.production.js",
     "build-webpack-viewer": "webpack --mode production --config ./webpack.config.viewer.js",
@@ -24,7 +24,7 @@
     "watch-viewer": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer\"",
     "watch-viewer-debug": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer-debug\"",
     "watch-tsc": "tsc --watch --incremental",
-    "watch-servers": "tsc --build src/servers --watch --incremental",
+    "watch-servers": "tsc --build tsconfig.servers.json --watch --incremental",
     "watch-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/ --watch",
     "watch-webpack": "webpack -w --mode development --display minimal",
     "watch-webpack-viewer": "webpack -w --mode development --display errors-only --info-verbosity verbose --config ./webpack.config.viewer.js",
@@ -45,7 +45,7 @@
     "cif2bcif": "lib/apps/cif2bcif/index.js",
     "cifschema": "lib/apps/cifschema/index.js",
     "model-server": "lib/servers/servers/model/server.js",
-    "model-server-query": "lib/servers/servers/model/local.js",
+    "model-server-query": "lib/servers/servers/model/query.js",
     "model-server-preprocess": "lib/servers/servers/model/preprocess.js",
     "volume-server": "lib/servers/servers/volume/server.js",
     "volume-server-query": "lib/servers/servers/volume/query.js",
@@ -82,51 +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-cli": "^3.3.11"
+    "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/volume.ts

@@ -34,9 +34,8 @@ function print(data: Volume) {
     const { volume_data_3d_info } = data.source;
     const row = Table.getRow(volume_data_3d_info, 0);
     console.log(row);
-    console.log(data.volume.cell);
+    if (data.volume.transform) console.log(data.volume.transform);
     console.log(data.volume.dataStats);
-    console.log(data.volume.fractionalBox);
 }
 
 async function doMesh(data: Volume, filename: string) {

src/examples/proteopedia-wrapper/index.html

@@ -176,16 +176,19 @@
 
             var snapshot;
             addControl('Set Snapshot', () => {
-                snapshot = PluginWrapper.snapshot.get();
-                // could use JSON.stringify(snapshot) and upload the data
+                // const options = { data: true, behavior: false, animation: false, interactivity: false, canvas3d: false, camera: false, cameraTransition: false };
+                snapshot = PluginWrapper.plugin.state.getSnapshot(/** options */);
                 // console.log(JSON.stringify(snapshot, null, 2));
             });
             addControl('Restore Snapshot', () => {
                 if (!snapshot) return;
                 PluginWrapper.snapshot.set(snapshot);
             });
-            addControl('Download Snapshot', () => {
-                snapshot = PluginWrapper.snapshot.download();
+            addControl('Download State', () => {
+                snapshot = PluginWrapper.snapshot.download('molj');
+            });
+            addControl('Download Session', () => {
+                snapshot = PluginWrapper.snapshot.download('molx');
             });
 
             ////////////////////////////////////////////////////////

src/examples/proteopedia-wrapper/index.ts

@@ -33,7 +33,7 @@ require('../../mol-plugin-ui/skin/light.scss');
 
 class MolStarProteopediaWrapper {
     static VERSION_MAJOR = 5;
-    static VERSION_MINOR = 2;
+    static VERSION_MINOR = 4;
 
     private _ev = RxEventHelper.create();
 
@@ -195,6 +195,7 @@ class MolStarProteopediaWrapper {
         return PluginCommands.State.Update(this.plugin, { state: this.plugin.state.data, tree });
     }
 
+    private emptyLoadedParams: LoadParams = { url: '', format: 'cif', isBinary: false, assemblyId: '' };
     private loadedParams: LoadParams = { url: '', format: 'cif', isBinary: false, assemblyId: '' };
     async load({ url, format = 'cif', assemblyId = 'deposited', isBinary = false, representationStyle }: LoadParams) {
         let loadType: 'full' | 'update' = 'full';
@@ -265,26 +266,7 @@ class MolStarProteopediaWrapper {
 
     camera = {
         toggleSpin: () => this.toggleSpin(),
-        resetPosition: () => PluginCommands.Camera.Reset(this.plugin, { }),
-        // setClip: (options?: { distance?: number, near?: number, far?: number }) => {
-        //     if (!options) {
-        //         PluginCommands.Canvas3D.SetSettings(this.plugin, {
-        //             settings: {
-        //                 cameraClipDistance: DefaultCanvas3DParams.cameraClipDistance,
-        //                 clip: DefaultCanvas3DParams.clip
-        //             }
-        //         });
-        //         return;
-        //     }
-
-        //     options = options || { };
-        //     const props = this.plugin.canvas3d.props;
-        //     const clipNear = typeof options.near === 'undefined' ? props.clip[0] : options.near;
-        //     const clipFar = typeof options.far === 'undefined' ? props.clip[1] : options.far;
-        //     PluginCommands.Canvas3D.SetSettings(this.plugin, {
-        //         settings: { cameraClipDistance: options.distance, clip: [clipNear, clipFar] }
-        //     });
-        // }
+        resetPosition: () => PluginCommands.Camera.Reset(this.plugin, { })
     }
 
     animate = {
@@ -305,11 +287,6 @@ class MolStarProteopediaWrapper {
             }
 
             const state = this.state;
-
-            // const visuals = state.selectQ(q => q.ofType(PluginStateObject.Molecule.Structure.Representation3D).filter(c => c.transform.transformer === StateTransforms.Representation.StructureRepresentation3D));
-            // for (const v of visuals) {
-            // }
-
             const tree = state.build();
             const colorTheme = { name: EvolutionaryConservation.propertyProvider.descriptor.name, params: this.plugin.representation.structure.themes.colorThemeRegistry.get(EvolutionaryConservation.propertyProvider.descriptor.name).defaultValues };
 
@@ -416,22 +393,21 @@ class MolStarProteopediaWrapper {
     }
 
     snapshot = {
-        get: () => {
-            return this.plugin.state.getSnapshot();
+        get: (params?: PluginState.SnapshotParams) => {
+            return this.plugin.state.getSnapshot(params);
         },
         set: (snapshot: PluginState.Snapshot) => {
             return this.plugin.state.setSnapshot(snapshot);
         },
-        download: () => {
-            const json = JSON.stringify(this.plugin.state.getSnapshot(), null, 2);
-            const blob = new Blob([json], {type : 'application/json;charset=utf-8'});
-            download(blob, `mol-star_state_${(name || getFormattedTime())}.json`);
+        download: async (type: 'molj' | 'molx' = 'molj', params?: PluginState.SnapshotParams) => {
+            const data = await this.plugin.managers.snapshot.serialize({ type, params });
+            download(data, `mol-star_state_${(name || getFormattedTime())}.${type}`);
         },
-        fetch: async (url: string) => {
+        fetch: async (url: string, type: 'molj' | 'molx' = 'molj') => {
             try {
-                const snapshot = await this.plugin.runTask(this.plugin.fetch({ url, type: 'json' }));
-                // TODO: is this OK to test for snapshots from server?
-                await this.plugin.state.setSnapshot(snapshot?.data?.entries?.[0]?.snapshot || snapshot);
+                const data = await this.plugin.runTask(this.plugin.fetch({ url, type: 'binary' }));
+                this.loadedParams = { ...this.emptyLoadedParams };
+                await this.plugin.managers.snapshot.open(new File([data], `state.${type}`));
             } catch (e) {
                 console.log(e);
             }

src/extensions/cellpack/data.ts

@@ -65,6 +65,7 @@ export interface Ingredient {
     principalAxis?: Vec3;
     /** offset along membrane */
     offset?: Vec3;
+    ingtype?: string;
 }
 
 export interface IngredientSource {

src/extensions/cellpack/model.ts

@@ -9,7 +9,7 @@ import { PluginContext } from '../../mol-plugin/context';
 import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Ingredient, IngredientSource, CellPacking } from './data';
-import { getFromPdb, getFromCellPackDB, IngredientFiles, parseCif, parsePDBfile, getStructureMean } from './util';
+import { getFromPdb, getFromCellPackDB, IngredientFiles, parseCif, parsePDBfile, getStructureMean, getFromOPM } from './util';
 import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit } from '../../mol-model/structure';
 import { trajectoryFromMmCIF, MmcifFormat } from '../../mol-model-formats/structure/mmcif';
 import { trajectoryFromPDB } from '../../mol-model-formats/structure/pdb';
@@ -26,56 +26,71 @@ import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
 import { Column } from '../../mol-data/db';
 import { createModels } from '../../mol-model-formats/structure/basic/parser';
 import { CellpackPackingPreset, CellpackMembranePreset } from './preset';
-import { Asset, AssetManager } from '../../mol-util/assets';
+import { Asset } from '../../mol-util/assets';
 
 function getCellPackModelUrl(fileName: string, baseUrl: string) {
     return `${baseUrl}/results/${fileName}`;
 }
 
-async function getModel(assetManager: AssetManager, id: string, model_id: number, baseUrl: string, file?: Asset.File) {
+async function getModel(plugin: PluginContext, id: string, ingredient: Ingredient, baseUrl: string, file?: Asset.File) {
+    const assetManager = plugin.managers.asset;
+    const model_id = (ingredient.source.model) ? parseInt(ingredient.source.model) : 0;
+    const surface = (ingredient.ingtype) ? (ingredient.ingtype === 'transmembrane') : false;
     let model: Model;
     let assets: Asset.Wrapper[] = [];
     if (file) {
         if (file.name.endsWith('.cif')) {
-            const text = await assetManager.resolve(file, 'string').run();
+            const text = await plugin.runTask(assetManager.resolve(file, 'string'));
             assets.push(text);
-            const cif = (await parseCif(text.data)).blocks[0];
-            model = (await trajectoryFromMmCIF(cif).run())[model_id];
+            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 assetManager.resolve(file, 'binary').run();
+            const binary = await plugin.runTask(assetManager.resolve(file, 'binary'));
             assets.push(binary);
-            const cif = (await parseCif(binary.data)).blocks[0];
-            model = (await trajectoryFromMmCIF(cif).run())[model_id];
+            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 assetManager.resolve(file, 'string').run();
+            const text = await plugin.runTask(assetManager.resolve(file, 'string'));
             assets.push(text);
-            const pdb = await parsePDBfile(text.data, id);
-            model = (await trajectoryFromPDB(pdb).run())[model_id];
+            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)) {
-        const { mmcif, asset } = await getFromPdb(id, assetManager);
-        assets.push(asset);
-        model = (await trajectoryFromMmCIF(mmcif).run())[model_id];
+        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];
+            } else {
+                const { mmcif, asset } = await getFromPdb(plugin, id, assetManager);
+                assets.push(asset);
+                model = (await plugin.runTask(trajectoryFromMmCIF(mmcif)))[model_id];
+            }
+        } 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(id, baseUrl, assetManager);
+        const data = await getFromCellPackDB(plugin, id, baseUrl, assetManager);
         assets.push(data.asset);
         if ('pdb' in data) {
-            model = (await trajectoryFromPDB(data.pdb).run())[model_id];
+            model = (await plugin.runTask(trajectoryFromPDB(data.pdb)))[model_id];
         } else {
-            model = (await trajectoryFromMmCIF(data.mmcif).run())[model_id];
+            model = (await plugin.runTask(trajectoryFromMmCIF(data.mmcif)))[model_id];
         }
     }
     return { model, assets };
 }
 
-async function getStructure(model: Model, source: IngredientSource, props: { assembly?: string } = {}) {
+async function getStructure(plugin: PluginContext, model: Model, source: IngredientSource, props: { assembly?: string } = {}) {
     let structure = Structure.ofModel(model);
     const { assembly } = props;
 
     if (assembly) {
-        structure = await StructureSymmetry.buildAssembly(structure, assembly).run();
+        structure = await plugin.runTask(StructureSymmetry.buildAssembly(structure, assembly));
     }
     let query;
     if (source.selection){
@@ -260,7 +275,7 @@ function getCifCurve(name: string, transforms: Mat4[], model: Model) {
     };
 }
 
-async function getCurve(name: string, ingredient: Ingredient, transforms: Mat4[], model: Model) {
+async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredient, transforms: Mat4[], model: Model) {
     const cif = getCifCurve(name, transforms, model);
 
     const curveModelTask = Task.create('Curve Model', async ctx => {
@@ -269,11 +284,11 @@ async function getCurve(name: string, ingredient: Ingredient, transforms: Mat4[]
         return models[0];
     });
 
-    const curveModel = await curveModelTask.run();
-    return getStructure(curveModel, ingredient.source);
+    const curveModel = await plugin.runTask(curveModelTask);
+    return getStructure(plugin, curveModel, ingredient.source);
 }
 
-async function getIngredientStructure(assetManager: AssetManager, ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles) {
+async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles) {
     const { name, source, results, nbCurve } = ingredient;
     if (source.pdb === 'None') return;
 
@@ -288,13 +303,12 @@ async function getIngredientStructure(assetManager: AssetManager, ingredient: In
     }
 
     // model id in case structure is NMR
-    const model_id = (ingredient.source.model) ? parseInt(ingredient.source.model) : 0;
-    const { model, assets } = await getModel(assetManager, source.pdb || name, model_id, baseUrl, file);
+    const { model, assets } = await getModel(plugin, source.pdb || name, ingredient, baseUrl, file);
     if (!model) return;
 
     let structure: Structure;
     if (nbCurve) {
-        structure = await getCurve(name, ingredient, getCurveTransforms(ingredient), model);
+        structure = await getCurve(plugin, name, ingredient, getCurveTransforms(ingredient), model);
     } else {
         let bu: string|undefined = source.bu ? source.bu : undefined;
         if (bu){
@@ -304,7 +318,7 @@ async function getIngredientStructure(assetManager: AssetManager, ingredient: In
                 bu = bu.slice(2);
             }
         }
-        structure = await getStructure(model, source, { assembly: bu });
+        structure = await getStructure(plugin, model, source, { assembly: bu });
         // transform with offset and pcp
         let legacy: boolean = true;
         if (ingredient.offset || ingredient.principalAxis){
@@ -336,14 +350,14 @@ async function getIngredientStructure(assetManager: AssetManager, ingredient: In
     return { structure, assets };
 }
 
-export function createStructureFromCellPack(assetManager: AssetManager, packing: CellPacking, baseUrl: string, ingredientFiles: IngredientFiles) {
+export function createStructureFromCellPack(plugin: PluginContext, packing: CellPacking, baseUrl: string, ingredientFiles: IngredientFiles) {
     return Task.create('Create Packing Structure', async ctx => {
         const { ingredients, name } = packing;
         const assets: Asset.Wrapper[] = [];
         const structures: Structure[] = [];
         for (const iName in ingredients) {
             if (ctx.shouldUpdate) await ctx.update(iName);
-            const ingredientStructure = await getIngredientStructure(assetManager, ingredients[iName], baseUrl, ingredientFiles);
+            const ingredientStructure = await getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles);
             if (ingredientStructure) {
                 structures.push(ingredientStructure.structure);
                 assets.push(...ingredientStructure.assets);

src/extensions/cellpack/state.ts

@@ -71,7 +71,7 @@ const StructureFromCellpack = PluginStateTransform.BuiltIn({
                     ingredientFiles[file.name] = file;
                 }
             }
-            const { structure, assets } = await createStructureFromCellPack(plugin.managers.asset, packing, params.baseUrl, ingredientFiles).runInContext(ctx);
+            const { structure, assets } = await createStructureFromCellPack(plugin, packing, params.baseUrl, ingredientFiles).runInContext(ctx);
 
             await CellPackInfoProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, structure, {
                 info: { packingsCount: a.data.packings.length, packingIndex: params.packing }

src/extensions/cellpack/util.ts

@@ -9,52 +9,56 @@ import { parsePDB } from '../../mol-io/reader/pdb/parser';
 import { AssetManager, Asset } from '../../mol-util/assets';
 import { Structure } from '../../mol-model/structure';
 import { Vec3 } from '../../mol-math/linear-algebra';
+import { PluginContext } from '../../mol-plugin/context';
 
-export async function parseCif(data: string|Uint8Array) {
+export async function parseCif(plugin: PluginContext, data: string | Uint8Array) {
     const comp = CIF.parse(data);
-    const parsed = await comp.run();
+    const parsed = await plugin.runTask(comp);
     if (parsed.isError) throw parsed;
     return parsed.result;
 }
 
-export async function parsePDBfile(data: string, id: string) {
+export async function parsePDBfile(plugin: PluginContext, data: string, id: string) {
     const comp = parsePDB(data, id);
-    const parsed = await comp.run();
+    const parsed = await plugin.runTask(comp);
     if (parsed.isError) throw parsed;
     return parsed.result;
 }
 
-async function downloadCif(url: string, isBinary: boolean, assetManager: AssetManager) {
+async function downloadCif(plugin: PluginContext, url: string, isBinary: boolean, assetManager: AssetManager) {
     const type = isBinary ? 'binary' : 'string';
-    const asset = await assetManager.resolve(Asset.getUrlAsset(assetManager, url), type).run();
-    return { cif: await parseCif(asset.data), asset };
+    const asset = await plugin.runTask(assetManager.resolve(Asset.getUrlAsset(assetManager, url), type));
+    return { cif: await parseCif(plugin, asset.data), asset };
 }
 
-async function downloadPDB(url: string, id: string, assetManager: AssetManager) {
+async function downloadPDB(plugin: PluginContext, url: string, id: string, assetManager: AssetManager) {
     const asset = await assetManager.resolve(Asset.getUrlAsset(assetManager, url), 'string').run();
-    return { pdb: await parsePDBfile(asset.data, id), asset };
+    return { pdb: await parsePDBfile(plugin, asset.data, id), asset };
 }
 
-export async function getFromPdb(pdbId: string, assetManager: AssetManager) {
-    const { cif, asset } = await downloadCif(`https://models.rcsb.org/${pdbId.toUpperCase()}.bcif`, true, assetManager);
+export async function getFromPdb(plugin: PluginContext, pdbId: string, assetManager: AssetManager) {
+    const { cif, asset } = await downloadCif(plugin, `https://models.rcsb.org/${pdbId.toUpperCase()}.bcif`, true, assetManager);
     return { mmcif: cif.blocks[0], asset };
 }
 
-export async function getFromCellPackDB(id: string, baseUrl: string, assetManager: AssetManager) {
+export async function getFromOPM(plugin: PluginContext, pdbId: string, assetManager: AssetManager){
+    const asset = await plugin.runTask(assetManager.resolve(Asset.getUrlAsset(assetManager, `https://opm-assets.storage.googleapis.com/pdb/${pdbId.toLowerCase()}.pdb`), 'string'));
+    return { pdb: await parsePDBfile(plugin, asset.data, pdbId), asset };
+}
+
+export async function getFromCellPackDB(plugin: PluginContext, id: string, baseUrl: string, assetManager: AssetManager) {
     if (id.toLowerCase().endsWith('.cif') || id.toLowerCase().endsWith('.bcif')) {
         const isBinary = id.toLowerCase().endsWith('.bcif');
-        const { cif, asset } = await downloadCif(`${baseUrl}/other/${id}`, isBinary, assetManager);
+        const { cif, asset } = await downloadCif(plugin, `${baseUrl}/other/${id}`, isBinary, assetManager);
         return { mmcif: cif.blocks[0], asset };
     } else {
         const name = id.endsWith('.pdb') ? id.substring(0, id.length - 4) : id;
-        return await downloadPDB(`${baseUrl}/other/${name}.pdb`, name, assetManager);
+        return await downloadPDB(plugin, `${baseUrl}/other/${name}.pdb`, name, assetManager);
     }
 }
 
 export type IngredientFiles = { [name: string]: Asset.File }
 
-//
-
 export function getStructureMean(structure: Structure) {
     let xSum = 0, ySum = 0, zSum = 0;
     for (let i = 0, il = structure.units.length; i < il; ++i) {

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/assembly-symmetry/ui.tsx

@@ -16,7 +16,8 @@ import { StateAction, StateSelection } from '../../../mol-state';
 import { PluginStateObject } from '../../../mol-plugin-state/objects';
 import { PluginContext } from '../../../mol-plugin/context';
 import { Task } from '../../../mol-task';
-import { Check, Extension } from '@material-ui/icons';
+import Check from '@material-ui/icons/Check';
+import Extension from '@material-ui/icons/Extension';
 
 interface AssemblySymmetryControlState extends CollapsableState {
     isBusy: boolean

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

@@ -71,8 +71,7 @@ export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean,
         }
 
         unregister() {
-            // TODO
-            // DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
+            DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
 
             this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
 
@@ -341,7 +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/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-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/geometry.ts

@@ -21,8 +21,9 @@ import { TransformData } from './transform-data';
 import { Theme } from '../../mol-theme/theme';
 import { RenderObjectValues } from '../../mol-gl/render-object';
 import { TextureMesh } from './texture-mesh/texture-mesh';
+import { Image } from './image/image';
 
-export type GeometryKind = 'mesh' | 'points' | 'spheres' | 'text' | 'lines' | 'direct-volume' | 'texture-mesh'
+export type GeometryKind = 'mesh' | 'points' | 'spheres' | 'text' | 'lines' | 'direct-volume' | 'image' | 'texture-mesh'
 
 export type Geometry<T extends GeometryKind = GeometryKind> =
     T extends 'mesh' ? Mesh :
@@ -31,7 +32,8 @@ export type Geometry<T extends GeometryKind = GeometryKind> =
                 T extends 'text' ? Text :
                     T extends 'lines' ? Lines :
                         T extends 'direct-volume' ? DirectVolume :
-                            T extends 'texture-mesh' ? TextureMesh : never
+                            T extends 'image' ? Image :
+                                T extends 'texture-mesh' ? TextureMesh : never
 
 type GeometryParams<T extends GeometryKind> =
     T extends 'mesh' ? Mesh.Params :
@@ -40,7 +42,8 @@ type GeometryParams<T extends GeometryKind> =
                 T extends 'text' ? Text.Params :
                     T extends 'lines' ? Lines.Params :
                         T extends 'direct-volume' ? DirectVolume.Params :
-                            T extends 'texture-mesh' ? TextureMesh.Params : never
+                            T extends 'image' ? Image.Params :
+                                T extends 'texture-mesh' ? TextureMesh.Params : never
 
 export interface GeometryUtils<G extends Geometry, P extends PD.Params = GeometryParams<G['kind']>, V = RenderObjectValues<G['kind']>> {
     Params: P
@@ -64,6 +67,7 @@ export namespace Geometry {
             case 'text': return geometry.charCount * 2 * 3;
             case 'lines': return geometry.lineCount * 2 * 3;
             case 'direct-volume': return 12 * 3;
+            case 'image': return 2 * 3;
             case 'texture-mesh': return geometry.vertexCount;
         }
     }
@@ -78,6 +82,8 @@ export namespace Geometry {
                 return getDrawCount(geometry) === 0 ? 0 : (arrayMax(geometry.groupBuffer.ref.value) + 1);
             case 'direct-volume':
                 return 1;
+            case 'image':
+                return arrayMax(geometry.groupTexture.ref.value.array) + 1;
             case 'texture-mesh':
                 return geometry.groupCount;
         }
@@ -92,6 +98,7 @@ export namespace Geometry {
             case 'text': return Text.Utils as any;
             case 'lines': return Lines.Utils as any;
             case 'direct-volume': return DirectVolume.Utils as any;
+            case 'image': return Image.Utils as any;
             case 'texture-mesh': return TextureMesh.Utils as any;
         }
     }

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

@@ -0,0 +1,210 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { hashFnv32a } from '../../../mol-data/util';
+import { LocationIterator } from '../../../mol-geo/util/location-iterator';
+import { RenderableState } from '../../../mol-gl/renderable';
+import { calculateInvariantBoundingSphere, calculateTransformBoundingSphere, TextureImage } from '../../../mol-gl/renderable/util';
+import { Sphere3D } from '../../../mol-math/geometry';
+import { Vec2 } from '../../../mol-math/linear-algebra';
+import { Theme } from '../../../mol-theme/theme';
+import { ValueCell } from '../../../mol-util';
+import { Color } from '../../../mol-util/color';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { BaseGeometry } from '../base';
+import { createColors } from '../color-data';
+import { GeometryUtils } from '../geometry';
+import { createMarkers } from '../marker-data';
+import { createEmptyOverpaint } from '../overpaint-data';
+import { TransformData } from '../transform-data';
+import { createEmptyTransparency } from '../transparency-data';
+import { ImageValues } from '../../../mol-gl/renderable/image';
+import { fillSerial } from '../../../mol-util/array';
+
+const QuadIndices = new Uint32Array([
+    0, 1, 2,
+    1, 3, 2
+]);
+
+const QuadUvs = new Float32Array([
+    0, 1,
+    0, 0,
+    1, 1,
+    1, 0
+]);
+
+export const InterpolationTypes = {
+    'nearest': 'Nearest',
+    'catmulrom': 'Catmulrom (Cubic)',
+    'mitchell': 'Mitchell (Cubic)',
+    'bspline': 'B-Spline (Cubic)'
+};
+export type InterpolationTypes = keyof typeof InterpolationTypes;
+export const InterpolationTypeNames = Object.keys(InterpolationTypes) as InterpolationTypes[];
+
+export { Image };
+
+interface Image {
+    readonly kind: 'image',
+
+    readonly imageTexture: ValueCell<TextureImage<Float32Array>>,
+    readonly imageTextureDim: ValueCell<Vec2>,
+    readonly cornerBuffer: ValueCell<Float32Array>,
+    readonly groupTexture: ValueCell<TextureImage<Float32Array>>,
+
+    /** Bounding sphere of the image */
+    boundingSphere: Sphere3D
+}
+
+namespace Image {
+    export function create(imageTexture: TextureImage<Float32Array>, corners: Float32Array, groupTexture: TextureImage<Float32Array>, image?: Image): Image {
+        return image ?
+            update(imageTexture, corners, groupTexture, image) :
+            fromData(imageTexture, corners, groupTexture);
+    }
+
+    function hashCode(image: Image) {
+        return hashFnv32a([
+            image.cornerBuffer.ref.version
+        ]);
+    }
+
+    function fromData(imageTexture: TextureImage<Float32Array>, corners: Float32Array, groupTexture: TextureImage<Float32Array>): Image {
+        const boundingSphere = Sphere3D();
+        let currentHash = -1;
+
+        const width = imageTexture.width;
+        const height = imageTexture.height;
+
+        const image = {
+            kind: 'image' as const,
+            imageTexture: ValueCell.create(imageTexture),
+            imageTextureDim: ValueCell.create(Vec2.create(width, height)),
+            cornerBuffer: ValueCell.create(corners),
+            groupTexture: ValueCell.create(groupTexture),
+            get boundingSphere() {
+                const newHash = hashCode(image);
+                if (newHash !== currentHash) {
+                    const b = getBoundingSphere(image.cornerBuffer.ref.value);
+                    Sphere3D.copy(boundingSphere, b);
+                    currentHash = newHash;
+                }
+                return boundingSphere;
+            },
+        };
+        return image;
+    }
+
+    function update(imageTexture: TextureImage<Float32Array>, corners: Float32Array, groupTexture: TextureImage<Float32Array>, image: Image): Image {
+        const width = imageTexture.width;
+        const height = imageTexture.height;
+
+        ValueCell.update(image.imageTexture, imageTexture);
+        ValueCell.update(image.imageTextureDim, Vec2.set(image.imageTextureDim.ref.value, width, height));
+        ValueCell.update(image.cornerBuffer, corners);
+        ValueCell.update(image.groupTexture, groupTexture);
+        return image;
+    }
+
+    export function createEmpty(image?: Image): Image {
+        return {} as Image; // TODO
+    }
+
+    export const Params = {
+        ...BaseGeometry.Params,
+        interpolation: PD.Select('bspline', PD.objectToOptions(InterpolationTypes)),
+    };
+    export type Params = typeof Params
+
+    export const Utils: GeometryUtils<Image, Params> = {
+        Params,
+        createEmpty,
+        createValues,
+        createValuesSimple,
+        updateValues,
+        updateBoundingSphere,
+        createRenderableState,
+        updateRenderableState
+    };
+
+    function createValues(image: Image, transform: TransformData, locationIt: LocationIterator, theme: Theme, props: PD.Values<Params>): ImageValues {
+
+        const { instanceCount, groupCount } = locationIt;
+        const color = createColors(locationIt, theme.color);
+        const marker = createMarkers(instanceCount * groupCount);
+        const overpaint = createEmptyOverpaint();
+        const transparency = createEmptyTransparency();
+
+        const counts = { drawCount: QuadIndices.length, groupCount, instanceCount };
+
+        const invariantBoundingSphere = Sphere3D.clone(image.boundingSphere);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
+
+        return {
+            ...color,
+            ...marker,
+            ...overpaint,
+            ...transparency,
+            ...transform,
+            ...BaseGeometry.createValues(props, counts),
+
+            aPosition: image.cornerBuffer,
+            aUv: ValueCell.create(QuadUvs),
+            elements: ValueCell.create(QuadIndices),
+
+            // aGroup is used as a vertex index here, group id is in tGroupTex
+            aGroup: ValueCell.create(fillSerial(new Float32Array(4))),
+            boundingSphere: ValueCell.create(boundingSphere),
+            invariantBoundingSphere: ValueCell.create(invariantBoundingSphere),
+
+            dInterpolation: ValueCell.create(props.interpolation),
+
+            uImageTexDim: image.imageTextureDim,
+            tImageTex: image.imageTexture,
+            tGroupTex: image.groupTexture,
+        };
+    }
+
+    function createValuesSimple(image: Image, props: Partial<PD.Values<Params>>, colorValue: Color, sizeValue: number, transform?: TransformData) {
+        const s = BaseGeometry.createSimple(colorValue, sizeValue, transform);
+        const p = { ...PD.getDefaultValues(Params), ...props };
+        return createValues(image, s.transform, s.locationIterator, s.theme, p);
+    }
+
+    function updateValues(values: ImageValues, props: PD.Values<Params>) {
+        BaseGeometry.updateValues(values, props);
+        ValueCell.updateIfChanged(values.dInterpolation, props.interpolation);
+    }
+
+    function updateBoundingSphere(values: ImageValues, image: Image) {
+        const invariantBoundingSphere = Sphere3D.clone(image.boundingSphere);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
+
+        if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
+            ValueCell.update(values.boundingSphere, boundingSphere);
+        }
+        if (!Sphere3D.equals(invariantBoundingSphere, values.invariantBoundingSphere.ref.value)) {
+            ValueCell.update(values.invariantBoundingSphere, invariantBoundingSphere);
+        }
+    }
+
+    function createRenderableState(props: PD.Values<Params>): RenderableState {
+        const state = BaseGeometry.createRenderableState(props);
+        state.opaque = false;
+        return state;
+    }
+
+    function updateRenderableState(state: RenderableState, props: PD.Values<Params>) {
+        BaseGeometry.updateRenderableState(state, props);
+        state.opaque = false;
+    }
+}
+
+//
+
+function getBoundingSphere(corners: Float32Array) {
+    return calculateInvariantBoundingSphere(corners, corners.length / 3, 1);
+}

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-geo/util/marching-cubes/algorithm.ts

@@ -196,11 +196,16 @@ class MarchingCubesState {
         const n1y = sfg(sf, hi, Math.max(0, hj - 1), hk) - sfg(sf, hi, Math.min(this.nY - 1, hj + 1), hk);
         const n1z = sfg(sf, hi, hj, Math.max(0, hk - 1)) - sfg(sf, hi, hj, Math.min(this.nZ - 1, hk + 1));
 
-        this.builder.addNormal(
-            n0x + t * (n0x - n1x),
-            n0y + t * (n0y - n1y),
-            n0z + t * (n0z - n1z)
-        );
+        const nx = n0x + t * (n0x - n1x);
+        const ny = n0y + t * (n0y - n1y);
+        const nz = n0z + t * (n0z - n1z);
+
+        // ensure normal-direction is the same for negative and positive iso-levels
+        if (this.isoLevel >= 0) {
+            this.builder.addNormal(nx, ny, nz);
+        } else {
+            this.builder.addNormal(-nx, -ny, -nz);
+        }
 
         return id;
     }
@@ -255,7 +260,13 @@ class MarchingCubesState {
 
         const triInfo = TriTable[tableIndex];
         for (let t = 0; t < triInfo.length; t += 3) {
-            this.builder.addTriangle(this.vertList, triInfo[t], triInfo[t + 1], triInfo[t + 2], edgeFilter);
+            const l = triInfo[t], m = triInfo[t + 1], n = triInfo[t + 2];
+            // ensure winding-order is the same for negative and positive iso-levels
+            if (this.isoLevel >= 0) {
+                this.builder.addTriangle(this.vertList, l, m, n, edgeFilter);
+            } else {
+                this.builder.addTriangle(this.vertList, n, m, l, edgeFilter);
+            }
         }
     }
 }

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/render-object.ts

@@ -14,6 +14,7 @@ import { LinesValues, LinesRenderable } from './renderable/lines';
 import { SpheresValues, SpheresRenderable } from './renderable/spheres';
 import { TextValues, TextRenderable } from './renderable/text';
 import { TextureMeshValues, TextureMeshRenderable } from './renderable/texture-mesh';
+import { ImageValues, ImageRenderable } from './renderable/image';
 
 const getNextId = idFactory(0, 0x7FFFFFFF);
 
@@ -27,7 +28,7 @@ export interface GraphicsRenderObject<T extends RenderObjectType = RenderObjectT
     readonly materialId: number
 }
 
-export type RenderObjectType = 'mesh' | 'points' | 'spheres' | 'text' | 'lines' | 'direct-volume' | 'texture-mesh'
+export type RenderObjectType = 'mesh' | 'points' | 'spheres' | 'text' | 'lines' | 'direct-volume' | 'image' | 'texture-mesh'
 
 export type RenderObjectValues<T extends RenderObjectType> =
     T extends 'mesh' ? MeshValues :
@@ -36,7 +37,8 @@ export type RenderObjectValues<T extends RenderObjectType> =
                 T extends 'text' ? TextValues :
                     T extends 'lines' ? LinesValues :
                         T extends 'direct-volume' ? DirectVolumeValues :
-                            T extends 'texture-mesh' ? TextureMeshValues : never
+                            T extends 'image' ? ImageValues :
+                                T extends 'texture-mesh' ? TextureMeshValues : never
 
 //
 
@@ -52,6 +54,7 @@ export function createRenderable<T extends RenderObjectType>(ctx: WebGLContext,
         case 'text': return TextRenderable(ctx, o.id, o.values as TextValues, o.state, o.materialId);
         case 'lines': return LinesRenderable(ctx, o.id, o.values as LinesValues, o.state, o.materialId);
         case 'direct-volume': return DirectVolumeRenderable(ctx, o.id, o.values as DirectVolumeValues, o.state, o.materialId);
+        case 'image': return ImageRenderable(ctx, o.id, o.values as ImageValues, o.state, o.materialId);
         case 'texture-mesh': return TextureMeshRenderable(ctx, o.id, o.values as TextureMeshValues, o.state, o.materialId);
     }
     throw new Error('unsupported type');

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> {

src/mol-gl/renderable/image.ts

@@ -0,0 +1,41 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Renderable, RenderableState, createRenderable } from '../renderable';
+import { WebGLContext } from '../webgl/context';
+import { createGraphicsRenderItem } from '../webgl/render-item';
+import { AttributeSpec, Values, GlobalUniformSchema, InternalSchema, TextureSpec, ElementsSpec, DefineSpec, InternalValues, BaseSchema, UniformSpec } from './schema';
+import { ImageShaderCode } from '../shader-code';
+import { ValueCell } from '../../mol-util';
+import { InterpolationTypeNames } from '../../mol-geo/geometry/image/image';
+
+export const ImageSchema = {
+    ...BaseSchema,
+
+    aPosition: AttributeSpec('float32', 3, 0),
+    aUv: AttributeSpec('float32', 2, 0),
+
+    elements: ElementsSpec('uint32'),
+
+    uImageTexDim: UniformSpec('v2'),
+    tImageTex: TextureSpec('image-float32', 'rgba', 'float', 'nearest'),
+    tGroupTex: TextureSpec('image-float32', 'alpha', 'float', 'nearest'),
+
+    dInterpolation: DefineSpec('string', InterpolationTypeNames),
+};
+export type ImageSchema = typeof ImageSchema
+export type ImageValues = Values<ImageSchema>
+
+export function ImageRenderable(ctx: WebGLContext, id: number, values: ImageValues, state: RenderableState, materialId: number): Renderable<ImageValues> {
+    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);
+    return createRenderable(renderItem, values, state);
+}

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

@@ -212,6 +212,10 @@ namespace Renderer {
                     state.cullFace(gl.BACK);
                 }
 
+                if (variant === 'color') {
+                    state.depthMask(r.state.writeDepth);
+                }
+
                 r.render(variant);
             }
         };
@@ -245,11 +249,11 @@ 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 +272,11 @@ 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-code.ts

@@ -126,6 +126,10 @@ import direct_volume_vert from './shader/direct-volume.vert';
 import direct_volume_frag from './shader/direct-volume.frag';
 export const DirectVolumeShaderCode = ShaderCode('direct-volume', direct_volume_vert, direct_volume_frag, { fragDepth: true });
 
+import image_vert from './shader/image.vert';
+import image_frag from './shader/image.frag';
+export const ImageShaderCode = ShaderCode('image', image_vert, image_frag, { fragDepth: true });
+
 //
 
 export type ShaderDefines = {

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-color-varying.glsl.ts

@@ -1,26 +1,30 @@
 export default `
-#if defined(dColorType_attribute)
-    vColor.rgb = aColor;
-#elif defined(dColorType_instance)
-    vColor.rgb = readFromTexture(tColor, aInstance, uColorTexDim).rgb;
-#elif defined(dColorType_group)
-    vColor.rgb = readFromTexture(tColor, group, uColorTexDim).rgb;
-#elif defined(dColorType_groupInstance)
-    vColor.rgb = readFromTexture(tColor, aInstance * float(uGroupCount) + group, uColorTexDim).rgb;
-#elif defined(dColorType_objectPicking)
-    vColor = vec4(encodeFloatRGB(float(uObjectId)), 1.0);
-#elif defined(dColorType_instancePicking)
-    vColor = vec4(encodeFloatRGB(aInstance), 1.0);
-#elif defined(dColorType_groupPicking)
-    vColor = vec4(encodeFloatRGB(group), 1.0);
-#endif
+#if defined(dRenderVariant_color)
+    #if defined(dColorType_attribute)
+        vColor.rgb = aColor;
+    #elif defined(dColorType_instance)
+        vColor.rgb = readFromTexture(tColor, aInstance, uColorTexDim).rgb;
+    #elif defined(dColorType_group)
+        vColor.rgb = readFromTexture(tColor, group, uColorTexDim).rgb;
+    #elif defined(dColorType_groupInstance)
+        vColor.rgb = readFromTexture(tColor, aInstance * float(uGroupCount) + group, uColorTexDim).rgb;
+    #endif
 
-#ifdef dOverpaint
-    vOverpaint = readFromTexture(tOverpaint, aInstance * float(uGroupCount) + group, uOverpaintTexDim);
-#endif
+    #ifdef dOverpaint
+        vOverpaint = readFromTexture(tOverpaint, aInstance * float(uGroupCount) + group, uOverpaintTexDim);
+    #endif
 
-#ifdef dTransparency
-    vGroup = group;
-    vTransparency = readFromTexture(tTransparency, aInstance * float(uGroupCount) + group, uTransparencyTexDim).a;
+    #ifdef dTransparency
+        vGroup = group;
+        vTransparency = readFromTexture(tTransparency, aInstance * float(uGroupCount) + group, uTransparencyTexDim).a;
+    #endif
+#elif defined(dRenderVariant_pick)
+    #if defined(dRenderVariant_pickObject)
+        vColor = vec4(encodeFloatRGB(float(uObjectId)), 1.0);
+    #elif defined(dRenderVariant_pickInstance)
+        vColor = vec4(encodeFloatRGB(aInstance), 1.0);
+    #elif defined(dRenderVariant_pickGroup)
+        vColor = vec4(encodeFloatRGB(group), 1.0);
+    #endif
 #endif
 `;

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

@@ -1,43 +1,45 @@
 export default `
-#if defined(dColorType_uniform)
-    vec4 material = vec4(uColor, uAlpha);
-#elif defined(dColorType_attribute) || defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance)
-    vec4 material = vec4(vColor.rgb, uAlpha);
-#elif defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+#if defined(dRenderVariant_color)
+    #if defined(dColorType_uniform)
+        vec4 material = vec4(uColor, uAlpha);
+    #elif defined(dColorType_varying)
+        vec4 material = vec4(vColor.rgb, uAlpha);
+    #endif
+
+    // mix material with overpaint
+    #if defined(dOverpaint)
+        material.rgb = mix(material.rgb, vOverpaint.rgb, vOverpaint.a);
+    #endif
+
+    // apply screendoor transparency
+    #if defined(dTransparency)
+        float ta = 1.0 - vTransparency;
+        float at = 0.0;
+
+        // shift by view-offset during multi-sample rendering to allow for blending
+        vec2 coord = gl_FragCoord.xy + uViewOffset * 0.25;
+
+        #if defined(dTransparencyVariant_single)
+            const mat4 thresholdMatrix = mat4(
+                1.0 / 17.0,  9.0 / 17.0,  3.0 / 17.0, 11.0 / 17.0,
+                13.0 / 17.0,  5.0 / 17.0, 15.0 / 17.0,  7.0 / 17.0,
+                4.0 / 17.0, 12.0 / 17.0,  2.0 / 17.0, 10.0 / 17.0,
+                16.0 / 17.0,  8.0 / 17.0, 14.0 / 17.0,  6.0 / 17.0
+            );
+            at = thresholdMatrix[int(intMod(coord.x, 4.0))][int(intMod(coord.y, 4.0))];
+        #elif defined(dTransparencyVariant_multi)
+            at = fract(dot(vec3(coord, vGroup + 0.5), vec3(2.0, 7.0, 23.0) / 17.0f));
+        #endif
+
+        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
-#elif defined(dColorType_depth)
+#elif defined(dRenderVariant_depth)
     #ifdef enabledFragDepth
         vec4 material = packDepthToRGBA(gl_FragDepthEXT);
     #else
         vec4 material = packDepthToRGBA(gl_FragCoord.z);
     #endif
 #endif
-
-// mix material with overpaint
-#if defined(dOverpaint) && (defined(dColorType_uniform) || defined(dColorType_attribute) || defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance))
-    material.rgb = mix(material.rgb, vOverpaint.rgb, vOverpaint.a);
-#endif
-
-// apply screendoor transparency
-#if defined(dTransparency) && (defined(dColorType_uniform) || defined(dColorType_attribute) || defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance))
-    float ta = 1.0 - vTransparency;
-    float at = 0.0;
-
-    // shift by view-offset during multi-sample rendering to allow for blending
-    vec2 coord = gl_FragCoord.xy + uViewOffset * 0.25;
-
-    #if defined(dTransparencyVariant_single)
-        const mat4 thresholdMatrix = mat4(
-            1.0 / 17.0,  9.0 / 17.0,  3.0 / 17.0, 11.0 / 17.0,
-            13.0 / 17.0,  5.0 / 17.0, 15.0 / 17.0,  7.0 / 17.0,
-            4.0 / 17.0, 12.0 / 17.0,  2.0 / 17.0, 10.0 / 17.0,
-            16.0 / 17.0,  8.0 / 17.0, 14.0 / 17.0,  6.0 / 17.0
-        );
-        at = thresholdMatrix[int(intMod(coord.x, 4.0))][int(intMod(coord.y, 4.0))];
-    #elif defined(dTransparencyVariant_multi)
-        at = fract(dot(vec3(coord, vGroup + 0.5), vec3(2.0, 7.0, 23.0) / 17.0f));
-    #endif
-
-    if (ta < 0.99 && (ta < 0.01 || ta < at)) discard;
-#endif
 `;

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

@@ -1,22 +1,24 @@
 export default `
-#if defined(dColorType_uniform)
-    uniform vec3 uColor;
-#elif defined(dColorType_attribute) || defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance)
-    varying vec4 vColor;
-#elif defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+#if defined(dRenderVariant_color)
+    #if defined(dColorType_uniform)
+        uniform vec3 uColor;
+    #elif defined(dColorType_varying)
+        varying vec4 vColor;
+    #endif
+
+    #ifdef dOverpaint
+        varying vec4 vOverpaint;
+    #endif
+
+    #ifdef dTransparency
+        varying float vGroup;
+        varying float vTransparency;
+    #endif
+#elif defined(dRenderVariant_pick)
     #if __VERSION__ != 300
         varying vec4 vColor;
     #else
         flat in vec4 vColor;
     #endif
 #endif
-
-#ifdef dOverpaint
-    varying vec4 vOverpaint;
-#endif
-
-#ifdef dTransparency
-    varying float vGroup;
-    varying float vTransparency;
-#endif
 `;

src/mol-gl/shader/chunks/color-vert-params.glsl.ts

@@ -1,31 +1,33 @@
 export default `
-#if defined(dColorType_uniform)
-    uniform vec3 uColor;
-#elif defined(dColorType_attribute)
-    varying vec4 vColor;
-    attribute vec3 aColor;
-#elif defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance)
-    varying vec4 vColor;
-    uniform vec2 uColorTexDim;
-    uniform sampler2D tColor;
-#elif defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+#if defined(dRenderVariant_color)
+    #if defined(dColorType_uniform)
+        uniform vec3 uColor;
+    #elif defined(dColorType_attribute)
+        varying vec4 vColor;
+        attribute vec3 aColor;
+    #elif defined(dColorType_texture)
+        varying vec4 vColor;
+        uniform vec2 uColorTexDim;
+        uniform sampler2D tColor;
+    #endif
+
+    #ifdef dOverpaint
+        varying vec4 vOverpaint;
+        uniform vec2 uOverpaintTexDim;
+        uniform sampler2D tOverpaint;
+    #endif
+
+    #ifdef dTransparency
+        varying float vGroup;
+        varying float vTransparency;
+        uniform vec2 uTransparencyTexDim;
+        uniform sampler2D tTransparency;
+    #endif
+#elif defined(dRenderVariant_pick)
     #if __VERSION__ != 300
         varying vec4 vColor;
     #else
         flat out vec4 vColor;
     #endif
 #endif
-
-#ifdef dOverpaint
-    varying vec4 vOverpaint;
-    uniform vec2 uOverpaintTexDim;
-    uniform sampler2D tOverpaint;
-#endif
-
-#ifdef dTransparency
-    varying float vGroup;
-    varying float vTransparency;
-    uniform vec2 uTransparencyTexDim;
-    uniform sampler2D tTransparency;
-#endif
 `;

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

@@ -1,4 +1,20 @@
 export default `
+// TODO find a better place for these convenience defines
+
+#if defined(dRenderVariant_pickObject) || defined(dRenderVariant_pickInstance) || defined(dRenderVariant_pickGroup)
+    #define dRenderVariant_pick
+#endif
+
+#if defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance)
+    #define dColorType_texture
+#endif
+
+#if defined(dColorType_attribute) || defined(dColorType_texture)
+    #define dColorType_varying
+#endif
+
+//
+
 #define PI 3.14159265
 #define RECIPROCAL_PI 0.31830988618
 #define EPSILON 1e-6

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

@@ -41,7 +41,7 @@ uniform int uPickable;
 
 #if defined(dColorType_uniform)
     uniform vec3 uColor;
-#elif defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance)
+#elif defined(dColorType_varying)
     uniform vec2 uColorTexDim;
     uniform sampler2D tColor;
 #endif
@@ -114,23 +114,23 @@ vec4 raymarch(vec3 startLoc, vec3 step, vec3 viewDir) {
                 tmp = ((prevValue - uIsoValue) / ((prevValue - uIsoValue) - (value - uIsoValue)));
                 isoPos = mix(pos - step, pos, tmp);
 
-                #if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+                #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(dColorType_objectPicking)
+                #if defined(dRenderVariant_pickObject)
                     return vec4(encodeFloatRGB(float(uObjectId)), 1.0);
-                #elif defined(dColorType_instancePicking)
+                #elif defined(dRenderVariant_pickInstance)
                     return vec4(encodeFloatRGB(instance), 1.0);
-                #elif defined(dColorType_groupPicking)
+                #elif defined(dRenderVariant_pickGroup)
                     float group = floor(decodeFloatRGB(textureGroup(isoPos).rgb) + 0.5);
                     return vec4(encodeFloatRGB(group), 1.0);
-                #elif defined(dColorType_depth)
+                #elif defined(dRenderVariant_depth)
                     return packDepthToRGBA(gl_FragCoord.z); // TODO calculate isosurface depth
-                #else
+                #elif defined(dRenderVariant_color)
                     // compute gradient by central differences
                     gradient.x = textureVal(isoPos - dx).a - textureVal(isoPos + dx).a;
                     gradient.y = textureVal(isoPos - dy).a - textureVal(isoPos + dy).a;

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

@@ -0,0 +1,136 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+export default `
+precision highp float;
+precision highp int;
+
+#include common
+#include read_from_texture
+#include common_frag_params
+
+uniform vec2 uImageTexDim;
+uniform sampler2D tImageTex;
+uniform sampler2D tGroupTex;
+
+uniform vec2 uMarkerTexDim;
+uniform sampler2D tMarker;
+
+varying vec2 vUv;
+varying float vInstance;
+
+#if defined(dInterpolation_catmulrom) || defined(dInterpolation_mitchell) || defined(dInterpolation_bspline)
+    #define dInterpolation_cubic
+#endif
+
+#if defined(dInterpolation_cubic)
+    #if defined(dInterpolation_catmulrom) || defined(dInterpolation_mitchell)
+        #if defined(dInterpolation_catmulrom)
+            const float B = 0.0;
+            const float C = 0.5;
+        #elif defined(dInterpolation_mitchell)
+            const float B = 0.333;
+            const float C = 0.333;
+        #endif
+
+        float cubicFilter(float x){
+            float f = x;
+            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;
+            }else{
+                return 0.0;
+            }
+        }
+    #elif defined(dInterpolation_bspline)
+        float cubicFilter(float x) {
+            float f = x;
+            if (f < 0.0) {
+                f = -f;
+            }
+            if (f >= 0.0 && f <= 1.0){
+                return (2.0 / 3.0) + (0.5) * (f * f * f) - (f * f);
+            } else if (f > 1.0 && f <= 2.0) {
+                return 1.0 / 6.0 * pow((2.0 - f), 3.0);
+            }
+            return 1.0;
+        }
+    #endif
+
+    vec4 biCubic(sampler2D tex, vec2 texCoord) {
+        vec2 texelSize = 1.0 / uImageTexDim;
+        texCoord -= texelSize / 2.0;
+        vec4 nSum = vec4(0.0);
+        float nDenom = 0.0;
+        vec2 cell = fract(texCoord * uImageTexDim);
+        for (float m = -1.0; m <= 2.0; ++m) {
+            for (float n = -1.0; n <= 2.0; ++n) {
+                vec4 vecData = texture2D(tex, texCoord + texelSize * vec2(m, n));
+                float c = cubicFilter(m - cell.x) * cubicFilter(-n + cell.y);
+                nSum += vecData * c;
+                nDenom += c;
+            }
+        }
+        return nSum / nDenom;
+    }
+#endif
+
+void main() {
+    #if defined(dInterpolation_cubic)
+        vec4 imageData = biCubic(tImageTex, vUv);
+    #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
+        }
+    #elif defined(dRenderVariant_depth)
+        if (imageData.a < 0.05)
+            discard;
+
+        #ifdef enabledFragDepth
+            gl_FragColor = packDepthToRGBA(gl_FragDepthEXT);
+        #else
+            gl_FragColor = packDepthToRGBA(gl_FragCoord.z);
+        #endif
+    #elif defined(dRenderVariant_color)
+        if (imageData.a < 0.05)
+            discard;
+
+        gl_FragColor = imageData;
+        gl_FragColor.a *= uAlpha;
+
+        float group = texture2D(tGroupTex, vUv).r;
+        float vMarker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;
+        #include apply_marker_color
+        #include apply_fog
+    #endif
+}
+`;

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

@@ -0,0 +1,27 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+export default `
+precision highp float;
+precision highp int;
+
+#include common
+#include common_vert_params
+
+attribute vec3 aPosition;
+attribute vec2 aUv;
+attribute mat4 aTransform;
+attribute float aInstance;
+
+varying vec2 vUv;
+varying float vInstance;
+
+void main() {
+    #include assign_position
+
+    vUv = aUv;
+    vInstance = aInstance;
+}
+`;

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

@@ -15,12 +15,12 @@ precision highp int;
 void main(){
     #include assign_material_color
 
-    #if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+    #if defined(dRenderVariant_pick)
         #include check_picking_alpha
         gl_FragColor = material;
-    #elif defined(dColorType_depth)
+    #elif defined(dRenderVariant_depth)
         gl_FragColor = material;
-    #else
+    #elif defined(dRenderVariant_color)
         gl_FragColor = material;
 
         #include apply_marker_color

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

@@ -33,12 +33,12 @@ void main() {
 
     #include assign_material_color
 
-    #if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+    #if defined(dRenderVariant_pick)
         #include check_picking_alpha
         gl_FragColor = material;
-    #elif defined(dColorType_depth)
+    #elif defined(dRenderVariant_depth)
         gl_FragColor = material;
-    #else
+    #elif defined(dRenderVariant_color)
         #ifdef dIgnoreLight
             gl_FragColor = material;
         #else

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

@@ -22,12 +22,12 @@ const float radius = 0.5;
 void main(){
     #include assign_material_color
 
-    #if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+    #if defined(dRenderVariant_pick)
         #include check_picking_alpha
         gl_FragColor = material;
-    #elif defined(dColorType_depth)
+    #elif defined(dRenderVariant_depth)
         gl_FragColor = material;
-    #else
+    #elif defined(dRenderVariant_color)
         gl_FragColor = material;
 
         #ifdef dPointFilledCircle

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

@@ -58,7 +58,7 @@ bool Impostor(out vec3 cameraPos, out vec3 cameraNormal){
 
     cameraPos = rayDirection * negT + rayOrigin;
 
-    
+
     if (calcDepth(cameraPos) <= 0.0) {
         cameraPos = rayDirection * posT + rayOrigin;
         interior = true;
@@ -94,12 +94,12 @@ void main(void){
 
     #include assign_material_color
 
-    #if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+    #if defined(dRenderVariant_pick)
         #include check_picking_alpha
         gl_FragColor = material;
-    #elif defined(dColorType_depth)
+    #elif defined(dRenderVariant_depth)
         gl_FragColor = material;
-    #else
+    #elif defined(dRenderVariant_color)
         #ifdef dIgnoreLight
             gl_FragColor = material;
         #else

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

@@ -56,11 +56,11 @@ void main(){
         gl_FragColor = material;
     }
 
-    #if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+    #if defined(dRenderVariant_pick)
         #include check_picking_alpha
-    #elif defined(dColorType_depth)
+    #elif defined(dRenderVariant_depth)
         gl_FragColor = material;
-    #else
+    #elif defined(dRenderVariant_color)
         #include apply_marker_color
         #include apply_fog
     #endif

src/mol-gl/webgl/render-item.ts

@@ -7,9 +7,9 @@
 import { createAttributeBuffers, ElementsBuffer, AttributeKind } from './buffer';
 import { createTextures, Texture } from './texture';
 import { WebGLContext, checkError } from './context';
-import { ShaderCode } from '../shader-code';
+import { ShaderCode, DefineValues } from '../shader-code';
 import { Program } from './program';
-import { RenderableSchema, RenderableValues, AttributeSpec, getValueVersions, splitValues, Values } from '../renderable/schema';
+import { RenderableSchema, RenderableValues, AttributeSpec, getValueVersions, splitValues, DefineSpec } from '../renderable/schema';
 import { idFactory } from '../../mol-util/id-factory';
 import { ValueCell } from '../../mol-util';
 import { TextureImage, TextureVolume } from '../../mol-gl/renderable/util';
@@ -46,21 +46,19 @@ export interface RenderItem<T extends string> {
 
 //
 
-const GraphicsRenderVariantDefines = {
-    'color': {},
-    'pickObject': { dColorType: ValueCell.create('objectPicking') },
-    'pickInstance': { dColorType: ValueCell.create('instancePicking') },
-    'pickGroup': { dColorType: ValueCell.create('groupPicking') },
-    'depth': { dColorType: ValueCell.create('depth') }
-};
-export type GraphicsRenderVariant = keyof typeof GraphicsRenderVariantDefines
+const GraphicsRenderVariant = { 'color': '', 'pickObject': '', 'pickInstance': '', 'pickGroup': '', 'depth': '' };
+export type GraphicsRenderVariant = keyof typeof GraphicsRenderVariant
+const GraphicsRenderVariants = Object.keys(GraphicsRenderVariant) as GraphicsRenderVariant[];
 
-const ComputeRenderVariantDefines = {
-    'compute': {},
-};
-export type ComputeRenderVariant = keyof typeof ComputeRenderVariantDefines
+const ComputeRenderVariant = { 'compute': '' };
+export type ComputeRenderVariant = keyof typeof ComputeRenderVariant
+const ComputeRenderVariants = Object.keys(ComputeRenderVariant) as ComputeRenderVariant[];
 
-type RenderVariantDefines = typeof GraphicsRenderVariantDefines | typeof ComputeRenderVariantDefines
+function createProgramVariant(ctx: WebGLContext, variant: string, defineValues: DefineValues, shaderCode: ShaderCode, schema: RenderableSchema) {
+    defineValues = { ...defineValues, dRenderVariant: ValueCell.create(variant) };
+    schema = { ...schema, dRenderVariant: DefineSpec('string') };
+    return ctx.resources.program(defineValues, shaderCode, schema);
+}
 
 //
 
@@ -90,14 +88,14 @@ function resetValueChanges(valueChanges: ValueChanges) {
 
 //
 
-export type GraphicsRenderItem = RenderItem<keyof typeof GraphicsRenderVariantDefines & string>
+export type GraphicsRenderItem = RenderItem<GraphicsRenderVariant>
 export function createGraphicsRenderItem(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId: number) {
-    return createRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, GraphicsRenderVariantDefines);
+    return createRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, GraphicsRenderVariants);
 }
 
-export type ComputeRenderItem = RenderItem<keyof typeof ComputeRenderVariantDefines & string>
+export type ComputeRenderItem = RenderItem<ComputeRenderVariant>
 export function createComputeRenderItem(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId = -1) {
-    return createRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, ComputeRenderVariantDefines);
+    return createRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, ComputeRenderVariants);
 }
 
 /**
@@ -105,7 +103,7 @@ export function createComputeRenderItem(ctx: WebGLContext, drawMode: DrawMode, s
  *
  * - assumes that `values.drawCount` and `values.instanceCount` exist
  */
-export function createRenderItem<T extends RenderVariantDefines, S extends keyof T & string>(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId: number, renderVariantDefines: T): RenderItem<S> {
+export function createRenderItem<T extends string>(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId: number, renderVariants: T[]): RenderItem<T> {
     const id = getNextRenderItemId();
     const { stats, state, resources } = ctx;
     const { instancedArrays, vertexArrayObject } = ctx.extensions;
@@ -121,10 +119,9 @@ export function createRenderItem<T extends RenderVariantDefines, S extends keyof
     const glDrawMode = getDrawMode(ctx, drawMode);
 
     const programs: ProgramVariants = {};
-    Object.keys(renderVariantDefines).forEach(k => {
-        const variantDefineValues: Values<RenderableSchema> = (renderVariantDefines as any)[k];
-        programs[k] = resources.program({ ...defineValues, ...variantDefineValues }, shaderCode, schema);
-    });
+    for (const k of renderVariants) {
+        programs[k] = createProgramVariant(ctx, k, defineValues, shaderCode, schema);
+    }
 
     const textures = createTextures(ctx, schema, textureValues);
     const attributeBuffers = createAttributeBuffers(ctx, schema, attributeValues);
@@ -136,9 +133,9 @@ export function createRenderItem<T extends RenderVariantDefines, S extends keyof
     }
 
     const vertexArrays: VertexArrayVariants = {};
-    Object.keys(renderVariantDefines).forEach(k => {
+    for (const k of renderVariants) {
         vertexArrays[k] = vertexArrayObject ? resources.vertexArray(programs[k], attributeBuffers, elementsBuffer) : null;
-    });
+    }
 
     let drawCount = values.drawCount.ref.value;
     let instanceCount = values.instanceCount.ref.value;
@@ -155,9 +152,9 @@ export function createRenderItem<T extends RenderVariantDefines, S extends keyof
     return {
         id,
         materialId,
-        getProgram: (variant: S) => programs[variant],
+        getProgram: (variant: T) => programs[variant],
 
-        render: (variant: S) => {
+        render: (variant: T) => {
             if (drawCount === 0 || instanceCount === 0 || ctx.isContextLost) return;
             const program = programs[variant];
             if (program.id === currentProgramId && state.currentRenderItemId === id) {
@@ -216,11 +213,10 @@ export function createRenderItem<T extends RenderVariantDefines, S extends keyof
 
             if (valueChanges.defines) {
                 // console.log('some defines changed, need to rebuild programs')
-                Object.keys(renderVariantDefines).forEach(k => {
-                    const variantDefineValues: Values<RenderableSchema> = (renderVariantDefines as any)[k];
+                for (const k of renderVariants) {
                     programs[k].destroy();
-                    programs[k] = resources.program({ ...defineValues, ...variantDefineValues }, shaderCode, schema);
-                });
+                    programs[k] = createProgramVariant(ctx, k, defineValues, shaderCode, schema);
+                }
             }
 
             if (values.drawCount.ref.version !== versions.drawCount) {
@@ -271,11 +267,11 @@ export function createRenderItem<T extends RenderVariantDefines, S extends keyof
 
             if (valueChanges.attributes || valueChanges.defines || valueChanges.elements) {
                 // console.log('program/defines or buffers changed, update vaos')
-                Object.keys(renderVariantDefines).forEach(k => {
+                for (const k of renderVariants) {
                     const vertexArray = vertexArrays[k];
                     if (vertexArray) vertexArray.destroy();
                     vertexArrays[k] = vertexArrayObject ? resources.vertexArray(programs[k], attributeBuffers, elementsBuffer) : null;
-                });
+                }
             }
 
             for (let i = 0, il = textures.length; i < il; ++i) {
@@ -298,11 +294,11 @@ export function createRenderItem<T extends RenderVariantDefines, S extends keyof
         },
         destroy: () => {
             if (!destroyed) {
-                Object.keys(renderVariantDefines).forEach(k => {
+                for (const k of renderVariants) {
                     programs[k].destroy();
                     const vertexArray = vertexArrays[k];
                     if (vertexArray) vertexArray.destroy();
-                });
+                }
                 textures.forEach(([k, texture]) => {
                     // lifetime of textures with kind 'texture' is defined externally
                     if (schema[k].kind !== 'texture') {

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/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/common/text/tokenizer.ts

@@ -107,13 +107,22 @@ namespace Tokenizer {
         return read;
     }
 
-    /** Advance the state by the given number of lines and return line starts/ends as tokens. */
-    export function readLines(state: Tokenizer, count: number): Tokens {
+    /** Advance the state by the given number of lines and return them*/
+    export function markLines(state: Tokenizer, count: number): Tokens {
         const lineTokens = TokenBuilder.create(state.data, count * 2);
         readLinesChunk(state, count, lineTokens);
         return lineTokens;
     }
 
+    /** Advance the state by the given number of lines and return them */
+    export function readLines(state: Tokenizer, count: number): string[] {
+        const ret: string[] = [];
+        for (let i = 0; i < count; i++) {
+            ret.push(Tokenizer.readLine(state));
+        }
+        return ret;
+    }
+
     /** Advance the state by the given number of lines and return line starts/ends as tokens. */
     export async function readLinesAsync(state: Tokenizer, count: number, ctx: RuntimeContext, initialLineCount = 100000): Promise<Tokens> {
         const { length } = state;

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

@@ -0,0 +1,141 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted from NGL.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { Tokenizer } from '../common/text/tokenizer';
+import { Column } from '../../../mol-data/db';
+import { Task, chunkedSubtask, RuntimeContext } from '../../../mol-task';
+import { ReaderResult as Result } from '../result';
+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
+}
+
+export namespace CubeFile {
+    export interface Header {
+        orbitals: boolean,
+        comment1: string,
+        comment2: string,
+        atomCount: number,
+        origin: Vec3,
+        dim: Vec3,
+        basisX: Vec3,
+        basisY: Vec3,
+        basisZ: Vec3,
+        dataSetIds: number[]
+    }
+
+    export interface Atoms {
+        count: number,
+        number: Column<number>,
+        nuclearCharge: Column<number>,
+        x: Column<number>,
+        y: Column<number>,
+        z: Column<number>
+    }
+}
+
+const bohrToAngstromFactor = 0.529177210859;
+
+function readHeader(tokenizer: Tokenizer) {
+    const headerLines = Tokenizer.readLines(tokenizer, 6);
+    const h = (k: number, l: number) => {
+        const field = +headerLines[k].trim().split(/\s+/g)[ l ];
+        return Number.isNaN(field) ? 0 : field;
+    };
+    const basis = (i: number) => {
+        const n = h(i + 2, 0);
+        const s = bohrToAngstromFactor;
+        return [Math.abs(n), Vec3.create(h(i + 2, 1) * s, h(i + 2, 2) * s, h(i + 2, 3) * s), n] as const;
+    };
+
+    const comment1 = headerLines[0].trim();
+    const comment2 = headerLines[1].trim();
+
+    const [atomCount, origin, rawAtomCount] = basis(0);
+    const [NVX, basisX] = basis(1);
+    const [NVY, basisY] = basis(2);
+    const [NVZ, basisZ] = basis(3);
+
+    const atoms = readAtoms(tokenizer, atomCount, bohrToAngstromFactor);
+
+    const dataSetIds: number[] = [];
+    if (rawAtomCount >= 0) {
+        let nVal = h(2, 4);
+        if (nVal === 0) nVal = 1;
+        for (let i = 0; i < nVal; i++) dataSetIds.push(i);
+    } else {
+        const counts = Tokenizer.readLine(tokenizer).trim().split(/\s+/g);
+        for (let i = 0, _i = +counts[0]; i < _i; i++) dataSetIds.push(+counts[i + 1]);
+    }
+
+    const header: CubeFile.Header = { orbitals: rawAtomCount < 0, comment1, comment2, atomCount, origin, dim: Vec3.create(NVX, NVY, NVZ), basisX, basisY, basisZ, dataSetIds };
+    return { header, atoms };
+}
+
+function readAtoms(tokenizer: Tokenizer, count: number, scaleFactor: number): CubeFile.Atoms {
+    const number = new Int32Array(count);
+    const value = new Float64Array(count);
+    const x = new Float32Array(count);
+    const y = new Float32Array(count);
+    const z = new Float32Array(count);
+
+    for (let i = 0; i < count; i++) {
+        const fields = Tokenizer.readLine(tokenizer).trim().split(/\s+/g);
+        number[i] = +fields[0];
+        value[i] = +fields[1];
+        x[i] = +fields[2] * scaleFactor;
+        y[i] = +fields[3] * scaleFactor;
+        z[i] = +fields[4] * scaleFactor;
+    }
+
+    return {
+        count,
+        number: Column.ofArray({ array: number, schema: Column.Schema.int }),
+        nuclearCharge: Column.ofArray({ array: value, schema: Column.Schema.float }),
+        x: Column.ofArray({ array: x, schema: Column.Schema.float }),
+        y: Column.ofArray({ array: y, schema: Column.Schema.float }),
+        z: Column.ofArray({ array: z, schema: Column.Schema.float })
+    };
+}
+
+function readValues(ctx: RuntimeContext, tokenizer: Tokenizer, header: CubeFile.Header) {
+    const N = header.dim[0] * header.dim[1] * header.dim[2] * header.dataSetIds.length;
+    const chunkSize = 100 * 100 * 100;
+    const data = new Float64Array(N);
+    let offset = 0;
+
+    return chunkedSubtask(ctx, chunkSize, data, (count, data) => {
+        const max = Math.min(N, offset + count);
+        for (let i = offset; i < max; i++) {
+            Tokenizer.skipWhitespace(tokenizer);
+            tokenizer.tokenStart = tokenizer.position;
+            Tokenizer.eatValue(tokenizer);
+            data[i] = fastParseFloat(tokenizer.data, tokenizer.tokenStart, tokenizer.tokenEnd);
+        }
+        offset = max;
+        return max === N ? 0 : chunkSize;
+    }, (ctx, _, i) => ctx.update({ current: Math.min(i, N), max: N }));
+}
+
+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, 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

@@ -0,0 +1,129 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted from NGL.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { chunkedSubtask, RuntimeContext, Task } from '../../../mol-task';
+import { parseFloat as fastParseFloat } from '../common/text/number-parser';
+import { Tokenizer } from '../common/text/tokenizer';
+import { ReaderResult as Result } from '../result';
+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
+}
+
+export namespace DxFile {
+    export interface Header {
+        dim: Vec3,
+        min: Vec3,
+        h: Vec3
+    }
+}
+
+function readHeader(tokenizer: Tokenizer): { header: DxFile.Header, headerByteCount: number } {
+    const header: Partial<DxFile.Header> = { h: Vec3() };
+    let headerByteCount = 0;
+    let deltaLineCount = 0;
+
+    const reWhitespace = /\s+/g;
+
+    while (true) {
+        const line = Tokenizer.readLine(tokenizer);
+        let ls;
+
+        if (line.startsWith('object 1')) {
+            ls = line.split(reWhitespace);
+            header.dim = Vec3.create(parseInt(ls[5]), parseInt(ls[6]), parseInt(ls[7]));
+        } else if (line.startsWith('origin')) {
+            ls = line.split(reWhitespace);
+            header.min = Vec3.create(parseFloat(ls[1]), parseFloat(ls[2]), parseFloat(ls[3]));
+        } else if (line.startsWith('delta')) {
+            ls = line.split(reWhitespace);
+
+            if (deltaLineCount === 0) {
+                (header.h as any)[0] = parseFloat(ls[1]);
+            } else if (deltaLineCount === 1) {
+                (header.h as any)[1] = parseFloat(ls[2]);
+            } else if (deltaLineCount === 2) {
+                (header.h as any)[2] = parseFloat(ls[3]);
+            }
+
+            deltaLineCount += 1;
+        } else if (line.startsWith('object 3')) {
+            headerByteCount += line.length + 1;
+            break;
+        }
+
+        headerByteCount += line.length + 1;
+    }
+
+    return { header: header as DxFile.Header, headerByteCount };
+}
+
+function readValuesText(ctx: RuntimeContext, tokenizer: Tokenizer, header: DxFile.Header) {
+    const N = header.dim[0] * header.dim[1] * header.dim[2];
+    const chunkSize = 100 * 100 * 100;
+    const data = new Float64Array(N);
+    let offset = 0;
+
+    return chunkedSubtask(ctx, chunkSize, data, (count, data) => {
+        const max = Math.min(N, offset + count);
+        for (let i = offset; i < max; i++) {
+            Tokenizer.skipWhitespace(tokenizer);
+            tokenizer.tokenStart = tokenizer.position;
+            Tokenizer.eatValue(tokenizer);
+            data[i] = fastParseFloat(tokenizer.data, tokenizer.tokenStart, tokenizer.tokenEnd);
+        }
+        offset = max;
+        return max === N ? 0 : chunkSize;
+    }, (ctx, _, i) => ctx.update({ current: Math.min(i, N), max: N }));
+}
+
+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, name });
+}
+
+async function parseBinary(taskCtx: RuntimeContext, data: Uint8Array, name: string) {
+    await taskCtx.update('Reading header...');
+
+    const headerString = utf8Read(data, 0, 1000);
+
+    const tokenizer = Tokenizer(headerString);
+    const { header, headerByteCount } = readHeader(tokenizer);
+
+    await taskCtx.update('Reading values...');
+
+    const size = header.dim[0] * header.dim[1] * header.dim[2];
+    const dv = new DataView(data.buffer, data.byteOffset + headerByteCount);
+    const values = new Float64Array(size);
+
+    for (let i = 0; i < size; i++) {
+        values[i] = dv.getFloat64(i * 8, true);
+    }
+
+    // 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, name });
+}
+
+export function parseDx(data: string | Uint8Array, name: string) {
+    return Task.create<Result<DxFile>>('Parse Cube', taskCtx => {
+        if (typeof data === 'string') return parseText(taskCtx, data, name);
+        return parseBinary(taskCtx, data, name);
+    });
+}

src/mol-io/writer/cif/encoder.ts

@@ -108,6 +108,11 @@ export namespace Field {
             return this;
         }
 
+        add(field: Field<K, D>) {
+            this.fields.push(field);
+            return this;
+        }
+
         getFields() { return this.fields; }
     }
 
@@ -222,6 +227,8 @@ export namespace Category {
 }
 
 export interface Encoder<T = string | Uint8Array> extends EncoderBase {
+    readonly isBinary: boolean,
+
     setFilter(filter?: Category.Filter): void,
     isCategoryIncluded(name: string): boolean,
     setFormatter(formatter?: Category.Formatter): void,

src/mol-io/writer/cif/encoder/binary.ts

@@ -28,6 +28,8 @@ export default class BinaryEncoder implements Encoder<Uint8Array> {
     private filter: Category.Filter = Category.DefaultFilter;
     private formatter: Category.Formatter = Category.DefaultFormatter;
 
+    readonly isBinary = true;
+
     binaryEncodingProvider: BinaryEncodingProvider | undefined = void 0;
 
     setFilter(filter?: Category.Filter) {

src/mol-io/writer/cif/encoder/text.ts

@@ -19,6 +19,8 @@ export default class TextEncoder implements Encoder<string> {
     private filter: Category.Filter = Category.DefaultFilter;
     private formatter: Category.Formatter = Category.DefaultFormatter;
 
+    readonly isBinary = false;
+
     binaryEncodingProvider = void 0;
 
     setFilter(filter?: Category.Filter) {

src/mol-math/linear-algebra/3d/mat4.ts

@@ -164,6 +164,21 @@ namespace Mat4 {
         return a;
     }
 
+    export function fromBasis(a: Mat4, x: Vec3, y: Vec3, z: Vec3) {
+        Mat4.setZero(a);
+        Mat4.setValue(a, 0, 0, x[0]);
+        Mat4.setValue(a, 1, 0, x[1]);
+        Mat4.setValue(a, 2, 0, x[2]);
+        Mat4.setValue(a, 0, 1, y[0]);
+        Mat4.setValue(a, 1, 1, y[1]);
+        Mat4.setValue(a, 2, 1, y[2]);
+        Mat4.setValue(a, 0, 2, z[0]);
+        Mat4.setValue(a, 1, 2, z[1]);
+        Mat4.setValue(a, 2, 2, z[2]);
+        Mat4.setValue(a, 3, 3, 1);
+        return a;
+    }
+
     export function copy(out: Mat4, a: Mat4) {
         out[0] = a[0];
         out[1] = a[1];

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/cube.ts

@@ -0,0 +1,83 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Column, Table } from '../../mol-data/db';
+import { Model } from '../../mol-model/structure/model';
+import { MoleculeType, getElementFromAtomicNumber, ElementSymbol } 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 { CubeFile } from '../../mol-io/reader/cube/parser';
+
+async function getModels(cube: CubeFile, ctx: RuntimeContext): Promise<Model[]> {
+    const { atoms } = cube;
+
+    const MOL = Column.ofConst('MOL', cube.atoms.count, Column.Schema.str);
+    const A = Column.ofConst('A', cube.atoms.count, Column.Schema.str);
+    const type_symbol = Column.ofArray({ array: Column.mapToArray(atoms.number, n => getElementFromAtomicNumber(n)), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) });
+    const seq_id = Column.ofConst(1, atoms.count, Column.Schema.int);
+
+    const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
+        auth_asym_id: A,
+        auth_atom_id: type_symbol,
+        auth_comp_id: MOL,
+        auth_seq_id: seq_id,
+        Cartn_x: Column.asArrayColumn(atoms.x, Float32Array),
+        Cartn_y: Column.asArrayColumn(atoms.y, Float32Array),
+        Cartn_z: Column.asArrayColumn(atoms.z, Float32Array),
+        id: Column.range(0, atoms.count - 1),
+
+        label_asym_id: A,
+        label_atom_id: type_symbol,
+        label_comp_id: MOL,
+        label_seq_id: seq_id,
+        label_entity_id: Column.ofConst('1', atoms.count, Column.Schema.str),
+
+        occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
+        type_symbol,
+
+        pdbx_PDB_model_num: Column.ofConst(1, 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(seq_id, type_symbol);
+    componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
+    componentBuilder.add('MOL', 0);
+
+    const basics = createBasic({
+        entity: entityBuilder.getEntityTable(),
+        chem_comp: componentBuilder.getChemCompTable(),
+        atom_site
+    });
+
+    return await createModels(basics, MolFormat.create(cube), ctx);
+}
+
+//
+
+export { CubeFormat };
+
+type CubeFormat = ModelFormat<CubeFile>
+
+namespace MolFormat {
+    export function is(x: ModelFormat): x is CubeFormat {
+        return x.kind === 'cube';
+    }
+
+    export function create(cube: CubeFile): CubeFormat {
+        return { kind: 'cube', name: cube.header.comment1, data: cube };
+    }
+}
+
+export function trajectoryFromCube(cube: CubeFile): Task<Model.Trajectory> {
+    return Task.create('Parse Cube', ctx => getModels(cube, ctx));
+}

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

@@ -59,13 +59,13 @@ export function parseRemark350(lines: Tokens, lineStart: number, lineEnd: number
     const assemblies: PdbAssembly[] = [];
 
     // Read the assemblies
-    let current: PdbAssembly, group: PdbAssembly['groups'][0], matrix: Mat4, operId = 1;
+    let current: PdbAssembly, group: PdbAssembly['groups'][0], matrix: Mat4, operId = 1, asmId = 1;
     const getLine = (n: number) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]);
     for (let i = lineStart; i < lineEnd; i++) {
         let line = getLine(i);
         if (line.substr(11, 12) === 'BIOMOLECULE:') {
             const id = line.substr(23).trim();
-            let details: string = `Biomolecule ` + id;
+            let details = `Biomolecule ${id}`;
             line = getLine(i + 1);
             if (line.substr(11, 30) !== 'APPLY THE FOLLOWING TO CHAINS:') {
                 i++;
@@ -100,6 +100,23 @@ export function parseRemark350(lines: Tokens, lineStart: number, lineEnd: number
                 const c = chainList[j].trim();
                 if (c) group!.chains.push(c);
             }
+        } else if (line.substr(11, 33) === 'APPLYING THE FOLLOWING TO CHAINS:') {
+            // variant in older PDB format version
+            current = PdbAssembly(`${asmId}`, `Biomolecule ${asmId}`);
+            assemblies.push(current);
+            asmId += 1;
+
+            group = { chains: [], operators: [] };
+            current!.groups.push(group);
+
+            i++;
+            line = getLine(i);
+
+            const chainList = line.substr(11, 69).split(',');
+            for (let j = 0, jl = chainList.length; j < jl; ++j) {
+                const c = chainList[j].trim();
+                if (c) group!.chains.push(c);
+            }
         }
     }
 

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

@@ -38,7 +38,7 @@ function getTypedArrayCtor(header: Ccp4Header) {
     throw Error(`${valueType} is not a supported value format.`);
 }
 
-export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, offset?: Vec3 }): Task<VolumeData> {
+export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, offset?: Vec3, label?: string }): Task<VolumeData> {
     return Task.create<VolumeData>('Create Volume Data', async ctx => {
         const { header, values } = source;
         const size = Vec3.create(header.xLength, header.yLength, header.zLength);
@@ -67,8 +67,8 @@ export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, of
         // These, however, calculate sigma, so no data on that.
 
         return {
-            cell,
-            fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)),
+            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,

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

@@ -0,0 +1,57 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { CubeFile } from '../../mol-io/reader/cube/parser';
+import { Mat4, Tensor } from '../../mol-math/linear-algebra';
+import { VolumeData } from '../../mol-model/volume/data';
+import { Task } from '../../mol-task';
+import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
+
+export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string }): Task<VolumeData> {
+    return Task.create<VolumeData>('Create Volume Data', async () => {
+        const { header, values: sourceValues } = source;
+        const space = Tensor.Space(header.dim, [0, 1, 2], Float64Array);
+
+        let values: Float64Array;
+        if (header.dataSetIds.length === 0) {
+            values = sourceValues;
+        } else {
+            // get every nth value from the source values
+            const [h, k, l] = header.dim;
+            const nth = (params?.dataIndex || 0) + 1;
+
+            let o = 0, s = 0;
+
+            values = new Float64Array(h * k * l);
+            for (let u = 0; u < h; u++) {
+                for (let v = 0; v < k; v++) {
+                    for (let w = 0; w < l; w++) {
+                        values[o++] = sourceValues[s];
+                        s += nth;
+                    }
+                }
+            }
+        }
+
+        const data = Tensor.create(space, Tensor.Data1(values));
+
+        const matrix = Mat4.fromTranslation(Mat4(), header.origin);
+        const basis = Mat4.fromBasis(Mat4(), header.basisX, header.basisY, header.basisZ);
+        Mat4.mul(matrix, matrix, basis);
+
+        return {
+            label: params?.label,
+            transform: { kind: 'matrix', matrix },
+            data,
+            dataStats: {
+                min: arrayMin(values),
+                max: arrayMax(values),
+                mean: arrayMean(values),
+                sigma: arrayRms(values)
+            }
+        };
+    });
+}

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

@@ -34,8 +34,7 @@ function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<
         const dimensions = Vec3.ofArray(normalizeOrder(info.dimensions.value(0)));
 
         return {
-            cell,
-            fractionalBox: Box3D.create(origin, Vec3.add(Vec3.zero(), origin, dimensions)),
+            transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin, Vec3.add(Vec3.zero(), origin, dimensions)) },
             data,
             dataStats: {
                 min: info.min_sampled.value(0),

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

@@ -12,7 +12,7 @@ import { degToRad } from '../../mol-math/misc';
 import { Dsn6File } from '../../mol-io/reader/dsn6/schema';
 import { arrayMin, arrayMax, arrayMean, arrayRms } from '../../mol-util/array';
 
-function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3 }): Task<VolumeData> {
+function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, label?: string }): Task<VolumeData> {
     return Task.create<VolumeData>('Create Volume Data', async ctx => {
         const { header, values } = source;
         const size = Vec3.create(header.xlen, header.ylen, header.zlen);
@@ -32,8 +32,8 @@ function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3 }): Task<V
         const data = Tensor.create(space, Tensor.Data1(values));
 
         return {
-            cell,
-            fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)),
+            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),

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

@@ -0,0 +1,34 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { DxFile } from '../../mol-io/reader/dx/parser';
+import { Mat4, Tensor } from '../../mol-math/linear-algebra';
+import { VolumeData } from '../../mol-model/volume/data';
+import { Task } from '../../mol-task';
+import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
+
+export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<VolumeData> {
+    return Task.create<VolumeData>('Create Volume Data', async () => {
+        const { header, values } = source;
+        const space = Tensor.Space(header.dim, [0, 1, 2], Float64Array);
+        const data = Tensor.create(space, Tensor.Data1(values));
+        const matrix = Mat4.fromTranslation(Mat4(), header.min);
+        const basis = Mat4.fromScaling(Mat4(), header.h);
+        Mat4.mul(matrix, matrix, basis);
+
+        return {
+            label: params?.label,
+            transform: { kind: 'matrix', matrix },
+            data,
+            dataStats: {
+                min: arrayMin(values),
+                max: arrayMax(values),
+                mean: arrayMean(values),
+                sigma: arrayRms(values)
+            }
+        };
+    });
+}

src/mol-model/loci.ts

@@ -16,6 +16,7 @@ import { shallowEqual } from '../mol-util';
 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';
 
 /** A Loci that includes every loci */
 export const EveryLoci = { kind: 'every-loci' as 'every-loci' };
@@ -62,7 +63,7 @@ export function DataLoci<T = unknown, E = unknown>(tag: string, data: T, element
 
 export { Loci };
 
-type Loci = StructureElement.Loci | Structure.Loci | Bond.Loci | EveryLoci | EmptyLoci | DataLoci | Shape.Loci | ShapeGroup.Loci
+type Loci = StructureElement.Loci | Structure.Loci | Bond.Loci | EveryLoci | EmptyLoci | DataLoci | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci
 
 namespace Loci {
     export interface Bundle<L extends number> { loci: FiniteArray<Loci, L> }
@@ -98,6 +99,15 @@ namespace Loci {
         if (ShapeGroup.isLoci(lociA) && ShapeGroup.isLoci(lociB)) {
             return ShapeGroup.areLociEqual(lociA, lociB);
         }
+        if (Volume.isLoci(lociA) && Volume.isLoci(lociB)) {
+            return Volume.areLociEqual(lociA, lociB);
+        }
+        if (Volume.Isosurface.isLoci(lociA) && Volume.Isosurface.isLoci(lociB)) {
+            return Volume.Isosurface.areLociEqual(lociA, lociB);
+        }
+        if (Volume.Cell.isLoci(lociA) && Volume.Cell.isLoci(lociB)) {
+            return Volume.Cell.areLociEqual(lociA, lociB);
+        }
         return false;
     }
 
@@ -114,6 +124,9 @@ namespace Loci {
         if (Bond.isLoci(loci)) return Bond.isLociEmpty(loci);
         if (Shape.isLoci(loci)) return Shape.isLociEmpty(loci);
         if (ShapeGroup.isLoci(loci)) return ShapeGroup.isLociEmpty(loci);
+        if (Volume.isLoci(loci)) return Volume.isLociEmpty(loci);
+        if (Volume.Isosurface.isLoci(loci)) return Volume.Isosurface.isLociEmpty(loci);
+        if (Volume.Cell.isLoci(loci)) return Volume.Cell.isLociEmpty(loci);
         return false;
     }
 
@@ -147,6 +160,12 @@ namespace Loci {
             return ShapeGroup.getBoundingSphere(loci, boundingSphere);
         } else if (loci.kind === 'data-loci') {
             return loci.getBoundingSphere(boundingSphere);
+        } else if (loci.kind === 'volume-loci') {
+            return Volume.getBoundingSphere(loci.volume, boundingSphere);
+        } else if (loci.kind === 'isosurface-loci') {
+            return Volume.Isosurface.getBoundingSphere(loci.volume, loci.isoValue, boundingSphere);
+        } else if (loci.kind === 'cell-loci') {
+            return Volume.Cell.getBoundingSphere(loci.volume, loci.indices, boundingSphere);
         }
     }
 
@@ -175,6 +194,15 @@ namespace Loci {
         } else if (loci.kind === 'data-loci') {
             // TODO maybe add loci.getPrincipalAxes()???
             return void 0;
+        } else if (loci.kind === 'volume-loci') {
+            // TODO
+            return void 0;
+        } else if (loci.kind === 'isosurface-loci') {
+            // TODO
+            return void 0;
+        } else if (loci.kind === 'cell-loci') {
+            // TODO
+            return void 0;
         }
     }
 

src/mol-model/shape/shape.ts

@@ -100,7 +100,7 @@ export namespace Shape {
     export function Loci(shape: Shape): Loci { return { kind: 'shape-loci', shape }; }
     export function isLoci(x: any): x is Loci { return !!x && x.kind === 'shape-loci'; }
     export function areLociEqual(a: Loci, b: Loci) { return a.shape === b.shape; }
-    export function isLociEmpty(loci: Loci) { return loci.shape.groupCount === 0 ? true : false; }
+    export function isLociEmpty(loci: Loci) { return loci.shape.groupCount === 0; }
 }
 
 export namespace ShapeGroup {

src/mol-model/structure/export/categories/atom_site_operator_mapping.ts

@@ -6,18 +6,21 @@
 
 import { SymmetryOperator } from '../../../../mol-math/geometry';
 import { CifExportContext } from '../mmcif';
-import { StructureElement, StructureProperties as P } from '../../structure';
+import { StructureElement, StructureProperties as P, CifExportCategoryInfo } from '../../structure';
 import Unit from '../../structure/unit';
 import { Segmentation } from '../../../../mol-data/int';
 import { CifWriter } from '../../../../mol-io/writer/cif';
 import { Column } from '../../../../mol-data/db';
 
-export function atom_site_operator_mapping(encoder: CifWriter.Encoder, ctx: CifExportContext) {
+
+export function atom_site_operator_mapping(ctx: CifExportContext): CifExportCategoryInfo | undefined {
     const entries = getEntries(ctx);
     if (entries.length === 0) return;
-    encoder.writeCategory(Category, entries, { ignoreFilter: true });
+    return [Category, entries, { ignoreFilter: true }];
 }
 
+export const AtomSiteOperatorMappingCategoryName = 'molstar_atom_site_operator_mapping';
+
 export const AtomSiteOperatorMappingSchema = {
     molstar_atom_site_operator_mapping: {
         label_asym_id: Column.Schema.Str(),

src/mol-model/structure/export/categories/utils.ts

@@ -14,6 +14,7 @@ import { sortArray } from '../../../../mol-data/util';
 import { CifWriter } from '../../../../mol-io/writer/cif';
 import { CifExportContext } from '../mmcif';
 import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
+import { CifCategory, CifField, getCifFieldType } from '../../../../mol-io/reader/cif';
 
 export function getModelMmCifCategory<K extends keyof mmCIF_Schema>(model: Model, name: K): mmCIF_Database[K] | undefined {
     if (!MmcifFormat.is(model.sourceData)) return;
@@ -58,4 +59,41 @@ export function copy_mmCif_category(name: keyof mmCIF_Schema, condition?: (struc
             return CifWriter.Category.ofTable(table);
         }
     };
+}
+
+export function copy_source_mmCifCategory(encoder: CifWriter.Encoder, ctx: CifExportContext, category: CifCategory): CifWriter.Category<CifExportContext> | undefined {
+    if (!MmcifFormat.is(ctx.firstModel.sourceData)) return;
+
+    const fs = CifWriter.fields<number, undefined>();
+    if (encoder.isBinary) {
+        for (const f of category.fieldNames) {
+            // TODO: this could be optimized
+            const field = classifyField(f, category.getField(f)!);
+            fs.add(field);
+        }
+    } else {
+        for (const f of category.fieldNames) {
+            const field = category.getField(f)!;
+            fs.str(f, row => field.str(row));
+        }
+    }
+
+    const fields = fs.getFields();
+    return {
+        name: category.name,
+        instance() {
+            return { fields, source: [{ data: void 0, rowCount: category.rowCount }] };
+        }
+    };
+}
+
+function classifyField(name: string, field: CifField): CifWriter.Field {
+    const type = getCifFieldType(field);
+    if (type['@type'] === 'str') {
+        return { name, type: CifWriter.Field.Type.Str, value: field.str, valueKind: field.valueKind };
+    } else if (type['@type'] === 'float') {
+        return CifWriter.Field.float(name, field.float, { valueKind: field.valueKind, typedArray: Float64Array });
+    } else {
+        return CifWriter.Field.int(name, field.int, { valueKind: field.valueKind, typedArray: Int32Array });
+    }
 }

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

@@ -13,10 +13,11 @@ import CifCategory = CifWriter.Category
 import { _struct_conf, _struct_sheet_range } from './categories/secondary-structure';
 import { _chem_comp, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './categories/misc';
 import { Model } from '../model';
-import { getUniqueEntityIndicesFromStructures, copy_mmCif_category } from './categories/utils';
+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 { atom_site_operator_mapping } from './categories/atom_site_operator_mapping';
+import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
 
 export interface CifExportContext {
     structures: Structure[],
@@ -24,6 +25,10 @@ export interface CifExportContext {
     cache: any
 }
 
+export type CifExportCategoryInfo =
+    | [CifWriter.Category, any /** context */, CifWriter.Encoder.WriteCategoryOptions]
+    | [CifWriter.Category, any /** context */]
+
 export namespace CifExportContext {
     export function create(structures: Structure | Structure[]): CifExportContext {
         const structureArray = Array.isArray(structures) ? structures : [structures];
@@ -99,8 +104,8 @@ export const mmCIF_Export_Filters = {
     }
 };
 
-function encodeCustomProp(customProp: CustomPropertyDescriptor, ctx: CifExportContext, encoder: CifWriter.Encoder, params: encode_mmCIF_categories_Params) {
-    if (!customProp.cifExport || customProp.cifExport.categories.length === 0) return;
+function getCustomPropCategories(customProp: CustomPropertyDescriptor, ctx: CifExportContext, params?: encode_mmCIF_categories_Params): CifExportCategoryInfo[] {
+    if (!customProp.cifExport || customProp.cifExport.categories.length === 0) return [];
 
     const prefix = customProp.cifExport.prefix;
     const cats = customProp.cifExport.categories;
@@ -114,14 +119,21 @@ function encodeCustomProp(customProp: CustomPropertyDescriptor, ctx: CifExportCo
             ctx.cache[propId + '__ctx'] = propCtx;
         }
     }
+
+    const ret: CifExportCategoryInfo[] = [];
     for (const cat of cats) {
-        if (params.skipCategoryNames && params.skipCategoryNames.has(cat.name)) continue;
+        if (params?.skipCategoryNames?.has(cat.name)) continue;
         if (cat.name.indexOf(prefix) !== 0) throw new Error(`Custom category '${cat.name}' name must start with prefix '${prefix}.'`);
-        encoder.writeCategory(cat, propCtx);
+        ret.push([cat, propCtx]);
     }
+    return ret;
 }
 
-type encode_mmCIF_categories_Params = { skipCategoryNames?: Set<string>, exportCtx?: CifExportContext }
+type encode_mmCIF_categories_Params = {
+    skipCategoryNames?: Set<string>,
+    exportCtx?: CifExportContext,
+    copyAllCategories?: boolean
+}
 
 /** Doesn't start a data block */
 export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures: Structure | Structure[], params?: encode_mmCIF_categories_Params) {
@@ -129,30 +141,94 @@ export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures:
     const models = first.models;
     if (models.length !== 1) throw 'Can\'t export stucture composed from multiple models.';
 
-    const _params = params || { };
-    const ctx: CifExportContext = params && params.exportCtx ? params.exportCtx : CifExportContext.create(structures);
+    const ctx: CifExportContext = params?.exportCtx || CifExportContext.create(structures);
 
+    if (params?.copyAllCategories && MmcifFormat.is(models[0].sourceData)) {
+        encode_mmCIF_categories_copyAll(encoder, ctx);
+    } else {
+        encode_mmCIF_categories_default(encoder, ctx, params);
+    }
+}
+
+function encode_mmCIF_categories_default(encoder: CifWriter.Encoder, ctx: CifExportContext, params?: encode_mmCIF_categories_Params) {
     for (const cat of Categories) {
-        if (_params.skipCategoryNames && _params.skipCategoryNames.has(cat.name)) continue;
+        if (params?.skipCategoryNames && params?.skipCategoryNames.has(cat.name)) continue;
         encoder.writeCategory(cat, ctx);
     }
 
-    if ((!_params.skipCategoryNames || !_params.skipCategoryNames.has('atom_site')) && encoder.isCategoryIncluded('atom_site')) {
-        atom_site_operator_mapping(encoder, ctx);
+    if (!params?.skipCategoryNames?.has('atom_site') && encoder.isCategoryIncluded('atom_site')) {
+        const info = atom_site_operator_mapping(ctx);
+        if (info) encoder.writeCategory(info[0], info[1], info[2]);
     }
 
-    for (const customProp of models[0].customProperties.all) {
-        encodeCustomProp(customProp, ctx, encoder, _params);
+    const _params = params || { };
+    for (const customProp of ctx.firstModel.customProperties.all) {
+        for (const [cat, propCtx] of getCustomPropCategories(customProp, ctx, _params)) {
+            encoder.writeCategory(cat, propCtx);
+        }
     }
 
-    const structureCustomProps = new Set<CustomPropertyDescriptor>();
     for (const s of ctx.structures) {
         if (!s.hasCustomProperties) continue;
-        for (const p of s.customPropertyDescriptors.all) structureCustomProps.add(p);
+        for (const customProp of s.customPropertyDescriptors.all) {
+            for (const [cat, propCtx] of getCustomPropCategories(customProp, ctx, _params)) {
+                encoder.writeCategory(cat, propCtx);
+            }
+        }
     }
-    structureCustomProps.forEach(customProp => encodeCustomProp(customProp, ctx, encoder, _params));
 }
 
+function encode_mmCIF_categories_copyAll(encoder: CifWriter.Encoder, ctx: CifExportContext) {
+    const providedCategories = new Map<string, CifExportCategoryInfo>();
+
+    for (const cat of Categories) {
+        providedCategories.set(cat.name, [cat, ctx]);
+    }
+
+    const mapping = atom_site_operator_mapping(ctx);
+    if (mapping) providedCategories.set(mapping[0].name, mapping);
+
+    for (const customProp of ctx.firstModel.customProperties.all) {
+        for (const info of getCustomPropCategories(customProp, ctx)) {
+            providedCategories.set(info[0].name, info);
+        }
+    }
+
+    for (const s of ctx.structures) {
+        if (!s.hasCustomProperties) continue;
+        for (const customProp of s.customPropertyDescriptors.all) {
+            for (const info of getCustomPropCategories(customProp, ctx)) {
+                providedCategories.set(info[0].name, info);
+            }
+        }
+    }
+
+    const handled = new Set<string>();
+
+    const data = (ctx.firstModel.sourceData as MmcifFormat).data;
+    for (const catName of data.frame.categoryNames) {
+        handled.add(catName);
+
+        if (providedCategories.has(catName)) {
+            const info = providedCategories.get(catName)!;
+            encoder.writeCategory(info[0], info[1], info[2]);
+        } else {
+            if ((data.db as any)[catName]) {
+                const cat = copy_mmCif_category(catName as any);
+                encoder.writeCategory(cat, ctx);
+            } else {
+                const cat = copy_source_mmCifCategory(encoder, ctx, data.frame.categories[catName]);
+                if (cat) encoder.writeCategory(cat);
+            }
+        }
+    }
+
+    providedCategories.forEach((info, name) => {
+        if (!handled.has(name)) encoder.writeCategory(info[0], info[1], info[2]);
+    });
+}
+
+
 function to_mmCIF(name: string, structure: Structure, asBinary = false) {
     const enc = CifWriter.createEncoder({ binary: asBinary });
     enc.startDataBlock(name);

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

@@ -25,6 +25,7 @@ import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
 import { ChainIndex } from './indexing';
 import { SymmetryOperator } from '../../../mol-math/geometry';
 import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
+import { Column } from '../../../mol-data/db';
 
 /**
  * Interface to the "source data" of the molecule.
@@ -143,16 +144,19 @@ export namespace Model {
 
     //
 
-    export function isFromPdbArchive(model: Model) {
+    export function isFromPdbArchive(model: Model): boolean {
         if (!MmcifFormat.is(model.sourceData)) return false;
         const { db } = model.sourceData.data;
         return (
             db.database_2.database_id.isDefined ||
-            model.entryId.length === 4
+            // 4 character PDB id
+            model.entryId.match(/^[1-9][a-z0-9]{3,3}$/i) !== null ||
+            // long PDB id
+            model.entryId.match(/^pdb_[0-9]{4,4}[1-9][a-z0-9]{3,3}$/i) !== null
         );
     }
 
-    export function hasSecondaryStructure(model: Model) {
+    export function hasSecondaryStructure(model: Model): boolean {
         if (!MmcifFormat.is(model.sourceData)) return false;
         const { db } = model.sourceData.data;
         return (
@@ -163,7 +167,7 @@ export namespace Model {
 
     const tmpAngles90 = Vec3.create(1.5707963, 1.5707963, 1.5707963); // in radians
     const tmpLengths1 = Vec3.create(1, 1, 1);
-    export function hasCrystalSymmetry(model: Model) {
+    export function hasCrystalSymmetry(model: Model): boolean {
         const spacegroup = ModelSymmetry.Provider.get(model)?.spacegroup;
         return !!spacegroup && !(
             spacegroup.num === 1 &&
@@ -172,7 +176,7 @@ export namespace Model {
         );
     }
 
-    export function isFromXray(model: Model) {
+    export function isFromXray(model: Model): boolean {
         if (!MmcifFormat.is(model.sourceData)) return false;
         const { db } = model.sourceData.data;
         for (let i = 0; i < db.exptl.method.rowCount; i++) {
@@ -182,7 +186,7 @@ export namespace Model {
         return false;
     }
 
-    export function isFromEm(model: Model) {
+    export function isFromEm(model: Model): boolean {
         if (!MmcifFormat.is(model.sourceData)) return false;
         const { db } = model.sourceData.data;
         for (let i = 0; i < db.exptl.method.rowCount; i++) {
@@ -192,7 +196,7 @@ export namespace Model {
         return false;
     }
 
-    export function isFromNmr(model: Model) {
+    export function isFromNmr(model: Model): boolean {
         if (!MmcifFormat.is(model.sourceData)) return false;
         const { db } = model.sourceData.data;
         for (let i = 0; i < db.exptl.method.rowCount; i++) {
@@ -202,7 +206,7 @@ export namespace Model {
         return false;
     }
 
-    export function hasXrayMap(model: Model) {
+    export function hasXrayMap(model: Model): boolean {
         if (!MmcifFormat.is(model.sourceData)) return false;
         // Check exprimental method to exclude models solved with
         // 'ELECTRON CRYSTALLOGRAPHY' which also have structure factors
@@ -217,7 +221,7 @@ export namespace Model {
      * like 6TEK which are solved with 'X-RAY DIFFRACTION' but have an related
      * EMDB entry of type 'other EM volume'.
      */
-    export function hasEmMap(model: Model) {
+    export function hasEmMap(model: Model): boolean {
         if (!MmcifFormat.is(model.sourceData)) return false;
         const { db } = model.sourceData.data;
         const { db_name, content_type } = db.pdbx_database_related;
@@ -229,7 +233,26 @@ export namespace Model {
         return false;
     }
 
-    export function hasDensityMap(model: Model) {
+    export function hasDensityMap(model: Model): boolean {
+        if (!MmcifFormat.is(model.sourceData)) return false;
         return hasXrayMap(model) || hasEmMap(model);
     }
+
+    export function probablyHasDensityMap(model: Model): boolean {
+        if (!MmcifFormat.is(model.sourceData)) return false;
+        const { db } = model.sourceData.data;
+        return hasDensityMap(model) || (
+            // check if from pdb archive but missing relevant meta data
+            isFromPdbArchive(model) && (
+                !db.exptl.method.isDefined ||
+                (isFromXray(model) && (
+                    !db.pdbx_database_status.status_code_sf.isDefined ||
+                    db.pdbx_database_status.status_code_sf.valueKind(0) === Column.ValueKind.Unknown
+                )) ||
+                (isFromEm(model) && (
+                    !db.pdbx_database_related.db_name.isDefined
+                ))
+            )
+        );
+    }
 }

src/mol-model/structure/model/properties/atomic/types.ts

@@ -14,6 +14,10 @@ export const enum Elements {
     H = 'H', D = 'D', T = 'T', HE = 'HE', LI = 'LI', BE = 'BE', B = 'B', C = 'C', N = 'N', O = 'O', F = 'F', NE = 'NE', NA = 'NA', MG = 'MG', AL = 'AL', SI = 'SI', P = 'P', S = 'S', CL = 'CL', AR = 'AR', K = 'K', CA = 'CA', SC = 'SC', TI = 'TI', V = 'V', CR = 'CR', MN = 'MN', FE = 'FE', CO = 'CO', NI = 'NI', CU = 'CU', ZN = 'ZN', GA = 'GA', GE = 'GE', AS = 'AS', SE = 'SE', BR = 'BR', KR = 'KR', RB = 'RB', SR = 'SR', Y = 'Y', ZR = 'ZR', NB = 'NB', MO = 'MO', TC = 'TC', RU = 'RU', RH = 'RH', PD = 'PD', AG = 'AG', CD = 'CD', IN = 'IN', SN = 'SN', SB = 'SB', TE = 'TE', I = 'I', XE = 'XE', CS = 'CS', BA = 'BA', LA = 'LA', CE = 'CE', PR = 'PR', ND = 'ND', PM = 'PM', SM = 'SM', EU = 'EU', GD = 'GD', TB = 'TB', DY = 'DY', HO = 'HO', ER = 'ER', TM = 'TM', YB = 'YB', LU = 'LU', HF = 'HF', TA = 'TA', W = 'W', RE = 'RE', OS = 'OS', IR = 'IR', PT = 'PT', AU = 'AU', HG = 'HG', TL = 'TL', PB = 'PB', BI = 'BI', PO = 'PO', AT = 'AT', RN = 'RN', FR = 'FR', RA = 'RA', AC = 'AC', TH = 'TH', PA = 'PA', U = 'U', NP = 'NP', PU = 'PU', AM = 'AM', CM = 'CM', BK = 'BK', CF = 'CF', ES = 'ES', FM = 'FM', MD = 'MD', NO = 'NO', LR = 'LR', RF = 'RF', DB = 'DB', SG = 'SG', BH = 'BH', HS = 'HS', MT = 'MT', DS = 'DS', RG = 'RG', CN = 'CN', NH = 'NH', FL = 'FL', MC = 'MC', LV = 'LV', TS = 'TS', OG = 'OG'
 }
 
+export const ElementNames: { [k: string]: string } = {
+    H: 'Hydrogen', HE: 'Helium', LI: 'Lithium', BE: 'Beryllium', B: 'Boron', C: 'Carbon', N: 'Nitrogen', O: 'Oxygen', F: 'Fluorine', NE: 'Neon', NA: 'Sodium', MG: 'Magnesium', AL: 'Aluminum', SI: 'Silicon', P: 'Phosphorus', S: 'Sulfur', CL: 'Chlorine', AR: 'Argon', K: 'Potassium', CA: 'Calcium', SC: 'Scandium', TI: 'Titanium', V: 'Vanadium', CR: 'Chromium', MN: 'Manganese', FE: 'Iron', CO: 'Cobalt', NI: 'Nickel', CU: 'Copper', ZN: 'Zinc', GA: 'Gallium', GE: 'Germanium', AS: 'Arsenic', SE: 'Selenium', BR: 'Bromine', KR: 'Krypton', RB: 'Rubidium', SR: 'Strontium', Y: 'Yttrium', ZR: 'Zirconium', NB: 'Niobium', MO: 'Molybdenum', TC: 'Technetium', RU: 'Ruthenium', RH: 'Rhodium', PD: 'Palladium', AG: 'Silver', CD: 'Cadmium', IN: 'Indium', SN: 'Tin', SB: 'Antimony', TE: 'Tellurium', I: 'Iodine', XE: 'Xenon', CS: 'Cesium', BA: 'Barium', LA: 'Lanthanum', CE: 'Cerium', PR: 'Praseodymium', ND: 'Neodymium', PM: 'Promethium', SM: 'Samarium', EU: 'Europium', GD: 'Gadolinium', TB: 'Terbium', DY: 'Dysprosium', HO: 'Holmium', ER: 'Erbium', TM: 'Thulium', YB: 'Ytterbium', LU: 'Lutetium', HF: 'Hafnium', TA: 'Tantalum', W: 'Wolfram', RE: 'Rhenium', OS: 'Osmium', IR: 'Iridium', PT: 'Platinum', AU: 'Gold', HG: 'Mercury', TL: 'Thallium', PB: 'Lead', BI: 'Bismuth', PO: 'Polonium', AT: 'Astatine', RN: 'Radon', FR: 'Francium', RA: 'Radium', AC: 'Actinium', TH: 'Thorium', PA: 'Protactinium', U: 'Uranium', NP: 'Neptunium', PU: 'Plutonium', AM: 'Americium', CM: 'Curium', BK: 'Berkelium', CF: 'Californium', ES: 'Einsteinium', FM: 'Fermium', MD: 'Mendelevium', NO: 'Nobelium', LR: 'Lawrencium', RF: 'Rutherfordium', DB: 'Dubnium', SG: 'Seaborgium', BH: 'Bohrium', HS: 'Hassium', MT: 'Meitnerium', DS: 'Darmstadtium', RG: 'Roentgenium', CN: 'Copernicium', NH: 'Nihonium', FL: 'Flerovium', MC: 'Moscovium', LV: 'Livermorium', TS: 'Tennessine', OG: 'Oganesson'
+};
+
 export const AlkaliMetals = new Set<ElementSymbol>(['LI', 'NA', 'K', 'RB', 'CS', 'FR'] as ElementSymbol[]);
 export function isAlkaliMetal(element: ElementSymbol) { return AlkaliMetals.has(element); }
 

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

@@ -34,6 +34,15 @@ export function ElementSymbol(s: string): ElementSymbol {
     return _esCache[s] || s.toUpperCase();
 }
 
+const _elementByAtomicNumber = new Map(
+    ([[1, 'H'], [2, 'He'], [3, 'Li'], [4, 'Be'], [5, 'B'], [6, 'C'], [7, 'N'], [8, 'O'], [9, 'F'], [10, 'Ne'], [11, 'Na'], [12, 'Mg'], [13, 'Al'], [14, 'Si'], [15, 'P'], [16, 'S'], [17, 'Cl'], [18, 'Ar'], [19, 'K'], [20, 'Ca'], [21, 'Sc'], [22, 'Ti'], [23, 'V'], [24, 'Cr'], [25, 'Mn'], [26, 'Fe'], [27, 'Co'], [28, 'Ni'], [29, 'Cu'], [30, 'Zn'], [31, 'Ga'], [32, 'Ge'], [33, 'As'], [34, 'Se'], [35, 'Br'], [36, 'Kr'], [37, 'Rb'], [38, 'Sr'], [39, 'Y'], [40, 'Zr'], [41, 'Nb'], [42, 'Mo'], [43, 'Tc'], [44, 'Ru'], [45, 'Rh'], [46, 'Pd'], [47, 'Ag'], [48, 'Cd'], [49, 'In'], [50, 'Sn'], [51, 'Sb'], [52, 'Te'], [53, 'I'], [54, 'Xe'], [55, 'Cs'], [56, 'Ba'], [57, 'La'], [58, 'Ce'], [59, 'Pr'], [60, 'Nd'], [61, 'Pm'], [62, 'Sm'], [63, 'Eu'], [64, 'Gd'], [65, 'Tb'], [66, 'Dy'], [67, 'Ho'], [68, 'Er'], [69, 'Tm'], [70, 'Yb'], [71, 'Lu'], [72, 'Hf'], [73, 'Ta'], [74, 'W'], [75, 'Re'], [76, 'Os'], [77, 'Ir'], [78, 'Pt'], [79, 'Au'], [80, 'Hg'], [81, 'Tl'], [82, 'Pb'], [83, 'Bi'], [84, 'Po'], [85, 'At'], [86, 'Rn'], [87, 'Fr'], [88, 'Ra'], [89, 'Ac'], [90, 'Th'], [91, 'Pa'], [92, 'U'], [93, 'Np'], [94, 'Pu'], [95, 'Am'], [96, 'Cm'], [97, 'Bk'], [98, 'Cf'], [99, 'Es'], [100, 'Fm'], [101, 'Md'], [102, 'No'], [103, 'Lr'], [104, 'Rf'], [105, 'Db'], [106, 'Sg'], [107, 'Bh'], [108, 'Hs'], [109, 'Mt'], [110, 'Ds'], [111, 'Rg'], [112, 'Cn'], [113, 'Uut'], [114, 'Fl'], [115, 'Uup'], [116, 'Lv'], [117, 'Uus'], [118, 'Uuo']] as const)
+        .map(e => [e[0], ElementSymbol(e[1])]));
+
+export function getElementFromAtomicNumber(n: number) {
+    if (_elementByAtomicNumber.has(n as any)) return _elementByAtomicNumber.get(n as any)!;
+    return ElementSymbol('H');
+}
+
 /** Entity types as defined in the mmCIF dictionary */
 export const enum EntityType {
     'unknown', 'polymer', 'non-polymer', 'macrolide', 'water', 'branched'
@@ -256,9 +265,9 @@ export const DnaBaseNames = new Set([
     'DA', 'DC', 'DT', 'DG', 'DI', 'DU',
     'DN' // unknown DNA base from CCD
 ]);
-export const PeptideBaseNames = new Set([ 'APN', 'CPN', 'TPN', 'GPN' ]);
-export const PurineBaseNames = new Set([ 'A', 'G', 'I', 'DA', 'DG', 'DI', 'APN', 'GPN' ]);
-export const PyrimidineBaseNames = new Set([ 'C', 'T', 'U', 'DC', 'DT', 'DU', 'CPN', 'TPN' ]);
+export const PeptideBaseNames = new Set(['APN', 'CPN', 'TPN', 'GPN']);
+export const PurineBaseNames = new Set(['A', 'G', 'I', 'DA', 'DG', 'DI', 'APN', 'GPN']);
+export const PyrimidineBaseNames = new Set(['C', 'T', 'U', 'DC', 'DT', 'DU', 'CPN', 'TPN']);
 export const BaseNames = SetUtils.unionMany(RnaBaseNames, DnaBaseNames, PeptideBaseNames);
 
 export const isPurineBase = (compId: string) => PurineBaseNames.has(compId.toUpperCase());
@@ -596,13 +605,13 @@ export type BondType = BitFlags<BondType.Flag>
 export namespace BondType {
     export const is: (b: BondType, f: Flag) => boolean = BitFlags.has;
     export const enum Flag {
-        None                 = 0x0,
-        Covalent             = 0x1,
+        None = 0x0,
+        Covalent = 0x1,
         MetallicCoordination = 0x2,
-        HydrogenBond         = 0x4,
-        Disulfide            = 0x8,
-        Aromatic             = 0x10,
-        Computed             = 0x20
+        HydrogenBond = 0x4,
+        Disulfide = 0x8,
+        Aromatic = 0x10,
+        Computed = 0x20
         // currently at most 16 flags are supported!!
     }
 
@@ -656,28 +665,28 @@ export namespace BondType {
  */
 export const ResidueHydrophobicity = {
     // AA  DGwif   DGwoct  Oct-IF
-    'ALA': [ 0.17, 0.50, 0.33 ],
-    'ARG': [ 0.81, 1.81, 1.00 ],
-    'ASN': [ 0.42, 0.85, 0.43 ],
-    'ASP': [ 1.23, 3.64, 2.41 ],
-    'ASH': [ -0.07, 0.43, 0.50 ],
-    'CYS': [ -0.24, -0.02, 0.22 ],
-    'GLN': [ 0.58, 0.77, 0.19 ],
-    'GLU': [ 2.02, 3.63, 1.61 ],
-    'GLH': [ -0.01, 0.11, 0.12 ],
-    'GLY': [ 0.01, 1.15, 1.14 ],
+    'ALA': [0.17, 0.50, 0.33],
+    'ARG': [0.81, 1.81, 1.00],
+    'ASN': [0.42, 0.85, 0.43],
+    'ASP': [1.23, 3.64, 2.41],
+    'ASH': [-0.07, 0.43, 0.50],
+    'CYS': [-0.24, -0.02, 0.22],
+    'GLN': [0.58, 0.77, 0.19],
+    'GLU': [2.02, 3.63, 1.61],
+    'GLH': [-0.01, 0.11, 0.12],
+    'GLY': [0.01, 1.15, 1.14],
     // "His+": [  0.96,  2.33,  1.37 ],
-    'HIS': [ 0.17, 0.11, -0.06 ],
-    'ILE': [ -0.31, -1.12, -0.81 ],
-    'LEU': [ -0.56, -1.25, -0.69 ],
-    'LYS': [ 0.99, 2.80, 1.81 ],
-    'MET': [ -0.23, -0.67, -0.44 ],
-    'PHE': [ -1.13, -1.71, -0.58 ],
-    'PRO': [ 0.45, 0.14, -0.31 ],
-    'SER': [ 0.13, 0.46, 0.33 ],
-    'THR': [ 0.14, 0.25, 0.11 ],
-    'TRP': [ -1.85, -2.09, -0.24 ],
-    'TYR': [ -0.94, -0.71, 0.23 ],
-    'VAL': [ 0.07, -0.46, -0.53 ]
+    'HIS': [0.17, 0.11, -0.06],
+    'ILE': [-0.31, -1.12, -0.81],
+    'LEU': [-0.56, -1.25, -0.69],
+    'LYS': [0.99, 2.80, 1.81],
+    'MET': [-0.23, -0.67, -0.44],
+    'PHE': [-1.13, -1.71, -0.58],
+    'PRO': [0.45, 0.14, -0.31],
+    'SER': [0.13, 0.46, 0.33],
+    'THR': [0.14, 0.25, 0.11],
+    'TRP': [-1.85, -2.09, -0.24],
+    'TYR': [-0.94, -0.71, 0.23],
+    'VAL': [0.07, -0.46, -0.53]
 };
-export const DefaultResidueHydrophobicity = [ 0.00, 0.00, 0.00 ];
+export const DefaultResidueHydrophobicity = [0.00, 0.00, 0.00];

src/mol-model/structure/query/utils/structure-set.ts

@@ -40,6 +40,22 @@ function buildUnion(this: StructureSubsetBuilder, elements: StructureElement.Set
     this.setUnit(id, elements);
 }
 
+export function structureAreEqual(sA: Structure, sB: Structure): boolean {
+    if (sA === sB) return true;
+
+    if (sA.units.length !== sB.units.length) return false;
+
+    const aU = sA.units, bU = sB.unitMap;
+    for (let i = 0, _i = aU.length; i < _i; i++) {
+        const u = aU[i];
+        if (!bU.has(u.id)) return false;
+        const v = bU.get(u.id);
+        if (!SortedArray.areEqual(u.elements, v.elements)) return false;
+    }
+
+    return true;
+}
+
 export function structureAreIntersecting(sA: Structure, sB: Structure): boolean {
     if (sA === sB) return true;
 

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

@@ -29,6 +29,7 @@ import { CustomProperties } from '../common/custom-property';
 import { AtomicHierarchy } from '../model/properties/atomic';
 import { StructureSelection } from '../query/selection';
 import { getBoundary } from '../../../mol-math/geometry/boundary';
+import { ElementSymbol } from '../model/types';
 
 class Structure {
     /** Maps unit.id to unit */
@@ -50,6 +51,7 @@ class Structure {
         masterModel?: Model,
         representativeModel?: Model,
         uniqueResidueNames?: Set<string>,
+        uniqueElementSymbols?: Set<ElementSymbol>,
         entityIndices?: ReadonlyArray<EntityIndex>,
         uniqueAtomicResidueIndices?: ReadonlyMap<UUID, ReadonlyArray<ResidueIndex>>,
         serialMapping?: SerialMapping,
@@ -265,6 +267,11 @@ class Structure {
             || (this._props.uniqueResidueNames = getUniqueResidueNames(this));
     }
 
+    get uniqueElementSymbols() {
+        return this._props.uniqueElementSymbols
+            || (this._props.uniqueElementSymbols = getUniqueElementSymbols(this));
+    }
+
     get entityIndices() {
         return this._props.entityIndices
             || (this._props.entityIndices = getEntityIndices(this));
@@ -403,7 +410,8 @@ function getUniqueResidueNames(s: Structure) {
     const prop = StructureProperties.residue.label_comp_id;
     const names = new Set<string>();
     const loc = StructureElement.Location.create(s);
-    for (const unit of s.units) {
+    for (const unitGroup of s.unitSymmetryGroups) {
+        const unit = unitGroup.units[0];
         // TODO: support coarse unit?
         if (!Unit.isAtomic(unit)) continue;
         const residues = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
@@ -417,6 +425,22 @@ function getUniqueResidueNames(s: Structure) {
     return names;
 }
 
+function getUniqueElementSymbols(s: Structure) {
+    const prop = StructureProperties.atom.type_symbol;
+    const symbols = new Set<ElementSymbol>();
+    const loc = StructureElement.Location.create(s);
+    for (const unitGroup of s.unitSymmetryGroups) {
+        const unit = unitGroup.units[0];
+        if (!Unit.isAtomic(unit)) continue;
+        loc.unit = unit;
+        for (let i = 0, il = unit.elements.length; i < il; ++i) {
+            loc.element = unit.elements[i];
+            symbols.add(prop(loc));
+        }
+    }
+    return symbols;
+}
+
 function getEntityIndices(structure: Structure): ReadonlyArray<EntityIndex> {
     const { units } = structure;
     const l = StructureElement.Location.create(structure);

src/mol-model/volume/data.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>
@@ -10,9 +10,9 @@ import { Tensor, Mat4, Vec3 } from '../../mol-math/linear-algebra';
 import { equalEps } from '../../mol-math/linear-algebra/3d/common';
 
 /** The basic unit cell that contains the data. */
-interface VolumeData {
-    readonly cell: SpacegroupCell,
-    readonly fractionalBox: Box3D,
+interface VolumeDataBase {
+    readonly label?: string,
+    readonly transform: { kind: 'spacegroup', cell: SpacegroupCell, fractionalBox: Box3D } | { kind: 'matrix', matrix: Mat4 },
     readonly data: Tensor,
     readonly dataStats: Readonly<{
         min: number,
@@ -22,20 +22,31 @@ interface VolumeData {
     }>
 }
 
+interface VolumeData extends VolumeDataBase {
+    readonly colorVolume?: VolumeDataBase
+}
+
 namespace VolumeData {
     export const One: VolumeData = {
-        cell: SpacegroupCell.Zero,
-        fractionalBox: Box3D.empty(),
+        transform: { kind: 'matrix', matrix: Mat4.identity() },
         data: Tensor.create(Tensor.Space([1, 1, 1], [0, 1, 2]), Tensor.Data1([0])),
         dataStats: { min: 0, max: 0, mean: 0, sigma: 0 }
     };
 
     const _scale = Mat4.zero(), _translate = Mat4.zero();
     export function getGridToCartesianTransform(volume: VolumeData) {
-        const { data: { space } } = volume;
-        const scale = Mat4.fromScaling(_scale, Vec3.div(Vec3.zero(), Box3D.size(Vec3.zero(), volume.fractionalBox), Vec3.ofArray(space.dimensions)));
-        const translate = Mat4.fromTranslation(_translate, volume.fractionalBox.min);
-        return Mat4.mul3(Mat4.zero(), volume.cell.fromFractional, translate, scale);
+        if (volume.transform.kind === 'matrix') {
+            return Mat4.copy(Mat4(), volume.transform.matrix);
+        }
+
+        if (volume.transform.kind === 'spacegroup') {
+            const { data: { space } } = volume;
+            const scale = Mat4.fromScaling(_scale, Vec3.div(Vec3.zero(), Box3D.size(Vec3.zero(), volume.transform.fractionalBox), Vec3.ofArray(space.dimensions)));
+            const translate = Mat4.fromTranslation(_translate, volume.transform.fractionalBox.min);
+            return Mat4.mul3(Mat4.zero(), volume.transform.cell.fromFractional, translate, scale);
+        }
+
+        return Mat4.identity();
     }
 
     export function areEquivalent(volA: VolumeData, volB: VolumeData) {
@@ -74,8 +85,8 @@ namespace VolumeIsoValue {
 
     export function toString(value: VolumeIsoValue) {
         return value.kind === 'relative'
-            ? `${value.relativeValue} σ`
-            : `${value.absoluteValue}`;
+            ? `${value.relativeValue.toFixed(2)} σ`
+            : `${value.absoluteValue.toPrecision(4)}`;
     }
 }
 

src/mol-model/volume/volume.ts

@@ -0,0 +1,92 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { VolumeData, VolumeIsoValue } from './data';
+import { OrderedSet } from '../../mol-data/int';
+import { Sphere3D } from '../../mol-math/geometry';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
+
+export namespace Volume {
+    export type CellIndex = { readonly '@type': 'cell-index' } & number
+
+    export interface Loci { readonly kind: 'volume-loci', readonly volume: VolumeData }
+    export function Loci(volume: VolumeData): Loci { return { kind: 'volume-loci', volume }; }
+    export function isLoci(x: any): x is Loci { return !!x && x.kind === 'volume-loci'; }
+    export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume; }
+    export function isLociEmpty(loci: Loci) { return loci.volume.data.data.length === 0; }
+
+    export function getBoundingSphere(volume: VolumeData, boundingSphere?: Sphere3D) {
+        if (!boundingSphere) boundingSphere = Sphere3D();
+
+        const transform = VolumeData.getGridToCartesianTransform(volume);
+        const [x, y, z] = volume.data.space.dimensions;
+
+        const cpA = Vec3.create(0, 0, 0); Vec3.transformMat4(cpA, cpA, transform);
+        const cpB = Vec3.create(x, y, z); Vec3.transformMat4(cpB, cpB, transform);
+        const cpC = Vec3.create(x, 0, 0); Vec3.transformMat4(cpC, cpC, transform);
+        const cpD = Vec3.create(0, y, z); Vec3.transformMat4(cpD, cpC, transform);
+
+        const cpE = Vec3.create(0, 0, z); Vec3.transformMat4(cpE, cpE, transform);
+        const cpF = Vec3.create(x, 0, z); Vec3.transformMat4(cpF, cpF, transform);
+        const cpG = Vec3.create(x, y, 0); Vec3.transformMat4(cpG, cpG, transform);
+        const cpH = Vec3.create(0, y, 0); Vec3.transformMat4(cpH, cpH, transform);
+
+        const center = Vec3();
+        Vec3.add(center, cpA, cpB);
+        Vec3.scale(center, center, 0.5);
+        const d = Math.max(Vec3.distance(cpA, cpB), Vec3.distance(cpC, cpD));
+        Sphere3D.set(boundingSphere, center, d / 2);
+        Sphere3D.setExtrema(boundingSphere, [cpA, cpB, cpC, cpD, cpE, cpF, cpG, cpH]);
+
+        return boundingSphere;
+    }
+
+    export namespace Isosurface {
+        export interface Loci { readonly kind: 'isosurface-loci', readonly volume: VolumeData, readonly isoValue: VolumeIsoValue }
+        export function Loci(volume: VolumeData, isoValue: VolumeIsoValue): Loci { return { kind: 'isosurface-loci', volume, isoValue }; }
+        export function isLoci(x: any): x is Loci { return !!x && x.kind === 'isosurface-loci'; }
+        export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume && VolumeIsoValue.areSame(a.isoValue, b.isoValue, a.volume.dataStats); }
+        export function isLociEmpty(loci: Loci) { return loci.volume.data.data.length === 0; }
+
+        export function getBoundingSphere(volume: VolumeData, isoValue: VolumeIsoValue, boundingSphere?: Sphere3D) {
+            // TODO get bounding sphere for subgrid with values >= isoValue
+            return Volume.getBoundingSphere(volume, boundingSphere);
+        }
+    }
+
+    export namespace Cell {
+        export interface Loci { readonly kind: 'cell-loci', readonly volume: VolumeData, readonly indices: OrderedSet<CellIndex> }
+        export function Loci(volume: VolumeData, indices: OrderedSet<CellIndex>): Loci { return { kind: 'cell-loci', volume, indices }; }
+        export function isLoci(x: any): x is Loci { return !!x && x.kind === 'cell-loci'; }
+        export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume && OrderedSet.areEqual(a.indices, b.indices); }
+        export function isLociEmpty(loci: Loci) { return OrderedSet.size(loci.indices) === 0; }
+
+        const boundaryHelper = new BoundaryHelper('98');
+        const tmpBoundaryPos = Vec3();
+        export function getBoundingSphere(volume: VolumeData, indices: OrderedSet<CellIndex>, boundingSphere?: Sphere3D) {
+            boundaryHelper.reset();
+            const transform = VolumeData.getGridToCartesianTransform(volume);
+            const { getCoords } = volume.data.space;
+
+            for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
+                const o = OrderedSet.getAt(indices, i);
+                getCoords(o, tmpBoundaryPos);
+                Vec3.transformMat4(tmpBoundaryPos, tmpBoundaryPos, transform);
+                boundaryHelper.includePosition(tmpBoundaryPos);
+            }
+            boundaryHelper.finishedIncludeStep();
+            for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
+                const o = OrderedSet.getAt(indices, i);
+                getCoords(o, tmpBoundaryPos);
+                Vec3.transformMat4(tmpBoundaryPos, tmpBoundaryPos, transform);
+                boundaryHelper.radiusPosition(tmpBoundaryPos);
+            }
+
+            return boundaryHelper.getSphere(boundingSphere);
+        }
+    }
+}

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

@@ -18,7 +18,10 @@ export const OpenFiles = StateAction.build({
         const { extensions, options } = ctx.dataFormats;
         return {
             files: PD.FileList({ accept: Array.from(extensions.values()).map(e => `.${e}`).join(',') + ',.gz,.zip', multiple: true }),
-            format: PD.Select('auto', options),
+            format: PD.MappedStatic('auto', {
+                auto: PD.EmptyGroup(),
+                specific: PD.Select(options[0][0], options)
+            }),
             visuals: PD.Boolean(true, { description: 'Add default visuals' }),
         };
     }
@@ -35,9 +38,9 @@ export const OpenFiles = StateAction.build({
                 const info = getFileInfo(file.file!);
                 const isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
                 const { data } = await plugin.builders.data.readFile({ file, isBinary });
-                const provider = params.format === 'auto'
+                const provider = params.format.name === 'auto'
                     ? plugin.dataFormats.auto(info, data.cell?.obj!)
-                    : plugin.dataFormats.get(params.format);
+                    : plugin.dataFormats.get(params.format.params);
 
                 if (!provider) {
                     plugin.log.warn(`OpenFiles: could not find data provider for '${info.name}.${info.ext}'`);
@@ -54,4 +57,38 @@ export const OpenFiles = StateAction.build({
             }
         }
     }).runInContext(taskCtx);
+}));
+
+export const DownloadFile = StateAction.build({
+    display: { name: 'Download File', description: 'Load one or more file from an URL' },
+    from: PluginStateObject.Root,
+    params: (a, ctx: PluginContext) => {
+        const { options } = ctx.dataFormats;
+        return {
+            url: PD.Url(''),
+            format: PD.Select(options[0][0], options),
+            isBinary: PD.Boolean(false),
+            visuals: PD.Boolean(true, { description: 'Add default visuals' }),
+        };
+    }
+})(({ params, state }, plugin: PluginContext) => Task.create('Open Files', async taskCtx => {
+    plugin.behaviors.layout.leftPanelTabName.next('data');
+
+    await state.transaction(async () => {
+        try {
+            const provider = plugin.dataFormats.get(params.format);
+            if (!provider) {
+                plugin.log.warn(`DownloadFile: could not find data provider for '${params.format}'`);
+                return;
+            }
+
+            const data = await plugin.builders.data.download({ url: params.url, isBinary: params.isBinary });
+            const parsed = await provider.parse(plugin, data);
+            if (params.visuals) {
+                await provider.visuals?.(plugin, parsed);
+            }
+        } catch (e) {
+            plugin.log.error(e);
+        }
+    }).runInContext(taskCtx);
 }));

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

@@ -37,7 +37,7 @@ const DownloadStructure = StateAction.build({
             source: PD.MappedStatic('pdb', {
                 'pdb': PD.Group({
                     provider: PD.Group({
-                        id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma separated PDB ids.' }),
+                        id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma/space separated PDB ids.' }),
                         server: PD.MappedStatic('pdbe', {
                             'rcsb': PD.Group({
                                 encoding: PD.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']] as ['cif' | 'bcif', string][]),
@@ -50,19 +50,19 @@ const DownloadStructure = StateAction.build({
                     options
                 }, { isFlat: true, label: 'PDB' }),
                 'pdb-dev': PD.Group({
-                    id: PD.Text('PDBDEV_00000001', { label: 'PDBDev Id(s)', description: 'One or more comma separated ids.' }),
+                    id: PD.Text('PDBDEV_00000001', { label: 'PDBDev Id(s)', description: 'One or more comma/space separated ids.' }),
                     options
                 }, { isFlat: true, label: 'PDBDEV' }),
                 'bcif-static': PD.Group({
-                    id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma separated PDB ids.' }),
+                    id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma/space separated PDB ids.' }),
                     options
                 }, { isFlat: true, label: 'BinaryCIF (static PDBe Updated)' }),
                 'swissmodel': PD.Group({
-                    id: PD.Text('Q9Y2I8', { label: 'UniProtKB AC(s)', description: 'One or more comma separated ACs.' }),
+                    id: PD.Text('Q9Y2I8', { label: 'UniProtKB AC(s)', description: 'One or more comma/space separated ACs.' }),
                     options
                 }, { isFlat: true, label: 'SWISS-MODEL', description: 'Loads the best homology model or experimental structure' }),
                 'pubchem': PD.Group({
-                    id: PD.Text('2244,2245', { label: 'PubChem ID', description: 'One or more comma separated IDs.' }),
+                    id: PD.Text('2244,2245', { label: 'PubChem ID', description: 'One or more comma/space separated IDs.' }),
                     options
                 }, { isFlat: true, label: 'PubChem', description: 'Loads 3D conformer from PubChem.' }),
                 'url': PD.Group({
@@ -160,7 +160,7 @@ const DownloadStructure = StateAction.build({
 }));
 
 function getDownloadParams(src: string, url: (id: string) => string, label: (id: string) => string, isBinary: boolean): StateTransformer.Params<Download>[] {
-    const ids = src.split(',').map(id => id.trim()).filter(id => !!id && (id.length >= 4 || /^[1-9][0-9]*$/.test(id)));
+    const ids = src.split(/[,\s]/).map(id => id.trim()).filter(id => !!id && (id.length >= 4 || /^[1-9][0-9]*$/.test(id)));
     const ret: StateTransformer.Params<Download>[] = [];
     for (const id of ids) {
         ret.push({ url: Asset.Url(url(id)), isBinary, label: label(id) });

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

@@ -6,7 +6,7 @@
  */
 
 import { PluginContext } from '../../mol-plugin/context';
-import { StateAction, StateTransformer } from '../../mol-state';
+import { StateAction, StateTransformer, StateSelection } from '../../mol-state';
 import { Task } from '../../mol-task';
 import { getFileInfo } from '../../mol-util/file-info';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
@@ -14,6 +14,7 @@ import { PluginStateObject } from '../objects';
 import { Download } from '../transforms/data';
 import { DataFormatProvider } from '../formats/provider';
 import { Asset } from '../../mol-util/assets';
+import { StateTransforms } from '../transforms';
 
 export { DownloadDensity };
 type DownloadDensity = typeof DownloadDensity
@@ -135,4 +136,17 @@ const DownloadDensity = StateAction.build({
 
     const volumes = await provider.parse(plugin, data);
     await provider.visuals?.(plugin, volumes);
-}));
+}));
+
+export const AssignColorVolume = StateAction.build({
+    display: { name: 'Assign Volume Colors', description: 'Assigns another volume to be available for coloring.' },
+    from: PluginStateObject.Volume.Data,
+    isApplicable(a) { return !a.data.colorVolume; },
+    params(a, plugin: PluginContext) {
+        const cells = plugin.state.data.select(StateSelection.Generators.root.subtree().ofType(PluginStateObject.Volume.Data).filter(cell => !!cell.obj && !cell.obj?.data.colorVolume && cell.obj !== a));
+        if (cells.length === 0) return { ref: PD.Text('', { isHidden: true, label: 'Volume' }) };
+        return { ref: PD.Select(cells[0].transform.ref, cells.map(c => [c.transform.ref, c.obj!.label]), { label: 'Volume' }) };
+    }
+})(({ ref, params, state }, plugin: PluginContext) => {
+    return plugin.build().to(ref).apply(StateTransforms.Volume.AssignColorVolume, { ref: params.ref }, { dependsOn: [ params.ref ] }).commit();
+});

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

@@ -75,7 +75,8 @@ const auto = StructureRepresentationPresetProvider({
             case Structure.Size.Medium:
                 return polymerAndLigand.apply(ref, params, plugin);
             case Structure.Size.Small:
-                return atomicDetail.apply(ref, params, plugin);
+                // `showCarbohydrateSymbol: true` is nice e.g. for PDB 1aga
+                return atomicDetail.apply(ref, { ...params, showCarbohydrateSymbol: true }, plugin);
         }
     }
 });
@@ -105,7 +106,7 @@ const polymerAndLigand = StructureRepresentationPresetProvider({
             polymer: await presetStaticComponent(plugin, structureCell, 'polymer'),
             ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
             nonStandard: await presetStaticComponent(plugin, structureCell, 'non-standard'),
-            branched: await presetStaticComponent(plugin, structureCell, 'branched'),
+            branched: await presetStaticComponent(plugin, structureCell, 'branched', { label: 'Carbohydrate' }),
             water: await presetStaticComponent(plugin, structureCell, 'water'),
             coarse: await presetStaticComponent(plugin, structureCell, 'coarse')
         };
@@ -115,9 +116,9 @@ const polymerAndLigand = StructureRepresentationPresetProvider({
             polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams, color }, { tag: 'polymer' }),
             ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams, color }, { tag: 'ligand' }),
             nonStandard: builder.buildRepresentation(update, components.nonStandard, { type: 'ball-and-stick', typeParams, color: color || 'polymer-id' }, { tag: 'non-standard' }),
-            branchedBallAndStick: builder.buildRepresentation(update, components.branched, { type: 'ball-and-stick', typeParams: { ...typeParams, alpha: 0.15 }, color }, { tag: 'branched-ball-and-stick' }),
+            branchedBallAndStick: builder.buildRepresentation(update, components.branched, { type: 'ball-and-stick', typeParams: { ...typeParams, alpha: 0.3 }, color }, { tag: 'branched-ball-and-stick' }),
             branchedSnfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams, color }, { tag: 'branched-snfg-3d' }),
-            water: builder.buildRepresentation(update, components.water, { type: 'ball-and-stick', typeParams: { ...typeParams, alpha: 0.51 }, color }, { tag: 'water' }),
+            water: builder.buildRepresentation(update, components.water, { type: 'ball-and-stick', typeParams: { ...typeParams, alpha: 0.6 }, color }, { tag: 'water' }),
             coarse: builder.buildRepresentation(update, components.coarse, { type: 'spacefill', typeParams, color: color || 'polymer-id' }, { tag: 'coarse' })
         };
 
@@ -226,7 +227,10 @@ const atomicDetail = StructureRepresentationPresetProvider({
         name: 'Atomic Detail', group: BuiltInPresetGroupName,
         description: 'Shows everything in atomic detail with Ball & Stick.'
     },
-    params: () => CommonParams,
+    params: () => ({
+        ...CommonParams,
+        showCarbohydrateSymbol: PD.Boolean(false)
+    }),
     async apply(ref, params, plugin) {
         const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
         if (!structureCell) return {};
@@ -237,8 +241,13 @@ const atomicDetail = StructureRepresentationPresetProvider({
 
         const { update, builder, typeParams, color } = reprBuilder(plugin, params);
         const representations = {
-            all: builder.buildRepresentation(update, components.all, { type: 'ball-and-stick', typeParams, color }, { tag: 'all' })
+            all: builder.buildRepresentation(update, components.all, { type: 'ball-and-stick', typeParams, color }, { tag: 'all' }),
         };
+        if (params.showCarbohydrateSymbol) {
+            Object.assign(representations, {
+                snfg3d: builder.buildRepresentation(update, components.all, { type: 'carbohydrate', typeParams: { ...typeParams, alpha: 0.4, visuals: ['carbohydrate-symbol'] }, color }, { tag: 'snfg-3d' }),
+            });
+        }
 
         await update.commit({ revertOnError: true });
         return { components, representations };

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

@@ -45,7 +45,7 @@ export class DataFormatRegistry {
 
     get options() {
         if (this._options) return this._options;
-        const options: [string, string, string][] = [['auto', 'Automatic', '']];
+        const options: [string, string, string][] = [];
         this._list.forEach(({ name, provider }) => options.push([ name, provider.label, provider.category || '' ]));
         this._options = options;
         return options;

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

@@ -13,6 +13,8 @@ import { PluginStateObject } from '../objects';
 import { VolumeRepresentation3DHelpers } from '../transforms/representation';
 import { ColorNames } from '../../mol-util/color/names';
 import { VolumeIsoValue } from '../../mol-model/volume';
+import { createVolumeRepresentationParams } from '../helpers/volume-representation-params';
+import { objectForEach } from '../../mol-util/object';
 
 const Category = 'Volume';
 
@@ -59,6 +61,76 @@ export const Dsn6Provider = DataFormatProvider({
     visuals: defaultVisuals
 });
 
+export const DxProvider = DataFormatProvider({
+    label: 'DX',
+    description: 'DX',
+    category: Category,
+    stringExtensions: ['dx'],
+    binaryExtensions: ['dxbin'],
+    parse: async (plugin, data) => {
+        const format = plugin.build()
+            .to(data)
+            .apply(StateTransforms.Data.ParseDx, {}, { state: { isGhost: true } });
+
+        const volume = format.apply(StateTransforms.Volume.VolumeFromDx);
+
+        await volume.commit({ revertOnError: true });
+
+        return { volume: volume.selector };
+    },
+    visuals: defaultVisuals
+});
+
+export const CubeProvider = DataFormatProvider({
+    label: 'Cube',
+    description: 'Cube',
+    category: Category,
+    stringExtensions: ['cub', 'cube'],
+    parse: async (plugin, data) => {
+        const format = plugin.build()
+            .to(data)
+            .apply(StateTransforms.Data.ParseCube, {}, { state: { isGhost: true } });
+
+        const volume = format.apply(StateTransforms.Volume.VolumeFromCube);
+        const structure = format
+            .apply(StateTransforms.Model.TrajectoryFromCube, void 0, { state: { isGhost: true } })
+            .apply(StateTransforms.Model.ModelFromTrajectory)
+            .apply(StateTransforms.Model.StructureFromModel);
+
+        await format.commit({ revertOnError: true });
+
+        return { format: format.selector, volume: volume.selector, structure: structure.selector };
+    },
+    visuals: async (plugin: PluginContext, data: { volume: StateObjectSelector<PluginStateObject.Volume.Data>, structure: StateObjectSelector<PluginStateObject.Molecule.Structure> }) => {
+        const surfaces = plugin.build();
+
+        const volumeData = data.volume.cell?.obj?.data;
+        const volumePos = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
+            type: 'isosurface',
+            typeParams: { isoValue: VolumeIsoValue.relative(1), alpha: 0.4 },
+            color: 'uniform',
+            colorParams: { value: ColorNames.blue }
+        }));
+        const volumeNeg = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
+            type: 'isosurface',
+            typeParams: { isoValue: VolumeIsoValue.relative(-1), alpha: 0.4 },
+            color: 'uniform',
+            colorParams: { value: ColorNames.red }
+        }));
+
+        const structure = await plugin.builders.structure.representation.applyPreset(data.structure, 'auto');
+        await surfaces.commit();
+
+        const structureReprs: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D>[] = [];
+
+        objectForEach(structure?.representations as any, (r: any) => {
+            if (r) structureReprs.push(r);
+        });
+
+        return [volumePos.selector, volumeNeg.selector, ...structureReprs];
+    }
+});
+
 export const DscifProvider = DataFormatProvider({
     label: 'DensityServer CIF',
     description: 'DensityServer CIF',
@@ -111,7 +183,9 @@ export const DscifProvider = DataFormatProvider({
 
 export const BuiltInVolumeFormats = [
     ['ccp4', Ccp4Provider] as const,
-    ['dns6', Dsn6Provider] as const,
+    ['dsn6', Dsn6Provider] as const,
+    ['cube', CubeProvider] as const,
+    ['dx', DxProvider] as const,
     ['dscif', DscifProvider] as const,
 ] as const;
 

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

@@ -6,8 +6,8 @@
  */
 
 import { CustomProperty } from '../../mol-model-props/common/custom-property';
-import { QueryContext, Structure, StructureQuery, StructureSelection } from '../../mol-model/structure';
-import { BondType, NucleicBackboneAtoms, ProteinBackboneAtoms, SecondaryStructureType } from '../../mol-model/structure/model/types';
+import { QueryContext, Structure, StructureQuery, StructureSelection, StructureProperties, StructureElement } from '../../mol-model/structure';
+import { BondType, NucleicBackboneAtoms, ProteinBackboneAtoms, SecondaryStructureType, AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames, ElementSymbol } from '../../mol-model/structure/model/types';
 import { PluginContext } from '../../mol-plugin/context';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import Expression from '../../mol-script/language/expression';
@@ -15,9 +15,9 @@ import { compile } from '../../mol-script/runtime/query/compiler';
 import { StateBuilder } from '../../mol-state';
 import { RuntimeContext } from '../../mol-task';
 import { SetUtils } from '../../mol-util/set';
-import { stringToWords } from '../../mol-util/string';
 import { PluginStateObject } from '../objects';
 import { StateTransforms } from '../transforms';
+import { ElementNames } from '../../mol-model/structure/model/properties/atomic/types';
 
 export enum StructureSelectionCategory {
     Type = 'Type',
@@ -41,6 +41,7 @@ interface StructureSelectionQuery {
     readonly description: string
     readonly category: string
     readonly isHidden: boolean
+    readonly priority: number
     readonly referencesCurrent: boolean
     readonly query: StructureQuery
     readonly ensureCustomProperties?: (ctx: CustomProperty.Context, structure: Structure) => Promise<void>
@@ -51,6 +52,7 @@ interface StructureSelectionQueryProps {
     description?: string
     category?: string
     isHidden?: boolean
+    priority?: number
     referencesCurrent?: boolean
     ensureCustomProperties?: (ctx: CustomProperty.Context, structure: Structure) => Promise<void>
 }
@@ -63,6 +65,7 @@ function StructureSelectionQuery(label: string, expression: Expression, props: S
         description: props.description || '',
         category: props.category ?? StructureSelectionCategory.Misc,
         isHidden: !!props.isHidden,
+        priority: props.priority || 0,
         referencesCurrent: !!props.referencesCurrent,
         get query() {
             if (!_query) _query = compile<StructureSelection>(expression);
@@ -81,7 +84,7 @@ function StructureSelectionQuery(label: string, expression: Expression, props: S
     };
 }
 
-const all = StructureSelectionQuery('All', MS.struct.generator.all(), { category: '' });
+const all = StructureSelectionQuery('All', MS.struct.generator.all(), { category: '', priority: 1000 });
 const current = StructureSelectionQuery('Current Selection', MS.internal.generator.current(), { category: '', referencesCurrent: true });
 
 const polymer = StructureSelectionQuery('Polymer', MS.struct.modifier.union([
@@ -229,14 +232,14 @@ const branchedPlusConnected = StructureSelectionQuery('Carbohydrate with Connect
     MS.struct.modifier.includeConnected({
         0: branched.expression, 'layer-count': 1, 'as-whole-residues': true
     })
-]), { category: StructureSelectionCategory.Internal });
+]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 const branchedConnectedOnly = StructureSelectionQuery('Connected to Carbohydrate', MS.struct.modifier.union([
     MS.struct.modifier.exceptBy({
         0: branchedPlusConnected.expression,
         by: branched.expression
     })
-]), { category: StructureSelectionCategory.Internal });
+]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 const ligand = StructureSelectionQuery('Ligand', MS.struct.modifier.union([
     MS.struct.combinator.merge([
@@ -264,7 +267,7 @@ const ligand = StructureSelectionQuery('Ligand', MS.struct.modifier.union([
                 'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
                 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
                 'residue-test': MS.core.str.match([
-                    MS.re('non-polymer|(amino|carboxy) terminus', 'i'),
+                    MS.re('non-polymer|(amino|carboxy) terminus|peptide-like', 'i'),
                     MS.ammp('chemCompType')
                 ])
             })
@@ -290,14 +293,14 @@ const ligandPlusConnected = StructureSelectionQuery('Ligand with Connected', MS.
         ]),
         by: branched.expression
     })
-]), { category: StructureSelectionCategory.Internal });
+]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 const ligandConnectedOnly = StructureSelectionQuery('Connected to Ligand', MS.struct.modifier.union([
     MS.struct.modifier.exceptBy({
         0: ligandPlusConnected.expression,
         by: ligand.expression
     })
-]), { category: StructureSelectionCategory.Internal });
+]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 // residues connected to ligands or branched entities
 const connectedOnly = StructureSelectionQuery('Connected to Ligand or Carbohydrate', MS.struct.modifier.union([
@@ -305,7 +308,7 @@ const connectedOnly = StructureSelectionQuery('Connected to Ligand or Carbohydra
         branchedConnectedOnly.expression,
         ligandConnectedOnly.expression
     ]),
-]), { category: StructureSelectionCategory.Internal });
+]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 const disulfideBridges = StructureSelectionQuery('Disulfide Bridges', MS.struct.modifier.union([
     MS.struct.modifier.wholeResidues([
@@ -380,6 +383,16 @@ const bonded = StructureSelectionQuery('Residues Bonded to Selection', MS.struct
     referencesCurrent: true
 });
 
+const wholeResidues = StructureSelectionQuery('Whole Residues of Selection', MS.struct.modifier.union([
+    MS.struct.modifier.wholeResidues({
+        0: MS.internal.generator.current()
+    })
+]), {
+    description: 'Expand current selection to whole residues.',
+    category: StructureSelectionCategory.Manipulate,
+    referencesCurrent: true
+});
+
 const StandardAminoAcids = [
     [['HIS'], 'HISTIDINE'],
     [['ARG'], 'ARGININE'],
@@ -390,6 +403,7 @@ const StandardAminoAcids = [
     [['TRP'], 'TRYPTOPHAN'],
     [['ALA'], 'ALANINE'],
     [['MET'], 'METHIONINE'],
+    [['PRO'], 'PROLINE'],
     [['CYS'], 'CYSTEINE'],
     [['ASN'], 'ASPARAGINE'],
     [['VAL'], 'VALINE'],
@@ -402,6 +416,7 @@ const StandardAminoAcids = [
     [['THR'], 'THREONINE'],
     [['SEC'], 'SELENOCYSTEINE'],
     [['PYL'], 'PYRROLYSINE'],
+    [['UNK'], 'UNKNOWN'],
 ].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0) as [string[], string][];
 
 const StandardNucleicBases = [
@@ -411,14 +426,99 @@ const StandardNucleicBases = [
     [['G', 'DG'], 'GUANOSINE'],
     [['I', 'DI'], 'INOSINE'],
     [['U', 'DU'], 'URIDINE'],
+    [['N', 'DN'], 'UNKNOWN'],
 ].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0) as [string[], string][];
 
-function ResidueQuery([names, label]: [string[], string], category: string) {
-    return StructureSelectionQuery(`${stringToWords(label)} (${names.join(', ')})`, MS.struct.modifier.union([
+export function ResidueQuery([names, label]: [string[], string], category: string, priority = 0) {
+    return StructureSelectionQuery(`${label} (${names.join(', ')})`, MS.struct.modifier.union([
         MS.struct.generator.atomGroups({
             'residue-test': MS.core.set.has([MS.set(...names), MS.ammp('auth_comp_id')])
         })
-    ]), { category });
+    ]), { category, priority, description: label });
+}
+
+export function ElementSymbolQuery([names, label]: [string[], string], category: string, priority: number) {
+    return StructureSelectionQuery(`${label} (${names.join(', ')})`, MS.struct.modifier.union([
+        MS.struct.generator.atomGroups({
+            'atom-test': MS.core.set.has([MS.set(...names), MS.acp('elementSymbol')])
+        })
+    ]), { category, priority });
+}
+
+export function EntityDescriptionQuery([description, label]: [string[], string], category: string, priority: number) {
+    return StructureSelectionQuery(`${label}`, MS.struct.modifier.union([
+        MS.struct.generator.atomGroups({
+            'entity-test': MS.core.list.equal([MS.list(...description), MS.ammp('entityDescription')])
+        })
+    ]), { category, priority, description: description.join(', ') });
+}
+
+const StandardResidues = SetUtils.unionMany(
+    AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames
+);
+
+export function getElementQueries(structures: Structure[]) {
+    const uniqueElements = new Set<ElementSymbol>();
+    for (const structure of structures) {
+        structure.uniqueElementSymbols.forEach(e => uniqueElements.add(e));
+    }
+
+    const queries: StructureSelectionQuery[] = [];
+    uniqueElements.forEach(e => {
+        const label = ElementNames[e] || e;
+        queries.push(ElementSymbolQuery([[e], label], 'Element Symbol', 0));
+    });
+    return queries;
+}
+
+export function getNonStandardResidueQueries(structures: Structure[]) {
+    const residueLabels = new Map<string, string>();
+    const uniqueResidues = new Set<string>();
+    for (const structure of structures) {
+        structure.uniqueResidueNames.forEach(r => uniqueResidues.add(r));
+        for (const m of structure.models) {
+            structure.uniqueResidueNames.forEach(r => {
+                const comp = m.properties.chemicalComponentMap.get(r);
+                if (comp) residueLabels.set(r, comp.name);
+            });
+        }
+    }
+
+    const queries: StructureSelectionQuery[] = [];
+    SetUtils.difference(uniqueResidues, StandardResidues).forEach(r => {
+        const label = residueLabels.get(r) || r;
+        queries.push(ResidueQuery([[r], label], 'Ligand/Non-standard Residue', 200));
+    });
+    return queries;
+}
+
+export function getPolymerAndBranchedEntityQueries(structures: Structure[]) {
+    const uniqueEntities = new Map<string, string[]>();
+    const l = StructureElement.Location.create();
+    for (const structure of structures) {
+        l.structure = structure;
+        for (const ug of structure.unitSymmetryGroups) {
+            l.unit = ug.units[0];
+            l.element = ug.elements[0];
+            const entityType = StructureProperties.entity.type(l);
+            if (entityType === 'polymer' || entityType === 'branched') {
+                const description = StructureProperties.entity.pdbx_description(l);
+                uniqueEntities.set(description.join(', '), description);
+            }
+        }
+    }
+
+    const queries: StructureSelectionQuery[] = [];
+    uniqueEntities.forEach((v, k) => {
+        queries.push(EntityDescriptionQuery([v, k], 'Polymer/Carbohydrate Entities', 300));
+    });
+    return queries;
+}
+
+export function applyBuiltInSelection(to: StateBuilder.To<PluginStateObject.Molecule.Structure>, query: keyof typeof StructureSelectionQueries, customTag?: string) {
+    return to.apply(StateTransforms.Model.StructureSelectionFromExpression,
+        { expression: StructureSelectionQueries[query].expression, label: StructureSelectionQueries[query].label },
+        { tags: customTag ? [query, customTag] : [query] });
 }
 
 export const StructureSelectionQueries = {
@@ -447,14 +547,9 @@ export const StructureSelectionQueries = {
     surroundings,
     complement,
     bonded,
+    wholeResidues,
 };
 
-export function applyBuiltInSelection(to: StateBuilder.To<PluginStateObject.Molecule.Structure>, query: keyof typeof StructureSelectionQueries, customTag?: string) {
-    return to.apply(StateTransforms.Model.StructureSelectionFromExpression,
-        { expression: StructureSelectionQueries[query].expression, label: StructureSelectionQueries[query].label },
-        { tags: customTag ? [query, customTag] : [query] });
-}
-
 export class StructureSelectionQueryRegistry {
     list: StructureSelectionQuery[] = []
     options: [StructureSelectionQuery, string, string][] = []

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

@@ -0,0 +1,121 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { VolumeData } from '../../mol-model/volume';
+import { PluginContext } from '../../mol-plugin/context';
+import { RepresentationProvider } from '../../mol-repr/representation';
+import { VolumeRepresentationRegistry } from '../../mol-repr/volume/registry';
+import { StateTransformer } from '../../mol-state';
+import { ColorTheme } from '../../mol-theme/color';
+import { SizeTheme } from '../../mol-theme/size';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { VolumeRepresentation3D } from '../transforms/representation';
+
+export interface VolumeRepresentationBuiltInProps<
+    R extends VolumeRepresentationRegistry.BuiltIn = VolumeRepresentationRegistry.BuiltIn,
+    C extends ColorTheme.BuiltIn = ColorTheme.BuiltIn,
+    S extends SizeTheme.BuiltIn = SizeTheme.BuiltIn> {
+    /** Using any registered name will work, but code completion will break */
+    type?: R,
+    typeParams?: VolumeRepresentationRegistry.BuiltInParams<R>,
+    /** Using any registered name will work, but code completion will break */
+    color?: C,
+    colorParams?: ColorTheme.BuiltInParams<C>,
+    /** Using any registered name will work, but code completion will break */
+    size?: S,
+    sizeParams?: SizeTheme.BuiltInParams<S>
+}
+
+export interface VolumeRepresentationProps<
+    R extends RepresentationProvider<VolumeData> = RepresentationProvider<VolumeData>,
+    C extends ColorTheme.Provider = ColorTheme.Provider,
+    S extends SizeTheme.Provider = SizeTheme.Provider> {
+    type?: R,
+    typeParams?: Partial<RepresentationProvider.ParamValues<R>>,
+    color?: C,
+    colorParams?: Partial<ColorTheme.ParamValues<C>>,
+    size?: S,
+    sizeParams?: Partial<SizeTheme.ParamValues<S>>
+}
+
+export function createVolumeRepresentationParams<R extends VolumeRepresentationRegistry.BuiltIn, C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(ctx: PluginContext, volume?: VolumeData, props?: VolumeRepresentationBuiltInProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
+export function createVolumeRepresentationParams<R extends RepresentationProvider<VolumeData>, C extends ColorTheme.Provider, S extends SizeTheme.Provider>(ctx: PluginContext, volume?: VolumeData, props?: VolumeRepresentationProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
+export function createVolumeRepresentationParams(ctx: PluginContext, volume?: VolumeData, props: any = {}): StateTransformer.Params<VolumeRepresentation3D>  {
+    const p = props as VolumeRepresentationBuiltInProps;
+    if (typeof p.type === 'string' || typeof p.color === 'string' || typeof p.size === 'string') return createParamsByName(ctx, volume || VolumeData.One, props);
+    return createParamsProvider(ctx, volume || VolumeData.One, props);
+}
+
+export function getVolumeThemeTypes(ctx: PluginContext, volume?: VolumeData) {
+    const { themes: themeCtx } = ctx.representation.volume;
+    if (!volume) return themeCtx.colorThemeRegistry.types;
+    return themeCtx.colorThemeRegistry.getApplicableTypes({ volume });
+}
+
+export function createVolumeColorThemeParams<T extends ColorTheme.BuiltIn>(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName: T, params?: ColorTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
+export function createVolumeColorThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
+export function createVolumeColorThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme'] {
+    const { registry, themes } = ctx.representation.volume;
+    const repr = registry.get(typeName || registry.default.name);
+    const color = themes.colorThemeRegistry.get(themeName || repr.defaultColorTheme.name);
+    const colorDefaultParams = PD.getDefaultValues(color.getParams({ volume: volume || VolumeData.One }));
+    if (color.name === repr.defaultColorTheme.name) Object.assign(colorDefaultParams, repr.defaultColorTheme.props);
+    return { name: color.name, params: Object.assign(colorDefaultParams, params) };
+}
+
+export function createVolumeSizeThemeParams<T extends SizeTheme.BuiltIn>(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName: T, params?: SizeTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
+export function createVolumeSizeThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
+export function createVolumeSizeThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme'] {
+    const { registry, themes } = ctx.representation.volume;
+    const repr = registry.get(typeName || registry.default.name);
+    const size = themes.sizeThemeRegistry.get(themeName || repr.defaultSizeTheme.name);
+    const sizeDefaultParams = PD.getDefaultValues(size.getParams({ volume: volume || VolumeData.One }));
+    if (size.name === repr.defaultSizeTheme.name) Object.assign(sizeDefaultParams, repr.defaultSizeTheme.props);
+    return { name: size.name, params: Object.assign(sizeDefaultParams, params) };
+}
+
+function createParamsByName(ctx: PluginContext, volume: VolumeData, props: VolumeRepresentationBuiltInProps): StateTransformer.Params<VolumeRepresentation3D> {
+    const typeProvider = (props.type && ctx.representation.volume.registry.get(props.type))
+        || ctx.representation.volume.registry.default.provider;
+    const colorProvider = (props.color && ctx.representation.volume.themes.colorThemeRegistry.get(props.color))
+        || ctx.representation.volume.themes.colorThemeRegistry.get(typeProvider.defaultColorTheme.name);
+    const sizeProvider = (props.size && ctx.representation.volume.themes.sizeThemeRegistry.get(props.size))
+        || ctx.representation.volume.themes.sizeThemeRegistry.get(typeProvider.defaultSizeTheme.name);
+
+    return createParamsProvider(ctx, volume, {
+        type: typeProvider,
+        typeParams: props.typeParams,
+        color: colorProvider,
+        colorParams: props.colorParams,
+        size: sizeProvider,
+        sizeParams: props.sizeParams
+    });
+}
+
+function createParamsProvider(ctx: PluginContext, volume: VolumeData, props: VolumeRepresentationProps = {}): StateTransformer.Params<VolumeRepresentation3D> {
+    const { themes: themeCtx } = ctx.representation.volume;
+    const themeDataCtx = { volume };
+
+    const repr = props.type || ctx.representation.volume.registry.default.provider;
+    const reprDefaultParams = PD.getDefaultValues(repr.getParams(themeCtx, volume));
+    const reprParams = Object.assign(reprDefaultParams, props.typeParams);
+
+    const color = props.color || themeCtx.colorThemeRegistry.get(repr.defaultColorTheme.name);
+    const colorDefaultParams = PD.getDefaultValues(color.getParams(themeDataCtx));
+    if (color.name === repr.defaultColorTheme.name) Object.assign(colorDefaultParams, repr.defaultColorTheme.props);
+    const colorParams = Object.assign(colorDefaultParams, props.colorParams);
+
+    const size = props.size || themeCtx.sizeThemeRegistry.get(repr.defaultSizeTheme.name);
+    const sizeDefaultParams = PD.getDefaultValues(size.getParams(themeDataCtx));
+    if (size.name === repr.defaultSizeTheme.name) Object.assign(sizeDefaultParams, repr.defaultSizeTheme.props);
+    const sizeParams = Object.assign(sizeDefaultParams, props.sizeParams);
+
+    return ({
+        type: { name: repr.name, params: reprParams },
+        colorTheme: { name: color.name, params: colorParams },
+        sizeTheme: { name: size.name, params: sizeParams }
+    });
+}

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

@@ -11,6 +11,7 @@ import { PrincipalAxes } from '../../mol-math/linear-algebra/matrix/principal-ax
 import { Camera } from '../../mol-canvas3d/camera';
 import { Loci } from '../../mol-model/loci';
 import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
+import { GraphicsRenderObject } from '../../mol-gl/render-object';
 
 // TODO: make this customizable somewhere?
 const DefaultCameraFocusOptions = {
@@ -24,6 +25,19 @@ export type CameraFocusOptions = typeof DefaultCameraFocusOptions
 export class CameraManager {
     private boundaryHelper = new BoundaryHelper('98');
 
+    focusRenderObjects(objects?: ReadonlyArray<GraphicsRenderObject>, options?: Partial<CameraFocusOptions>) {
+        if (!objects) return;
+        const spheres: Sphere3D[] = [];
+
+        for (const o of objects) {
+            const s = o.values.boundingSphere.ref.value;
+            if (s.radius === 0) continue;
+            spheres.push(s);
+        }
+
+        this.focusSpheres(spheres, s => s, options);
+    }
+
     focusLoci(loci: Loci | Loci[], options?: Partial<CameraFocusOptions>) {
         // TODO: allow computation of principal axes here?
         // perhaps have an optimized function, that does exact axes small Loci and approximate/sampled from big ones?

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

@@ -33,8 +33,6 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
         changed: this.ev()
     };
 
-    currentGetSnapshotParams: PluginState.GetSnapshotParams = PluginState.DefaultGetSnapshotParams as any;
-
     getIndex(e: PluginStateSnapshotManager.Entry) {
         return this.state.entries.indexOf(e);
     }
@@ -164,7 +162,7 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
         return next;
     }
 
-    private syncCurrent(options?: { name?: string, description?: string, params?: PluginState.GetSnapshotParams }) {
+    private syncCurrent(options?: { name?: string, description?: string, params?: PluginState.SnapshotParams }) {
         const snapshot = this.plugin.state.getSnapshot(options?.params);
         if (this.state.entries.size === 0 || !this.state.current) {
             this.add(PluginStateSnapshotManager.Entry(snapshot, { name: options?.name, description: options?.description }));
@@ -173,10 +171,8 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
         }
     }
 
-    getStateSnapshot(options?: { name?: string, description?: string, playOnLoad?: boolean, params?: PluginState.GetSnapshotParams }): PluginStateSnapshotManager.StateSnapshot {
+    getStateSnapshot(options?: { name?: string, description?: string, playOnLoad?: boolean, params?: PluginState.SnapshotParams }): PluginStateSnapshotManager.StateSnapshot {
         // TODO: diffing and all that fancy stuff
-
-        // TODO: the options need to be handled better, particularky options.params
         this.syncCurrent(options);
 
         return {
@@ -193,10 +189,10 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
         };
     }
 
-    async serialize(type: 'json' | 'zip' = 'json') {
-        const json = JSON.stringify(this.getStateSnapshot(), null, 2);
+    async serialize(options?: { type: 'json' | 'molj' | 'zip' | 'molx', params?: PluginState.SnapshotParams }) {
+        const json = JSON.stringify(this.getStateSnapshot({ params: options?.params }), null, 2);
 
-        if (type === 'json') {
+        if (!options?.type || options.type === 'json' || options.type === 'molj') {
             return new Blob([json], {type : 'application/json;charset=utf-8'});
         } else {
             const state = new Uint8Array(utf8ByteCount(json));
@@ -232,7 +228,12 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
             if (fn.endsWith('json') || fn.endsWith('molj')) {
                 const data = await this.plugin.runTask(readFromFile(file, 'string'));
                 const snapshot = JSON.parse(data);
-                return this.setStateSnapshot(snapshot);
+
+                if (PluginStateSnapshotManager.isStateSnapshot(snapshot)) {
+                    return this.setStateSnapshot(snapshot);
+                } else {
+                    this.plugin.state.setSnapshot(snapshot);
+                }
             } else {
                 const data = await this.plugin.runTask(readFromFile(file, 'zip'));
                 const assets = Object.create(null);
@@ -333,6 +334,11 @@ namespace PluginStateSnapshotManager {
         return { timestamp: +new Date(), snapshot, ...params };
     }
 
+    export function isStateSnapshot(x?: any): x is StateSnapshot {
+        const s = x as StateSnapshot;
+        return !!s && !!s.timestamp && !!s.entries;
+    }
+
     export interface StateSnapshot {
         timestamp: number,
         version: string,

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

@@ -6,11 +6,11 @@
 
 import { VisualQualityOptions } from '../../../mol-geo/geometry/base';
 import { InteractionsProvider } from '../../../mol-model-props/computed/interactions';
-import { Structure, StructureElement } from '../../../mol-model/structure';
-import { structureAreIntersecting, structureIntersect, structureSubtract, structureUnion } from '../../../mol-model/structure/query/utils/structure-set';
+import { Structure, StructureElement, StructureSelection } from '../../../mol-model/structure';
+import { structureAreEqual, structureAreIntersecting, structureIntersect, structureSubtract, structureUnion } from '../../../mol-model/structure/query/utils/structure-set';
 import { setSubtreeVisibility } from '../../../mol-plugin/behavior/static/state';
 import { PluginContext } from '../../../mol-plugin/context';
-import { StateBuilder, StateTransformer } from '../../../mol-state';
+import { StateBuilder, StateObjectRef, StateTransformer } from '../../../mol-state';
 import { Task } from '../../../mol-task';
 import { ColorTheme } from '../../../mol-theme/color';
 import { SizeTheme } from '../../../mol-theme/size';
@@ -25,7 +25,7 @@ import { clearStructureOverpaint, setStructureOverpaint } from '../../helpers/st
 import { createStructureColorThemeParams, createStructureSizeThemeParams } from '../../helpers/structure-representation-params';
 import { StructureSelectionQueries, StructureSelectionQuery } from '../../helpers/structure-selection-query';
 import { StructureRepresentation3D } from '../../transforms/representation';
-import { HierarchyRef, StructureComponentRef, StructureRef, StructureRepresentationRef } from './hierarchy-state';
+import { StructureHierarchyRef, StructureComponentRef, StructureRef, StructureRepresentationRef } from './hierarchy-state';
 
 export { StructureComponentManager };
 
@@ -132,7 +132,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
         let changed = false;
         const update = this.dataState.build();
 
-        const sync = (r: HierarchyRef) => {
+        const sync = (r: StructureHierarchyRef) => {
             if (!keptRefs.has(r.cell.transform.ref)) {
                 changed = true;
                 update.delete(r.cell);
@@ -169,7 +169,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
         }
     }
 
-    canBeModified(ref: HierarchyRef) {
+    canBeModified(ref: StructureHierarchyRef) {
         return this.plugin.builders.structure.isComponentTransform(ref.cell);
     }
 
@@ -211,7 +211,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
     removeRepresentations(components: ReadonlyArray<StructureComponentRef>, pivot?: StructureRepresentationRef) {
         if (components.length === 0) return;
 
-        const toRemove: HierarchyRef[] = [];
+        const toRemove: StructureHierarchyRef[] = [];
         if (pivot) {
             const index = components[0].representations.indexOf(pivot);
             if (index < 0) return;
@@ -308,6 +308,24 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
         }, { canUndo: 'Add Representation' });
     }
 
+    private tryFindComponent(structure: StructureRef, selection: StructureSelectionQuery) {
+        if (structure.components.length === 0) return;
+
+        return this.plugin.runTask(Task.create('Find Component', async taskCtx => {
+
+            const data = structure.cell.obj?.data;
+            if (!data) return;
+            const sel = StructureSelection.unionStructure(await selection.getSelection(this.plugin, taskCtx, data));
+
+            for (const c of structure.components) {
+                const comp = c.cell.obj?.data;
+                if (!comp || !c.cell.parent) continue;
+
+                if (structureAreEqual(sel, comp)) return c.cell;
+            }
+        }));
+    }
+
     async add(params: StructureComponentManager.AddParams, structures?: ReadonlyArray<StructureRef>) {
         return this.plugin.dataTransaction(async () => {
             const xs = structures || this.currentStructures;
@@ -319,9 +337,18 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
 
             const componentKey = UUID.create22();
             for (const s of xs) {
-                const component = await this.plugin.builders.structure.tryCreateComponentFromSelection(s.cell, params.selection, componentKey, {
-                    label: params.label || (params.selection === StructureSelectionQueries.current ? 'Custom Selection' : ''),
-                });
+                let component: StateObjectRef | undefined = void 0;
+
+                if (params.options.checkExisting) {
+                    component = await this.tryFindComponent(s, params.selection);
+                }
+
+                if (!component) {
+                    component = await this.plugin.builders.structure.tryCreateComponentFromSelection(s.cell, params.selection, componentKey, {
+                        label: params.options.label || (params.selection === StructureSelectionQueries.current ? 'Custom Selection' : ''),
+                    });
+                }
+
                 if (params.representation === 'none' || !component) continue;
                 await this.plugin.builders.structure.representation.addRepresentation(component, {
                     type: this.plugin.representation.structure.registry.get(params.representation),
@@ -400,15 +427,26 @@ namespace StructureComponentManager {
     };
     export type Options = PD.Values<typeof OptionsParams>
 
-    export function getAddParams(plugin: PluginContext) {
+    export function getAddParams(plugin: PluginContext, params?: { pivot?: StructureRef, allowNone: boolean, hideSelection?: boolean, checkExisting?: boolean, defaultSelection?: StructureSelectionQuery }) {
         const { options } = plugin.query.structure.registry;
+        params = {
+            pivot: plugin.managers.structure.component.pivotStructure,
+            allowNone: true,
+            hideSelection: false,
+            checkExisting: false,
+            defaultSelection: StructureSelectionQueries.current,
+            ...params
+        };
         return {
-            selection: PD.Select(options[1][0], options),
-            representation: getRepresentationTypesSelect(plugin, plugin.managers.structure.component.pivotStructure, [['none', '< Create Later >']]),
-            label: PD.Text('')
+            selection: PD.Select(options[1][0], options, { isHidden: params?.hideSelection }),
+            representation: getRepresentationTypesSelect(plugin, params?.pivot, params?.allowNone ? [['none', '< Create Later >']] : []),
+            options: PD.Group({
+                label: PD.Text(''),
+                checkExisting: PD.Boolean(!!params?.checkExisting, { help: () => ({ description: 'Checks if a selection with the specifield elements already exists to avoid creating duplicate components.' }) }),
+            })
         };
     }
-    export type AddParams = { selection: StructureSelectionQuery, label: string, representation: string }
+    export type AddParams = { selection: StructureSelectionQuery, options: { checkExisting: boolean, label: string }, representation: string }
 
     export function getColorParams(plugin: PluginContext, pivot: StructureRef | StructureComponentRef | undefined) {
         return {

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

@@ -21,7 +21,7 @@ export interface StructureHierarchy {
     trajectories: TrajectoryRef[],
     models: ModelRef[],
     structures: StructureRef[],
-    refs: Map<StateTransform.Ref, HierarchyRef>
+    refs: Map<StateTransform.Ref, StructureHierarchyRef>
     // TODO: might be needed in the future
     // decorators: Map<StateTransform.Ref, StateTransform>,
 }
@@ -36,7 +36,7 @@ interface RefBase<K extends string = string, O extends StateObject = StateObject
     version: StateTransform['version']
 }
 
-export type HierarchyRef =
+export type StructureHierarchyRef =
     | TrajectoryRef
     | ModelRef | ModelPropertiesRef | ModelUnitcellRef
     | StructureRef | StructurePropertiesRef | StructureTransformRef | StructureVolumeStreamingRef | StructureComponentRef | StructureRepresentationRef
@@ -140,10 +140,10 @@ function StructureRepresentationRef(cell: StateObjectCell<SO.Molecule.Structure.
 }
 
 export interface GenericRepresentationRef extends RefBase<'generic-representation', SO.Any> {
-    parent: HierarchyRef
+    parent: StructureHierarchyRef
 }
 
-function GenericRepresentationRef(cell: StateObjectCell<SO.Molecule.Structure.Representation3D>, parent: HierarchyRef): GenericRepresentationRef {
+function GenericRepresentationRef(cell: StateObjectCell<SO.Molecule.Structure.Representation3D>, parent: StructureHierarchyRef): GenericRepresentationRef {
     return { kind: 'generic-representation', cell, version: cell.transform.version, parent };
 }
 
@@ -166,7 +166,7 @@ function BuildState(state: State, oldHierarchy: StructureHierarchy): BuildState
     return { state, oldHierarchy, hierarchy: StructureHierarchy(), changed: false, added: new Set() };
 }
 
-function createOrUpdateRefList<R extends HierarchyRef, C extends any[]>(state: BuildState, cell: StateObjectCell, list: R[], ctor: (...args: C) => R, ...args: C) {
+function createOrUpdateRefList<R extends StructureHierarchyRef, C extends any[]>(state: BuildState, cell: StateObjectCell, list: R[], ctor: (...args: C) => R, ...args: C) {
     const ref: R = ctor(...args);
     list.push(ref);
     state.hierarchy.refs.set(cell.transform.ref, ref);
@@ -180,7 +180,7 @@ function createOrUpdateRefList<R extends HierarchyRef, C extends any[]>(state: B
     return ref;
 }
 
-function createOrUpdateRef<R extends HierarchyRef, C extends any[]>(state: BuildState, cell: StateObjectCell, ctor: (...args: C) => R, ...args: C) {
+function createOrUpdateRef<R extends StructureHierarchyRef, C extends any[]>(state: BuildState, cell: StateObjectCell, ctor: (...args: C) => R, ...args: C) {
     const ref: R = ctor(...args);
     state.hierarchy.refs.set(cell.transform.ref, ref);
     const old = state.oldHierarchy.refs.get(cell.transform.ref);
@@ -300,7 +300,7 @@ function isValidCell(cell?: StateObjectCell): cell is StateObjectCell {
     return true;
 }
 
-function isRemoved(this: BuildState, ref: HierarchyRef) {
+function isRemoved(this: BuildState, ref: StructureHierarchyRef) {
     const { cell } = ref;
     if (isValidCell(cell)) return;
     this.changed = true;

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

@@ -12,7 +12,7 @@ import { StateTransform, StateTree } from '../../../mol-state';
 import { SetUtils } from '../../../mol-util/set';
 import { TrajectoryHierarchyPresetProvider } from '../../builder/structure/hierarchy-preset';
 import { PluginComponent } from '../../component';
-import { buildStructureHierarchy, HierarchyRef, ModelRef, StructureComponentRef, StructureHierarchy, StructureRef, TrajectoryRef } from './hierarchy-state';
+import { buildStructureHierarchy, StructureHierarchyRef, ModelRef, StructureComponentRef, StructureHierarchy, StructureRef, TrajectoryRef } from './hierarchy-state';
 
 export class StructureHierarchyManager extends PluginComponent {
     private state = {
@@ -68,7 +68,18 @@ export class StructureHierarchyManager extends PluginComponent {
         return this.state.selection;
     }
 
-    private syncCurrent<T extends HierarchyRef>(all: ReadonlyArray<T>, added: Set<StateTransform.Ref>): T[] {
+    getStructuresWithSelection() {
+        const xs = this.plugin.managers.structure.hierarchy.current.structures;
+        const ret: StructureRef[] = [];
+        for (const s of xs) {
+            if (this.plugin.managers.structure.selection.structureHasSelection(s)) {
+                ret.push(s);
+            }
+        }
+        return ret;
+    }
+
+    private syncCurrent<T extends StructureHierarchyRef>(all: ReadonlyArray<T>, added: Set<StateTransform.Ref>): T[] {
         const current = this.seletionSet;
         const newCurrent: T[] = [];
 
@@ -121,7 +132,7 @@ export class StructureHierarchyManager extends PluginComponent {
         }
     }
 
-    updateCurrent(refs: HierarchyRef[], action: 'add' | 'remove') {
+    updateCurrent(refs: StructureHierarchyRef[], action: 'add' | 'remove') {
         const hierarchy = this.current;
         const set = action === 'add'
             ? SetUtils.union(this.seletionSet, new Set(refs.map(r => r.cell.transform.ref)))
@@ -151,14 +162,14 @@ export class StructureHierarchyManager extends PluginComponent {
         this.behaviors.selection.next({ hierarchy, trajectories, models, structures });
     }
 
-    remove(refs: (HierarchyRef | string)[], canUndo?: boolean) {
+    remove(refs: (StructureHierarchyRef | string)[], canUndo?: boolean) {
         if (refs.length === 0) return;
         const deletes = this.plugin.state.data.build();
         for (const r of refs) deletes.delete(typeof r === 'string' ? r : r.cell.transform.ref);
         return deletes.commit({ canUndo: canUndo ? 'Remove' : false });
     }
 
-    toggleVisibility(refs: ReadonlyArray<HierarchyRef>, action?: 'show' | 'hide') {
+    toggleVisibility(refs: ReadonlyArray<StructureHierarchyRef>, action?: 'show' | 'hide') {
         if (refs.length === 0) return;
 
         const isHidden = action !== void 0

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

@@ -21,6 +21,7 @@ import { StatefulPluginComponent } from '../../component';
 import { StructureSelectionQuery } from '../../helpers/structure-selection-query';
 import { PluginStateObject } from '../../objects';
 import { UUID } from '../../../mol-util';
+import { StructureRef } from './hierarchy-state';
 
 interface StructureSelectionManagerState {
     entries: Map<string, SelectionEntry>,
@@ -248,6 +249,13 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
         return entry.structure;
     }
 
+    structureHasSelection(structure: StructureRef) {
+        const s = structure.cell?.obj?.data;
+        if (!s) return false;
+        const entry = this.getEntry(s);
+        return !!entry && !StructureElement.Loci.isEmpty(entry.selection);
+    }
+
     has(loci: Loci) {
         if (StructureElement.Loci.is(loci)) {
             const entry = this.getEntry(loci.structure);

src/mol-plugin-state/manager/volume/hierarchy-state.ts

@@ -0,0 +1,170 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginStateObject as SO } from '../../objects';
+import { StateObject, StateTransform, State, StateObjectCell, StateTree, StateTransformer } from '../../../mol-state';
+import { StateTransforms } from '../../transforms';
+
+export function buildVolumeHierarchy(state: State, previous?: VolumeHierarchy) {
+    const build = BuildState(state, previous || VolumeHierarchy());
+    doPreOrder(state.tree, build);
+    if (previous) previous.refs.forEach(isRemoved, build);
+    return { hierarchy: build.hierarchy, added: build.added, changed: build.changed };
+}
+
+export interface VolumeHierarchy {
+    volumes: VolumeRef[],
+    refs: Map<StateTransform.Ref, VolumeHierarchyRef>
+    // TODO: might be needed in the future
+    // decorators: Map<StateTransform.Ref, StateTransform>,
+}
+
+export function VolumeHierarchy(): VolumeHierarchy {
+    return { volumes: [], refs: new Map() };
+}
+
+interface RefBase<K extends string = string, O extends StateObject = StateObject, T extends StateTransformer = StateTransformer> {
+    kind: K,
+    cell: StateObjectCell<O, StateTransform<T>>,
+    version: StateTransform['version']
+}
+
+export type VolumeHierarchyRef = VolumeRef | VolumeRepresentationRef
+
+export interface VolumeRef extends RefBase<'volume', SO.Volume.Data> {
+    representations: VolumeRepresentationRef[]
+}
+
+function VolumeRef(cell: StateObjectCell<SO.Volume.Data>): VolumeRef {
+    return { kind: 'volume', cell, version: cell.transform.version, representations: [] };
+}
+
+export interface VolumeRepresentationRef extends RefBase<'volume-representation', SO.Volume.Representation3D, StateTransforms['Representation']['VolumeRepresentation3D']> {
+    volume: VolumeRef
+}
+
+function VolumeRepresentationRef(cell: StateObjectCell<SO.Volume.Representation3D>, volume: VolumeRef): VolumeRepresentationRef {
+    return { kind: 'volume-representation', cell, version: cell.transform.version, volume };
+}
+
+interface BuildState {
+    state: State,
+    oldHierarchy: VolumeHierarchy,
+
+    hierarchy: VolumeHierarchy,
+
+    currentVolume?: VolumeRef,
+
+    changed: boolean,
+    added: Set<StateTransform.Ref>
+}
+
+function BuildState(state: State, oldHierarchy: VolumeHierarchy): BuildState {
+    return { state, oldHierarchy, hierarchy: VolumeHierarchy(), changed: false, added: new Set() };
+}
+
+function createOrUpdateRefList<R extends VolumeHierarchyRef, C extends any[]>(state: BuildState, cell: StateObjectCell, list: R[], ctor: (...args: C) => R, ...args: C) {
+    const ref: R = ctor(...args);
+    list.push(ref);
+    state.hierarchy.refs.set(cell.transform.ref, ref);
+    const old = state.oldHierarchy.refs.get(cell.transform.ref);
+    if (old) {
+        if (old.version !== cell.transform.version) state.changed = true;
+    } else {
+        state.added.add(ref.cell.transform.ref);
+        state.changed = true;
+    }
+    return ref;
+}
+
+type TestCell = (cell: StateObjectCell, state: BuildState) => boolean
+type ApplyRef = (state: BuildState, cell: StateObjectCell) => boolean | void
+type LeaveRef = (state: BuildState) => any
+
+function isTypeRoot(t: StateObject.Ctor, target: (state: BuildState) => any): TestCell {
+    return (cell, state) => !target(state) && t.is(cell.obj);
+}
+
+function noop() { }
+
+const Mapping: [TestCell, ApplyRef, LeaveRef][] = [
+    [isTypeRoot(SO.Volume.Data, t => t.currentVolume), (state, cell) => {
+        state.currentVolume = createOrUpdateRefList(state, cell, state.hierarchy.volumes, VolumeRef, cell);
+    }, state => state.currentVolume = void 0],
+
+    [(cell, state) => {
+        return !cell.state.isGhost && !!state.currentVolume && SO.Volume.Representation3D.is(cell.obj);
+    }, (state, cell) => {
+        if (state.currentVolume) {
+            createOrUpdateRefList(state, cell, state.currentVolume.representations, VolumeRepresentationRef, cell, state.currentVolume);
+        }
+        return false;
+    }, noop]
+];
+
+function isValidCell(cell?: StateObjectCell): cell is StateObjectCell {
+    if (!cell || !cell?.parent || !cell.parent.cells.has(cell.transform.ref)) return false;
+    const { obj } = cell;
+    if (!obj || obj === StateObject.Null || (cell.status !== 'ok' && cell.status !== 'error')) return false;
+    return true;
+}
+
+function isRemoved(this: BuildState, ref: VolumeHierarchyRef) {
+    const { cell } = ref;
+    if (isValidCell(cell)) return;
+    this.changed = true;
+}
+
+type VisitorCtx = { tree: StateTree, state: BuildState };
+
+function _preOrderFunc(this: VisitorCtx, c: StateTransform.Ref | undefined) { _doPreOrder(this, this.tree.transforms.get(c!)!); }
+function _doPreOrder(ctx: VisitorCtx, root: StateTransform) {
+    const { state } = ctx;
+    const cell = state.state.cells.get(root.ref);
+    if (!isValidCell(cell)) return;
+
+    let onLeave: undefined | ((state: BuildState) => any) = void 0;
+    let end = false;
+    for (const [test, f, l] of Mapping) {
+        if (test(cell, state)) {
+            const cont = f(state, cell);
+            if (cont === false) {
+                end = true;
+                break;
+            }
+            onLeave = l;
+            break;
+        }
+    }
+
+    // TODO: might be needed in the future
+    // const { currentComponent, currentModel, currentStructure, currentTrajectory } = ctx.state;
+    // const inTrackedSubtree = currentComponent || currentModel || currentStructure || currentTrajectory;
+
+    // if (inTrackedSubtree && cell.transform.transformer.definition.isDecorator) {
+    //     const ref = cell.transform.ref;
+    //     const old = ctx.state.oldHierarchy.decorators.get(ref);
+    //     if (old && old.version !== cell.transform.version) {
+    //         ctx.state.changed = true;
+    //     }
+    //     ctx.state.hierarchy.decorators.set(cell.transform.ref, cell.transform);
+    // }
+
+    if (end) return;
+
+    const children = ctx.tree.children.get(root.ref);
+    if (children && children.size) {
+        children.forEach(_preOrderFunc, ctx);
+    }
+
+    if (onLeave) onLeave(state);
+}
+
+function doPreOrder(tree: StateTree, state: BuildState): BuildState {
+    const ctx: VisitorCtx = { tree, state };
+    _doPreOrder(ctx, tree.root);
+    return ctx.state;
+}

src/mol-plugin-state/manager/volume/hierarchy.ts

@@ -0,0 +1,135 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { setSubtreeVisibility } from '../../../mol-plugin/behavior/static/state';
+import { PluginContext } from '../../../mol-plugin/context';
+import { PluginComponent } from '../../component';
+import { buildVolumeHierarchy, VolumeHierarchy, VolumeHierarchyRef, VolumeRef } from './hierarchy-state';
+import { createVolumeRepresentationParams } from '../../helpers/volume-representation-params';
+import { StateTransforms } from '../../transforms';
+
+export class VolumeHierarchyManager extends PluginComponent {
+    private state = {
+        syncedTree: this.dataState.tree,
+        notified: false,
+
+        hierarchy: VolumeHierarchy(),
+        selection: void 0 as VolumeRef | undefined
+    }
+
+    readonly behaviors = {
+        selection: this.ev.behavior({
+            hierarchy: this.current,
+            volume: this.selection
+        })
+    }
+
+    private get dataState() {
+        return this.plugin.state.data;
+    }
+
+    get current() {
+        this.sync(false);
+        return this.state.hierarchy;
+    }
+
+    get selection() {
+        this.sync(false);
+        return this.state.selection;
+    }
+
+    private sync(notify: boolean) {
+        if (!notify && this.dataState.inUpdate) return;
+
+        if (this.state.syncedTree === this.dataState.tree) {
+            if (notify && !this.state.notified) {
+                this.state.notified = true;
+                this.behaviors.selection.next({ hierarchy: this.state.hierarchy, volume: this.state.selection });
+            }
+
+            return;
+        }
+
+        this.state.syncedTree = this.dataState.tree;
+
+        const update = buildVolumeHierarchy(this.plugin.state.data, this.current);
+        if (!update.changed) {
+            return;
+        }
+
+        const { hierarchy } = update;
+
+        this.state.hierarchy = hierarchy;
+        if (!this.state.selection) {
+            this.state.selection = hierarchy.volumes[0];
+        } else {
+            this.state.selection = hierarchy.refs.has(this.state.selection.cell.transform.ref) ? hierarchy.refs.get(this.state.selection.cell.transform.ref) as VolumeRef : hierarchy.volumes[0];
+        }
+
+        if (notify) {
+            this.state.notified = true;
+            this.behaviors.selection.next({ hierarchy, volume: this.state.selection });
+        } else {
+            this.state.notified = false;
+        }
+    }
+
+    setCurrent(volume?: VolumeRef) {
+        this.state.selection = volume || this.state.hierarchy.volumes[0];
+        this.behaviors.selection.next({ hierarchy: this.state.hierarchy, volume: volume || this.state.hierarchy.volumes[0] });
+    }
+
+    // TODO: have common util
+    remove(refs: (VolumeHierarchyRef | string)[], canUndo?: boolean) {
+        if (refs.length === 0) return;
+        const deletes = this.plugin.state.data.build();
+        for (const r of refs) deletes.delete(typeof r === 'string' ? r : r.cell.transform.ref);
+        return deletes.commit({ canUndo: canUndo ? 'Remove' : false });
+    }
+
+    // TODO: have common util
+    toggleVisibility(refs: ReadonlyArray<VolumeHierarchyRef>, action?: 'show' | 'hide') {
+        if (refs.length === 0) return;
+
+        const isHidden = action !== void 0
+            ? (action === 'show' ? false : true)
+            : !refs[0].cell.state.isHidden;
+        for (const c of refs) {
+            setSubtreeVisibility(this.dataState, c.cell.transform.ref, isHidden);
+        }
+    }
+
+    addRepresentation(ref: VolumeRef, type: string) {
+        const update = this.dataState.build()
+            .to(ref.cell)
+            .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, ref.cell.obj?.data, {
+                type: type as any,
+            }));
+
+        return update.commit({ canUndo: 'Add Representation' });
+    }
+
+    constructor(private plugin: PluginContext) {
+        super();
+
+        this.subscribe(plugin.state.data.events.changed, e => {
+            if (e.inTransaction || plugin.behaviors.state.isAnimating.value) return;
+            this.sync(true);
+        });
+
+        this.subscribe(plugin.behaviors.state.isAnimating, isAnimating => {
+            if (!isAnimating && !plugin.behaviors.state.isUpdating.value) this.sync(true);
+        });
+    }
+}
+
+export namespace VolumeHierarchyManager {
+    export function getRepresentationTypes(plugin: PluginContext, pivot: VolumeRef | undefined) {
+        return pivot?.cell.obj?.data
+            ? plugin.representation.volume.registry.getApplicableTypes(pivot.cell.obj?.data!)
+            : plugin.representation.volume.registry.types;
+    }
+}

src/mol-plugin-state/objects.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>
@@ -21,6 +21,8 @@ import { ShapeRepresentation } from '../mol-repr/shape/representation';
 import { StructureRepresentation, StructureRepresentationState } from '../mol-repr/structure/representation';
 import { VolumeRepresentation } from '../mol-repr/volume/representation';
 import { StateObject, StateTransformer } from '../mol-state';
+import { CubeFile } from '../mol-io/reader/cube/parser';
+import { DxFile } from '../mol-io/reader/dx/parser';
 
 export type TypeClass = 'root' | 'data' | 'prop'
 
@@ -67,10 +69,12 @@ export namespace PluginStateObject {
     export namespace Format {
         export class Json extends Create<any>({ name: 'JSON Data', typeClass: 'Data' }) { }
         export class Cif extends Create<CifFile>({ name: 'CIF File', typeClass: 'Data' }) { }
+        export class Cube extends Create<CubeFile>({ name: 'Cube File', typeClass: 'Data' }) { }
         export class Psf extends Create<PsfFile>({ name: 'PSF File', typeClass: 'Data' }) { }
         export class Ply extends Create<PlyFile>({ name: 'PLY File', typeClass: 'Data' }) { }
         export class Ccp4 extends Create<Ccp4File>({ name: 'CCP4/MRC/MAP File', typeClass: 'Data' }) { }
         export class Dsn6 extends Create<Dsn6File>({ name: 'DSN6/BRIX File', typeClass: 'Data' }) { }
+        export class Dx extends Create<DxFile>({ name: 'DX File', typeClass: 'Data' }) { }
 
         export type BlobEntry = { id: string } & (
             { kind: 'json', data: unknown } |
@@ -83,6 +87,7 @@ export namespace PluginStateObject {
             { kind: 'dcd', data: DcdFile } |
             { kind: 'ccp4', data: Ccp4File } |
             { kind: 'dsn6', data: Dsn6File } |
+            { kind: 'dx', data: DxFile } |
             { kind: 'ply', data: PlyFile } |
             // For non-build in extensions
             { kind: 'custom', data: unknown, tag: string }

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

@@ -18,6 +18,8 @@ import { ajaxGetMany } from '../../mol-util/data-source';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject as SO, PluginStateTransform } from '../objects';
 import { Asset } from '../../mol-util/assets';
+import { parseCube } from '../../mol-io/reader/cube/parser';
+import { parseDx } from '../../mol-io/reader/dx/parser';
 
 export { Download };
 export { DownloadBlob };
@@ -25,10 +27,12 @@ export { RawData };
 export { ReadFile };
 export { ParseBlob };
 export { ParseCif };
+export { ParseCube };
 export { ParsePsf };
 export { ParsePly };
 export { ParseCcp4 };
 export { ParseDsn6 };
+export { ParseDx };
 export { ImportString };
 export { ImportJson };
 export { ParseJson };
@@ -255,6 +259,22 @@ const ParseCif = PluginStateTransform.BuiltIn({
     }
 });
 
+type ParseCube = typeof ParseCube
+const ParseCube = PluginStateTransform.BuiltIn({
+    name: 'parse-cube',
+    display: { name: 'Parse Cube', description: 'Parse Cube from String data' },
+    from: SO.Data.String,
+    to: SO.Format.Cube
+})({
+    apply({ a }) {
+        return Task.create('Parse Cube', async ctx => {
+            const parsed = await parseCube(a.data, a.label).runInContext(ctx);
+            if (parsed.isError) throw new Error(parsed.message);
+            return new SO.Format.Cube(parsed.result);
+        });
+    }
+});
+
 type ParsePsf = typeof ParsePsf
 const ParsePsf = PluginStateTransform.BuiltIn({
     name: 'parse-psf',
@@ -296,7 +316,7 @@ const ParseCcp4 = PluginStateTransform.BuiltIn({
 })({
     apply({ a }) {
         return Task.create('Parse CCP4/MRC/MAP', async ctx => {
-            const parsed = await CCP4.parse(a.data).runInContext(ctx);
+            const parsed = await CCP4.parse(a.data, a.label).runInContext(ctx);
             if (parsed.isError) throw new Error(parsed.message);
             return new SO.Format.Ccp4(parsed.result);
         });
@@ -312,13 +332,29 @@ const ParseDsn6 = PluginStateTransform.BuiltIn({
 })({
     apply({ a }) {
         return Task.create('Parse DSN6/BRIX', async ctx => {
-            const parsed = await DSN6.parse(a.data).runInContext(ctx);
+            const parsed = await DSN6.parse(a.data, a.label).runInContext(ctx);
             if (parsed.isError) throw new Error(parsed.message);
             return new SO.Format.Dsn6(parsed.result);
         });
     }
 });
 
+type ParseDx = typeof ParseDx
+const ParseDx = PluginStateTransform.BuiltIn({
+    name: 'parse-dx',
+    display: { name: 'Parse DX', description: 'Parse DX from Binary/String data' },
+    from: [SO.Data.Binary, SO.Data.String],
+    to: SO.Format.Dx
+})({
+    apply({ a }) {
+        return Task.create('Parse DX', async ctx => {
+            const parsed = await parseDx(a.data, a.label).runInContext(ctx);
+            if (parsed.isError) throw new Error(parsed.message);
+            return new SO.Format.Dx(parsed.result);
+        });
+    }
+});
+
 type ImportString = typeof ImportString
 const ImportString = PluginStateTransform.BuiltIn({
     name: 'import-string',

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

@@ -34,6 +34,7 @@ import { PluginStateObject as SO, PluginStateTransform } from '../objects';
 import { parseMol } from '../../mol-io/reader/mol/parser';
 import { trajectoryFromMol } from '../../mol-model-formats/structure/mol';
 import { trajectoryFromCifCore } from '../../mol-model-formats/structure/cif-core';
+import { trajectoryFromCube } from '../../mol-model-formats/structure/cube';
 
 export { CoordinatesFromDcd };
 export { TopologyFromPsf };
@@ -43,6 +44,7 @@ export { TrajectoryFromMmCif };
 export { TrajectoryFromPDB };
 export { TrajectoryFromGRO };
 export { TrajectoryFromMOL };
+export { TrajectoryFromCube };
 export { TrajectoryFromCifCore };
 export { TrajectoryFrom3DG };
 export { ModelFromTrajectory };
@@ -233,6 +235,22 @@ const TrajectoryFromMOL = PluginStateTransform.BuiltIn({
     }
 });
 
+type TrajectoryFromCube = typeof TrajectoryFromCube
+const TrajectoryFromCube = PluginStateTransform.BuiltIn({
+    name: 'trajectory-from-cube',
+    display: { name: 'Parse Cube', description: 'Parse Cube file to create a trajectory.' },
+    from: SO.Format.Cube,
+    to: SO.Molecule.Trajectory
+})({
+    apply({ a }) {
+        return Task.create('Parse MOL', async ctx => {
+            const models = await trajectoryFromCube(a.data).runInContext(ctx);
+            const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+            return new SO.Molecule.Trajectory(models, props);
+        });
+    }
+});
+
 type TrajectoryFromCifCore = typeof TrajectoryFromCifCore
 const TrajectoryFromCifCore = PluginStateTransform.BuiltIn({
     name: 'trajectory-from-cif-core',