0.7.0-dev.7

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

.npmignore

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

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.1",
+  "version": "0.7.0-dev.7",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -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/extensions/rcsb/assembly-symmetry/representation.ts

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

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

@@ -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/image/image.ts

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

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

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

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

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

src/mol-gl/renderable.ts

@@ -18,6 +18,7 @@ export type RenderableState = {
     alphaFactor: number
     pickable: boolean
     opaque: boolean
+    writeDepth: boolean,
 }
 
 export interface Renderable<T extends RenderableValues> {

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/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/image.frag.ts

@@ -35,20 +35,20 @@ varying float vInstance;
             const float C = 0.333;
         #endif
 
-        float cubicFilter( float x ){
+        float cubicFilter(float x){
             float f = x;
-            if( f < 0.0 ){
+            if (f < 0.0) {
                 f = -f;
             }
-            if( f < 1.0 ){
-                return ( ( 12.0 - 9.0 * B - 6.0 * C ) * ( f * f * f ) +
-                    ( -18.0 + 12.0 * B + 6.0 *C ) * ( f * f ) +
-                    ( 6.0 - 2.0 * B ) ) / 6.0;
-            }else if( f >= 1.0 && f < 2.0 ){
-                return ( ( -B - 6.0 * C ) * ( f * f * f )
-                    + ( 6.0 * B + 30.0 * C ) * ( f *f ) +
-                    ( - ( 12.0 * B ) - 48.0 * C  ) * f +
-                    8.0 * B + 24.0 * C ) / 6.0;
+            if (f < 1.0) {
+                return ((12.0 - 9.0 * B - 6.0 * C) * (f * f * f) +
+                    (-18.0 + 12.0 * B + 6.0 * C) * (f * f) +
+                    (6.0 - 2.0 * B)) / 6.0;
+            }else if (f >= 1.0 && f < 2.0){
+                return ((-B - 6.0 * C) * ( f * f * f)
+                    + (6.0 * B + 30.0 * C) * (f * f) +
+                    (-(12.0 * B) - 48.0 * C) * f +
+                    8.0 * B + 24.0 * C) / 6.0;
             }else{
                 return 0.0;
             }
@@ -92,6 +92,8 @@ void main() {
     #else
         vec4 imageData = texture2D(tImageTex, vUv);
     #endif
+    imageData.a = clamp(imageData.a, 0.0, 1.0);
+    if (imageData.a > 0.9) imageData.a = 1.0;
 
     #if defined(dRenderVariant_pick)
         if (imageData.a < 0.3)
@@ -110,7 +112,7 @@ void main() {
             gl_FragColor = vec4(0.0, 0.0, 0.0, 1.0); // set to empty picking id
         }
     #elif defined(dRenderVariant_depth)
-        if (imageData.a < 0.01)
+        if (imageData.a < 0.05)
             discard;
 
         #ifdef enabledFragDepth
@@ -119,7 +121,7 @@ void main() {
             gl_FragColor = packDepthToRGBA(gl_FragCoord.z);
         #endif
     #elif defined(dRenderVariant_color)
-        if (imageData.a < 0.01)
+        if (imageData.a < 0.05)
             discard;
 
         gl_FragColor = imageData;

src/mol-gl/webgl/texture.ts

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/mol-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/loci.ts

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

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

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

src/mol-model/structure/model/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/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

@@ -1,11 +1,11 @@
 /**
- * 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>
  */
 
-import { SpacegroupCell, Box3D, Sphere3D } from '../../mol-math/geometry';
+import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
 import { Tensor, Mat4, Vec3 } from '../../mol-math/linear-algebra';
 import { equalEps } from '../../mol-math/linear-algebra/3d/common';
 
@@ -28,7 +28,7 @@ interface VolumeData extends VolumeDataBase {
 
 namespace VolumeData {
     export const One: VolumeData = {
-        transform: { kind: 'matrix', matrix: Mat4() },
+        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 }
     };
@@ -52,12 +52,6 @@ namespace VolumeData {
     export function areEquivalent(volA: VolumeData, volB: VolumeData) {
         return volA === volB;
     }
-
-    export function getBoundingSphere(volume: VolumeData, boundingSphere?: Sphere3D) {
-        if (!boundingSphere) boundingSphere = Sphere3D();
-        // TODO
-        return boundingSphere;
-    }
 }
 
 type VolumeIsoValue = VolumeIsoValue.Absolute | VolumeIsoValue.Relative
@@ -91,8 +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

@@ -6,6 +6,9 @@
 
 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
@@ -16,12 +19,43 @@ export namespace Volume {
     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 {
@@ -30,5 +64,29 @@ export namespace Volume {
         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/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/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/volume.ts

@@ -68,9 +68,11 @@ export const DxProvider = DataFormatProvider({
     stringExtensions: ['dx'],
     binaryExtensions: ['dxbin'],
     parse: async (plugin, data) => {
-        const volume = plugin.build()
+        const format = plugin.build()
             .to(data)
-            .apply(StateTransforms.Volume.VolumeFromDx);
+            .apply(StateTransforms.Data.ParseDx, {}, { state: { isGhost: true } });
+
+        const volume = format.apply(StateTransforms.Volume.VolumeFromDx);
 
         await volume.commit({ revertOnError: true });
 
@@ -107,13 +109,13 @@ export const CubeProvider = DataFormatProvider({
             type: 'isosurface',
             typeParams: { isoValue: VolumeIsoValue.relative(1), alpha: 0.4 },
             color: 'uniform',
-            colorParams: { value: ColorNames.red }
+            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.blue }
+            colorParams: { value: ColorNames.red }
         }));
 
         const structure = await plugin.builders.structure.representation.applyPreset(data.structure, 'auto');

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/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>
@@ -22,6 +22,7 @@ import { StructureRepresentation, StructureRepresentationState } from '../mol-re
 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'
 
@@ -73,6 +74,7 @@ export namespace PluginStateObject {
         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 } |
@@ -85,6 +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

@@ -19,6 +19,7 @@ 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 };
@@ -31,6 +32,7 @@ export { ParsePsf };
 export { ParsePly };
 export { ParseCcp4 };
 export { ParseDsn6 };
+export { ParseDx };
 export { ImportString };
 export { ImportJson };
 export { ParseJson };
@@ -266,7 +268,7 @@ const ParseCube = PluginStateTransform.BuiltIn({
 })({
     apply({ a }) {
         return Task.create('Parse Cube', async ctx => {
-            const parsed = await parseCube(a.data).runInContext(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);
         });
@@ -314,7 +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);
         });
@@ -330,13 +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/volume.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>
@@ -14,7 +14,6 @@ import { Task } from '../../mol-task';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject as SO, PluginStateTransform } from '../objects';
 import { volumeFromCube } from '../../mol-model-formats/volume/cube';
-import { parseDx } from '../../mol-io/reader/dx/parser';
 import { volumeFromDx } from '../../mol-model-formats/volume/dx';
 import { VolumeData } from '../../mol-model/volume';
 import { PluginContext } from '../../mol-plugin/context';
@@ -42,7 +41,7 @@ const VolumeFromCcp4 = PluginStateTransform.BuiltIn({
 })({
     apply({ a, params }) {
         return Task.create('Create volume from CCP4/MRC/MAP', async ctx => {
-            const volume = await volumeFromCcp4(a.data, { ...params, label: a.label }).runInContext(ctx);
+            const volume = await volumeFromCcp4(a.data, { ...params, label: a.data.name || a.label }).runInContext(ctx);
             const props = { label: volume.label || 'Volume', description: 'Volume' };
             return new SO.Volume.Data(volume, props);
         });
@@ -63,7 +62,7 @@ const VolumeFromDsn6 = PluginStateTransform.BuiltIn({
 })({
     apply({ a, params }) {
         return Task.create('Create volume from DSN6/BRIX', async ctx => {
-            const volume = await volumeFromDsn6(a.data, { ...params, label: a.label }).runInContext(ctx);
+            const volume = await volumeFromDsn6(a.data, { ...params, label: a.data.name || a.label }).runInContext(ctx);
             const props = { label: volume.label || 'Volume', description: 'Volume' };
             return new SO.Volume.Data(volume, props);
         });
@@ -85,7 +84,7 @@ const VolumeFromCube = PluginStateTransform.BuiltIn({
 })({
     apply({ a, params }) {
         return Task.create('Create volume from Cube', async ctx => {
-            const volume = await volumeFromCube(a.data, { ...params, label: a.label }).runInContext(ctx);
+            const volume = await volumeFromCube(a.data, { ...params, label: a.data.name || a.label }).runInContext(ctx);
             const props = { label: volume.label || 'Volume', description: 'Volume' };
             return new SO.Volume.Data(volume, props);
         });
@@ -95,15 +94,15 @@ const VolumeFromCube = PluginStateTransform.BuiltIn({
 type VolumeFromDx = typeof VolumeFromDx
 const VolumeFromDx = PluginStateTransform.BuiltIn({
     name: 'volume-from-dx',
-    display: { name: 'Parse PX', description: 'Parse DX string/binary and create volume.' },
-    from: [SO.Data.String, SO.Data.Binary],
+    display: { name: 'Parse DX', description: 'Create volume from DX data.' },
+    from: SO.Format.Dx,
     to: SO.Volume.Data
 })({
     apply({ a }) {
         return Task.create('Parse DX', async ctx => {
-            const parsed = await parseDx(a.data).runInContext(ctx);
-            if (parsed.isError) throw new Error(parsed.message);
-            const volume = await volumeFromDx(parsed.result, { label: a.label }).runInContext(ctx);
+            console.log(a);
+            const volume = await volumeFromDx(a.data, { label: a.data.name || a.label }).runInContext(ctx);
+            console.log(volume);
             const props = { label: volume.label || 'Volume', description: 'Volume' };
             return new SO.Volume.Data(volume, props);
         });

src/mol-plugin-ui/controls/action-menu.tsx

@@ -20,7 +20,7 @@ export class ActionMenu extends React.PureComponent<ActionMenu.Props> {
         const cmd = this.props;
         const section = <Section items={cmd.items} onSelect={cmd.onSelect} current={cmd.current} multiselect={this.props.multiselect} noOffset={this.props.noOffset} noAccent={this.props.noAccent} />;
         return <div className={`msp-action-menu-options${cmd.header ? '' : ' msp-action-menu-options-no-header'}`}>
-            {cmd.header && <ControlGroup header={cmd.header} initialExpanded={true} hideExpander={true} hideOffset onHeaderClick={this.hide} topRightIcon={Close}>
+            {cmd.header && <ControlGroup header={cmd.header} title={cmd.title} initialExpanded={true} hideExpander={true} hideOffset onHeaderClick={this.hide} topRightIcon={Close}>
                 {section}
             </ControlGroup>}
             {!cmd.header && section}
@@ -33,6 +33,7 @@ export namespace ActionMenu {
         items: Items,
         onSelect: OnSelect | OnSelectMany,
         header?: string,
+        title?: string,
         current?: Item,
         multiselect?: boolean,
         noOffset?: boolean,

src/mol-plugin-ui/controls/common.tsx

@@ -16,6 +16,7 @@ export type ColorAccent = 'cyan' | 'red' | 'gray' | 'green' | 'purple' | 'blue'
 
 export class ControlGroup extends React.Component<{
     header: string,
+    title?: string,
     initialExpanded?: boolean,
     hideExpander?: boolean,
     hideOffset?: boolean,
@@ -41,7 +42,7 @@ export class ControlGroup extends React.Component<{
 
         // TODO: customize header style (bg color, togle button etc)
         return <div className='msp-control-group-wrapper' style={{ position: 'relative', marginTop: this.props.noTopMargin ? 0 : void 0 }}>
-            <div className='msp-control-group-header' style={{ marginLeft: this.props.headerLeftMargin }}>
+            <div className='msp-control-group-header' style={{ marginLeft: this.props.headerLeftMargin }} title={this.props.title}>
                 <Button onClick={this.headerClicked}>
                     {!this.props.hideExpander && <Icon svg={this.state.isExpanded ? ArrowRight : ArrowDropDown} />}
                     {this.props.topRightIcon && <Icon svg={this.props.topRightIcon} style={{ position: 'absolute', right: '2px', top: 0 }} />}

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

@@ -8,7 +8,7 @@ import { PluginUIComponent } from '../base';
 import { StateTransformParameters } from '../state/common';
 import * as React from 'react';
 import { VolumeStreaming } from '../../mol-plugin/behavior/dynamic/volume-streaming/behavior';
-import { ExpandableControlRow } from '../controls/common';
+import { ExpandableControlRow, IconButton } from '../controls/common';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ParameterControls, ParamOnChange } from '../controls/parameters';
 import { Slider } from '../controls/slider';
@@ -16,6 +16,10 @@ import { VolumeIsoValue, VolumeData } from '../../mol-model/volume';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { ColorNames } from '../../mol-util/color/names';
 import { toPrecision } from '../../mol-util/number';
+import VisibilityOffOutlined from '@material-ui/icons/VisibilityOffOutlined';
+import VisibilityOutlined from '@material-ui/icons/VisibilityOutlined';
+import { StateSelection, StateObjectCell } from '../../mol-state';
+import { setSubtreeVisibility } from '../../mol-plugin/behavior/static/state';
 
 const ChannelParams = {
     color: PD.Color(ColorNames.black, { description: 'Display color of the volume.' }),
@@ -24,36 +28,69 @@ const ChannelParams = {
 };
 type ChannelParams = PD.Values<typeof ChannelParams>
 
-function Channel(props: {
+class Channel extends PluginUIComponent<{
     label: string,
     name: VolumeStreaming.ChannelType,
     channels: { [k: string]: VolumeStreaming.ChannelParams },
     isRelative: boolean,
     params: StateTransformParameters.Props,
     stats: VolumeData['dataStats'],
-    changeIso: (name: string, value: number, isRelative: boolean) => void
-    changeParams: (name: string, param: string, value: any) => void
-}) {
-    const { isRelative, stats } = props;
-    const channel = props.channels[props.name]!;
+    changeIso: (name: string, value: number, isRelative: boolean) => void,
+    changeParams: (name: string, param: string, value: any) => void,
+    bCell: StateObjectCell,
+    isDisabled?: boolean
+}> {
+    private ref = StateSelection.findTagInSubtree(this.plugin.state.data.tree, this.props.bCell!.transform.ref, this.props.name);
 
-    const { min, max, mean, sigma } = stats;
-    const value = Math.round(100 * (channel.isoValue.kind === 'relative' ? channel.isoValue.relativeValue : channel.isoValue.absoluteValue)) / 100;
-    const relMin = (min - mean) / sigma;
-    const relMax = (max - mean) / sigma;
-    const step = toPrecision(isRelative ? Math.round(((max - min) / sigma)) / 100 : sigma / 100, 2);
+    componentDidUpdate() {
+        this.ref = StateSelection.findTagInSubtree(this.plugin.state.data.tree, this.props.bCell!.transform.ref, this.props.name);
+    }
 
-    return <ExpandableControlRow
-        label={props.label + (props.isRelative ? ' \u03C3' : '')}
-        colorStripe={channel.color}
-        pivot={<Slider value={value} min={isRelative ? relMin : min} max={isRelative ? relMax : max} step={step}
-            onChange={v => props.changeIso(props.name, v, isRelative)} disabled={props.params.isDisabled} onEnter={props.params.events.onEnter} />}
-        controls={<ParameterControls onChange={({ name, value }) => props.changeParams(props.name, name, value)} params={ChannelParams} values={channel} onEnter={props.params.events.onEnter} />}
-    />;
+    componentDidMount() {
+        this.subscribe(this.plugin.state.data.events.cell.stateUpdated, e => {
+            if (this.ref === e.ref) this.forceUpdate();
+        });
+    }
+
+    getVisible = () => {
+        const state = this.plugin.state.data;
+        const ref = this.ref;
+        if (!ref) return false;
+        return !state.cells.get(ref)!.state.isHidden;
+    };
+
+    toggleVisible = () => {
+        const state = this.plugin.state.data;
+        const ref = this.ref;
+        if (!ref) return;
+        setSubtreeVisibility(state, ref, !state.cells.get(ref)!.state.isHidden);
+    };
+
+    render() {
+        const props = this.props;
+        const { isRelative, stats } = props;
+        const channel = props.channels[props.name]!;
+
+        const { min, max, mean, sigma } = stats;
+        const value = Math.round(100 * (channel.isoValue.kind === 'relative' ? channel.isoValue.relativeValue : channel.isoValue.absoluteValue)) / 100;
+        const relMin = (min - mean) / sigma;
+        const relMax = (max - mean) / sigma;
+        const step = toPrecision(isRelative ? Math.round(((max - min) / sigma)) / 100 : sigma / 100, 2);
+
+        return <ExpandableControlRow
+            label={props.label + (props.isRelative ? ' \u03C3' : '')}
+            colorStripe={channel.color}
+            pivot={<div className='msp-volume-channel-inline-controls'>
+                <Slider value={value} min={isRelative ? relMin : min} max={isRelative ? relMax : max} step={step}
+                    onChange={v => props.changeIso(props.name, v, isRelative)} disabled={props.params.isDisabled} onEnter={props.params.events.onEnter} />
+                <IconButton svg={this.getVisible() ? VisibilityOutlined : VisibilityOffOutlined} onClick={this.toggleVisible} toggleState={false} disabled={props.params.isDisabled} />
+            </div>}
+            controls={<ParameterControls onChange={({ name, value }) => props.changeParams(props.name, name, value)} params={ChannelParams} values={channel} onEnter={props.params.events.onEnter} isDisabled={props.params.isDisabled} />}
+        />;
+    }
 }
 
 export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransformParameters.Props> {
-
     private areInitial(params: any) {
         return PD.areEqual(this.props.info.params, params, this.props.info.initialValues);
     }
@@ -170,8 +207,8 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
 
     render() {
         if (!this.props.b) return null;
-
         const b = (this.props.b as VolumeStreaming).data;
+
         const isEM = b.info.kind === 'em';
         const pivot = isEM ? 'em' : '2fo-fc';
 
@@ -225,16 +262,16 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
         };
 
         if (isOff) {
-            return <ParameterControls onChange={this.changeOption} params={OptionsParams} values={options} onEnter={this.props.events.onEnter} />;
+            return <ParameterControls onChange={this.changeOption} params={OptionsParams} values={options} onEnter={this.props.events.onEnter} isDisabled={this.props.isDisabled} />;
         }
 
         return <>
-            {!isEM && <Channel label='2Fo-Fc' name='2fo-fc' channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[0]} />}
-            {!isEM && <Channel label='Fo-Fc(+ve)' name='fo-fc(+ve)' channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[1]} />}
-            {!isEM && <Channel label='Fo-Fc(-ve)' name='fo-fc(-ve)' channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[1]} />}
-            {isEM && <Channel label='EM' name='em' channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[0]} />}
+            {!isEM && <Channel label='2Fo-Fc' name='2fo-fc' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[0]} />}
+            {!isEM && <Channel label='Fo-Fc(+ve)' name='fo-fc(+ve)' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[1]} />}
+            {!isEM && <Channel label='Fo-Fc(-ve)' name='fo-fc(-ve)' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[1]} />}
+            {isEM && <Channel label='EM' name='em' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[0]} />}
 
-            <ParameterControls onChange={this.changeOption} params={OptionsParams} values={options} onEnter={this.props.events.onEnter} />
+            <ParameterControls onChange={this.changeOption} params={OptionsParams} values={options} onEnter={this.props.events.onEnter} isDisabled={this.props.isDisabled} />
         </>;
     }
 }

src/mol-plugin-ui/skin/base/components/misc.scss

@@ -579,4 +579,35 @@
 @include accent('green', $color-accent-green);
 @include accent('purple', $color-accent-purple);
 @include accent('blue', $color-accent-blue);
-@include accent('orange', $color-accent-orange);
+@include accent('orange', $color-accent-orange);
+
+.msp-volume-channel-inline-controls {
+    > :first-child {
+        position: absolute;
+        left: 0;
+        top: 0;
+        height: $row-height;
+        right: 32px;
+    }
+
+    .msp-slider {
+        > div:first-child() {
+            right: 42px;
+        }
+        > div:last-child() {
+            width: 30px;
+        }
+    }
+
+    > button {
+        position: absolute;
+        right: 0;
+        width: 32px;
+        top: 0;
+        padding: 0;
+
+        .msp-material-icon {
+            margin-right: 0;
+        }
+    }
+}

src/mol-plugin-ui/state/common.tsx

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { State, StateTransform, StateTransformer, StateAction, StateObject } from '../../mol-state';
+import { State, StateTransform, StateTransformer, StateAction, StateObject, StateObjectCell } from '../../mol-state';
 import * as React from 'react';
 import { PurePluginUIComponent } from '../base';
 import { ParameterControls, ParamOnChange } from '../controls/parameters';
@@ -56,7 +56,8 @@ namespace StateTransformParameters {
         params: any,
         isDisabled?: boolean,
         a?: StateObject,
-        b?: StateObject
+        b?: StateObject,
+        bCell?: StateObjectCell
     }
 
     export type Class = React.ComponentClass<Props>
@@ -125,7 +126,7 @@ abstract class TransformControlBase<P, S extends TransformControlBase.ComponentS
     abstract canAutoApply(newParams: any): boolean;
     abstract applyText(): string;
     abstract isUpdate(): boolean;
-    abstract getSourceAndTarget(): { a?: StateObject, b?: StateObject };
+    abstract getSourceAndTarget(): { a?: StateObject, b?: StateObject, bCell?: StateObjectCell };
     abstract state: S;
 
     private busy: Subject<boolean> = new Subject();
@@ -224,10 +225,10 @@ abstract class TransformControlBase<P, S extends TransformControlBase.ComponentS
 
         let params = null;
         if (!isEmpty && !this.state.isCollapsed) {
-            const { a, b } = this.getSourceAndTarget();
+            const { a, b, bCell } = this.getSourceAndTarget();
             const applyControl = this.renderApply();
             params = <>
-                <ParamEditor info={info} a={a} b={b} events={this.events} params={this.state.params} isDisabled={this.state.busy} />
+                <ParamEditor info={info} a={a} b={b} bCell={bCell} events={this.events} params={this.state.params} isDisabled={this.state.busy} />
                 {applyControl}
             </>;
         }
@@ -266,11 +267,11 @@ abstract class TransformControlBase<P, S extends TransformControlBase.ComponentS
         const ParamEditor: StateTransformParameters.Class = this.plugin.customParamEditors.has(tId)
             ? this.plugin.customParamEditors.get(tId)!
             : StateTransformParameters;
-        const { a, b } = this.getSourceAndTarget();
+        const { a, b, bCell } = this.getSourceAndTarget();
 
         return <>
             {apply}
-            <ParamEditor info={info} a={a} b={b} events={this.events} params={this.state.params} isDisabled={this.state.busy} />
+            <ParamEditor info={info} a={a} b={b} bCell={bCell} events={this.events} params={this.state.params} isDisabled={this.state.busy} />
         </>;
     }
 

src/mol-plugin-ui/state/snapshots.tsx

@@ -175,7 +175,6 @@ class LocalStateSnapshotList extends PluginUIComponent<{}, {}> {
         return <ul style={{ listStyle: 'none', marginTop: '10px' }} className='msp-state-list'>
             {this.plugin.managers.snapshot.state.entries.map(e => <li key={e!.snapshot.id} className='msp-flex-row'>
                 <Button data-id={e!.snapshot.id} onClick={this.apply} className='msp-no-overflow'>
-                    {(console.log(e!.snapshot.durationInMs), false)}
                     <span style={{ fontWeight: e!.snapshot.id === current ? 'bold' : void 0 }}>
                         {e!.name || new Date(e!.timestamp).toLocaleString()}</span> <small>
                         {`${e!.snapshot.durationInMs ? formatTimespan(e!.snapshot.durationInMs, false) + `${e!.description ? ', ' : ''}` : ''}${e!.description ? e!.description : ''}`}

src/mol-plugin-ui/state/update-transform.tsx

@@ -49,9 +49,11 @@ class UpdateTransformControl extends TransformControlBase<UpdateTransformControl
     applyText() { return this.canApply() ? 'Update' : 'Nothing to Update'; }
     isUpdate() { return true; }
     getSourceAndTarget() {
+        const bCell = this.props.state.cells.get(this.props.transform.ref);
         return {
             a: this.props.state.cells.get(this.props.transform.parent)!.obj,
-            b: this.props.state.cells.has(this.props.transform.ref)! ? this.props.state.cells.get(this.props.transform.ref)!.obj : void 0
+            b: bCell?.obj,
+            bCell
         };
     }
 

src/mol-plugin-ui/structure/measurements.tsx

@@ -198,7 +198,6 @@ class MeasurementsOptions extends PurePluginUIComponent<{}, { isDisabled: boolea
         });
 
         this.subscribe(this.plugin.behaviors.state.isBusy, v => {
-            console.log('isBusy', 'measurement opt', v);
             this.setState({ isDisabled: v });
         });
     }

src/mol-plugin-ui/structure/selection.tsx

@@ -11,7 +11,7 @@ import Brush from '@material-ui/icons/Brush';
 import Restore from '@material-ui/icons/Restore';
 import Remove from '@material-ui/icons/Remove';
 import * as React from 'react';
-import { StructureSelectionQueries, StructureSelectionQuery } from '../../mol-plugin-state/helpers/structure-selection-query';
+import { StructureSelectionQueries, StructureSelectionQuery, getNonStandardResidueQueries, getElementQueries, getPolymerAndBranchedEntityQueries } from '../../mol-plugin-state/helpers/structure-selection-query';
 import { InteractivityManager } from '../../mol-plugin-state/manager/interactivity';
 import { StructureComponentManager } from '../../mol-plugin-state/manager/structure/component';
 import { StructureRef, StructureComponentRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
@@ -25,6 +25,7 @@ import { Button, ControlGroup, IconButton, ToggleButton } from '../controls/comm
 import { ParameterControls, ParamOnChange, PureSelectControl } from '../controls/parameters';
 import { Union, Subtract, Intersect, SetSvg as SetSvg, CubeSvg } from '../controls/icons';
 import { AddComponentControls } from './components';
+import Structure from '../../mol-model/structure/structure/structure';
 
 const StructureSelectionParams = {
     granularity: InteractivityManager.Params.granularity,
@@ -60,6 +61,9 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
             if (this.state.isEmpty !== isEmpty) {
                 this.setState({ isEmpty });
             }
+            // trigger elementQueries and nonStandardResidueQueries recalculation
+            this.queriesVersion = -1;
+            this.forceUpdate();
         });
 
         this.subscribe(this.plugin.behaviors.state.isBusy, v => {
@@ -83,15 +87,28 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
         this.plugin.managers.structure.selection.fromSelectionQuery(modifier, selectionQuery, false);
     }
 
-    selectQuery: ActionMenu.OnSelect = item => {
+    selectQuery: ActionMenu.OnSelect = (item, e) => {
         if (!item || !this.state.action) {
             this.setState({ action: void 0 });
             return;
         }
         const q = this.state.action! as StructureSelectionModifier;
-        this.setState({ action: void 0 }, () => {
+        if (e?.shiftKey) {
             this.set(q, item.value as StructureSelectionQuery);
-        });
+        } else {
+            this.setState({ action: void 0 }, () => {
+                this.set(q, item.value as StructureSelectionQuery);
+            });
+        }
+    }
+
+    get structures () {
+        const structures: Structure[] = [];
+        for (const s of this.plugin.managers.structure.hierarchy.selection.structures) {
+            const structure = s.cell.obj?.data;
+            if (structure) structures.push(structure);
+        }
+        return structures;
     }
 
     private queriesItems: ActionMenu.Items[] = []
@@ -99,8 +116,15 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
     get queries () {
         const { registry } = this.plugin.query.structure;
         if (registry.version !== this.queriesVersion) {
-            this.queriesItems = ActionMenu.createItems(registry.list, {
-                filter: q => q !== StructureSelectionQueries.current,
+            const structures = this.structures;
+            const queries = [
+                ...registry.list,
+                ...getPolymerAndBranchedEntityQueries(structures),
+                ...getNonStandardResidueQueries(structures),
+                ...getElementQueries(structures)
+            ].sort((a, b) => b.priority - a.priority);
+            this.queriesItems = ActionMenu.createItems(queries, {
+                filter: q => q !== StructureSelectionQueries.current && !q.isHidden,
                 label: q => q.label,
                 category: q => q.category,
                 description: q => q.description
@@ -148,29 +172,29 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
 
         return <>
             <div className='msp-flex-row' style={{ background: 'none' }}>
-                <PureSelectControl title={`Picking Level`} param={StructureSelectionParams.granularity} name='granularity' value={granularity} onChange={this.setGranuality} isDisabled={this.isDisabled} />
+                <PureSelectControl title={`Picking Level for selecting and highlighting`} param={StructureSelectionParams.granularity} name='granularity' value={granularity} onChange={this.setGranuality} isDisabled={this.isDisabled} />
                 <ToggleButton icon={Union} title={ActionHeader.get('add')} toggle={this.toggleAdd} isSelected={this.state.action === 'add'} disabled={this.isDisabled} />
                 <ToggleButton icon={Subtract} title={ActionHeader.get('remove')} toggle={this.toggleRemove} isSelected={this.state.action === 'remove'} disabled={this.isDisabled} />
                 <ToggleButton icon={Intersect} title={ActionHeader.get('intersect')} toggle={this.toggleIntersect} isSelected={this.state.action === 'intersect'} disabled={this.isDisabled} />
                 <ToggleButton icon={SetSvg} title={ActionHeader.get('set')} toggle={this.toggleSet} isSelected={this.state.action === 'set'} disabled={this.isDisabled} />
 
-                <ToggleButton icon={Brush} title='Color' toggle={this.toggleColor} isSelected={this.state.action === 'color'} disabled={this.isDisabled} style={{ marginLeft: '10px' }}  />
-                <ToggleButton icon={CubeSvg} title='Create Representation' toggle={this.toggleAddRepr} isSelected={this.state.action === 'add-repr'} disabled={this.isDisabled} />
-                <IconButton svg={Remove} title='Subtract from Representations' onClick={this.subtract} disabled={this.isDisabled} />
+                <ToggleButton icon={Brush} title='Color Selection' toggle={this.toggleColor} isSelected={this.state.action === 'color'} disabled={this.isDisabled} style={{ marginLeft: '10px' }}  />
+                <ToggleButton icon={CubeSvg} title='Create Representation of Selection' toggle={this.toggleAddRepr} isSelected={this.state.action === 'add-repr'} disabled={this.isDisabled} />
+                <IconButton svg={Remove} title='Subtract Selection from Representations' onClick={this.subtract} disabled={this.isDisabled} />
                 <IconButton svg={Restore} onClick={this.undo} disabled={!this.state.canUndo || this.isDisabled} title={undoTitle} />
 
                 <IconButton svg={CancelOutlined} title='Turn selection mode off' onClick={this.turnOff} style={{ marginLeft: '10px' }} />
             </div>
             {(this.state.action && this.state.action !== 'color' && this.state.action !== 'add-repr') && <div className='msp-selection-viewport-controls-actions'>
-                <ActionMenu header={ActionHeader.get(this.state.action as StructureSelectionModifier)} items={this.queries} onSelect={this.selectQuery} noOffset />
+                <ActionMenu header={ActionHeader.get(this.state.action as StructureSelectionModifier)} title='Click to close.' items={this.queries} onSelect={this.selectQuery} noOffset />
             </div>}
             {this.state.action === 'color' && <div className='msp-selection-viewport-controls-actions'>
-                <ControlGroup header='Color' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleColor} topRightIcon={Close}>
+                <ControlGroup header='Color' title='Click to close.' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleColor} topRightIcon={Close}>
                     <ApplyColorControls onApply={this.toggleColor} />
                 </ControlGroup>
             </div>}
             {this.state.action === 'add-repr' && <div className='msp-selection-viewport-controls-actions'>
-                <ControlGroup header='Add Representation' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleAddRepr} topRightIcon={Close}>
+                <ControlGroup header='Add Representation' title='Click to close.' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleAddRepr} topRightIcon={Close}>
                     <AddComponentControls onApply={this.toggleAddRepr} forSelection />
                 </ControlGroup>
             </div>}

src/mol-plugin-ui/viewport.tsx

@@ -104,8 +104,8 @@ export class ViewportControls extends PluginUIComponent<ViewportControlsProps, V
                 </div>
                 <div>
                     <div className='msp-semi-transparent-background' />
-                    {this.icon(BuildOutlined, this.toggleControls, 'Toggle Controls', this.plugin.layout.state.showControls)}
-                    {this.plugin.config.get(PluginConfig.Viewport.ShowExpand) && this.icon(Fullscreen, this.toggleExpanded, 'Toggle Expanded', this.plugin.layout.state.isExpanded)}
+                    {this.icon(BuildOutlined, this.toggleControls, 'Toggle Controls Panel', this.plugin.layout.state.showControls)}
+                    {this.plugin.config.get(PluginConfig.Viewport.ShowExpand) && this.icon(Fullscreen, this.toggleExpanded, 'Toggle Expanded Viewport', this.plugin.layout.state.isExpanded)}
                     {this.icon(Tune, this.toggleSettingsExpanded, 'Settings / Controls Info', this.state.isSettingsExpanded)}
                 </div>
                 {this.plugin.config.get(PluginConfig.Viewport.ShowSelectionMode) && <div>
@@ -114,13 +114,13 @@ export class ViewportControls extends PluginUIComponent<ViewportControlsProps, V
                 </div>}
             </div>
             {this.state.isScreenshotExpanded && <div className='msp-viewport-controls-panel'>
-                <ControlGroup header='Screenshot / State' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleScreenshotExpanded}
+                <ControlGroup header='Screenshot / State' title='Click to close.' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleScreenshotExpanded}
                     topRightIcon={Close} noTopMargin childrenClassName='msp-viewport-controls-panel-controls'>
                     <DownloadScreenshotControls close={this.toggleScreenshotExpanded} />
                 </ControlGroup>
             </div>}
             {this.state.isSettingsExpanded && <div className='msp-viewport-controls-panel'>
-                <ControlGroup header='Settings / Controls Info' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleSettingsExpanded}
+                <ControlGroup header='Settings / Controls Info' title='Click to close.' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleSettingsExpanded}
                     topRightIcon={Close} noTopMargin childrenClassName='msp-viewport-controls-panel-controls'>
                     <SimpleSettingsControl />
                 </ControlGroup>

src/mol-plugin/behavior/dynamic/camera.ts

@@ -11,6 +11,7 @@ import { PluginBehavior } from '../behavior';
 import { ButtonsType, ModifiersKeys } from '../../../mol-util/input/input-observer';
 import { Binding } from '../../../mol-util/binding';
 import { PluginCommands } from '../../commands';
+import { Structure, StructureElement, Bond } from '../../../mol-model/structure';
 
 const B = ButtonsType;
 const M = ModifiersKeys;
@@ -53,9 +54,13 @@ export const FocusLoci = PluginBehavior.create<FocusLociProps>({
                     }
 
                     // The focus is handled in structure-focus-representation
-                    // TODO: is there a better solution?
-                    // const loci = Loci.normalize(current.loci, this.ctx.managers.interactivity.props.granularity);
-                    // this.ctx.managers.camera.focusLoci(loci, this.params);
+                    // TODO: is there a better solution for structure-based loci?
+
+                    const loci = Loci.normalize(current.loci, this.ctx.managers.interactivity.props.granularity);
+
+                    if (!Structure.isLoci(loci) && !StructureElement.Loci.is(loci) && !Bond.isLoci(loci)) {
+                        this.ctx.managers.camera.focusLoci(loci, this.params);
+                    }
                 }
             });
         }

src/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.ts

@@ -51,8 +51,7 @@ export const AccessibleSurfaceArea = PluginBehavior.create<{ autoAttach: boolean
         }
 
         unregister() {
-            // TODO
-            // DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
+            DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
 
             this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
             this.ctx.representation.structure.themes.colorThemeRegistry.remove(AccessibleSurfaceAreaColorThemeProvider);

src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts

@@ -115,11 +115,11 @@ export const InitVolumeStreaming = StateAction.build({
         { ref: params.options.behaviorRef ? params.options.behaviorRef : void 0 });
 
     if (params.method === 'em') {
-        behTree.apply(VolumeStreamingVisual, { channel: 'em' }, { state: { isGhost: true } });
+        behTree.apply(VolumeStreamingVisual, { channel: 'em' }, { state: { isGhost: true }, tags: 'em' });
     } else {
-        behTree.apply(VolumeStreamingVisual, { channel: '2fo-fc' }, { state: { isGhost: true } });
-        behTree.apply(VolumeStreamingVisual, { channel: 'fo-fc(+ve)' }, { state: { isGhost: true } });
-        behTree.apply(VolumeStreamingVisual, { channel: 'fo-fc(-ve)' }, { state: { isGhost: true } });
+        behTree.apply(VolumeStreamingVisual, { channel: '2fo-fc' }, { state: { isGhost: true }, tags: '2fo-fc' });
+        behTree.apply(VolumeStreamingVisual, { channel: 'fo-fc(+ve)' }, { state: { isGhost: true }, tags: 'fo-fc(+ve)' });
+        behTree.apply(VolumeStreamingVisual, { channel: 'fo-fc(-ve)' }, { state: { isGhost: true }, tags: 'fo-fc(-ve)' });
     }
     await state.updateTree(behTree).runInContext(taskCtx);
 }));

src/mol-plugin/version.ts

@@ -5,11 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-/** version from package.json, to be filled in at bundle build time */
-declare const __VERSION__: string;
-export const PLUGIN_VERSION = __VERSION__;
+/** version from package.json, to be filled in at build time */
+export const PLUGIN_VERSION = '';
 
-/** unix time stamp, to be filled in at bundle build time */
-declare const __VERSION_TIMESTAMP__: number;
-export const PLUGIN_VERSION_TIMESTAMP = __VERSION_TIMESTAMP__;
-export const PLUGIN_VERSION_DATE = new Date(PLUGIN_VERSION_TIMESTAMP);
+/** to be filled in at build time */
+export const PLUGIN_VERSION_DATE = +new Date();

src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts

@@ -26,6 +26,7 @@ import { EmptyLoci, Loci } from '../../../mol-model/loci';
 import { VisualContext } from '../../../mol-repr/visual';
 import { Theme } from '../../../mol-theme/theme';
 import { getAltResidueLociFromId } from './util/common';
+import { BaseGeometry } from '../../../mol-geo/geometry/base';
 
 const t = Mat4.identity();
 const sVec = Vec3.zero();
@@ -162,7 +163,7 @@ function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure,
 
 export const CarbohydrateSymbolParams = {
     ...ComplexMeshParams,
-    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
     sizeFactor: PD.Numeric(1.75, { min: 0, max: 10, step: 0.01 }),
 };
 export type CarbohydrateSymbolParams = typeof CarbohydrateSymbolParams

src/mol-repr/structure/visual/element-sphere.ts

@@ -10,12 +10,13 @@ import { UnitsMeshParams, UnitsSpheresParams, UnitsVisual, UnitsSpheresVisual, U
 import { WebGLContext } from '../../../mol-gl/webgl/context';
 import { createElementSphereImpostor, ElementIterator, getElementLoci, eachElement, createElementSphereMesh } from './util/element';
 import { VisualUpdateState } from '../../util';
+import { BaseGeometry } from '../../../mol-geo/geometry/base';
 
 export const ElementSphereParams = {
     ...UnitsMeshParams,
     ...UnitsSpheresParams,
     sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }),
-    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
     ignoreHydrogens: PD.Boolean(false),
     traceOnly: PD.Boolean(false),
 };

src/mol-repr/structure/visual/ellipsoid-mesh.ts

@@ -21,11 +21,12 @@ import { AtomSiteAnisotrop } from '../../../mol-model-formats/structure/property
 import { equalEps } from '../../../mol-math/linear-algebra/3d/common';
 import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
 import { Sphere3D } from '../../../mol-math/geometry';
+import { BaseGeometry } from '../../../mol-geo/geometry/base';
 
 export const EllipsoidMeshParams = {
     ...UnitsMeshParams,
     sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }),
-    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
     ignoreHydrogens: PD.Boolean(false),
 };
 export type EllipsoidMeshParams = typeof EllipsoidMeshParams

src/mol-repr/structure/visual/orientation-ellipsoid-mesh.ts

@@ -21,11 +21,12 @@ import { EmptyLoci, Loci } from '../../../mol-model/loci';
 import { UnitIndex } from '../../../mol-model/structure/structure/element/element';
 import { LocationIterator } from '../../../mol-geo/util/location-iterator';
 import { MoleculeType } from '../../../mol-model/structure/model/types';
+import { BaseGeometry } from '../../../mol-geo/geometry/base';
 
 export const OrientationEllipsoidMeshParams = {
     ...UnitsMeshParams,
     sizeFactor: PD.Numeric(1, { min: 0, max: 2, step: 0.1 }),
-    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
 };
 export type OrientationEllipsoidMeshParams = typeof OrientationEllipsoidMeshParams
 
@@ -80,7 +81,7 @@ export function createOrientationEllipsoidMesh(ctx: VisualContext, unit: Unit, s
     const radiusScale = Vec3.create(size[2], size[1], size[0]);
 
     builderState.currentGroup = 0;
-    addEllipsoid(builderState, origin, dirA, dirB, radiusScale, detail);
+    addEllipsoid(builderState, origin, dirA, dirB, radiusScale, detail + 1);
 
     const m = MeshBuilder.getMesh(builderState);
 

src/mol-repr/util.ts

@@ -51,6 +51,7 @@ export interface QualityProps {
     linearSegments: number
     resolution: number
     doubleSided: boolean
+    alpha: number
 }
 
 export const DefaultQualityThresholds = {
@@ -151,6 +152,10 @@ export function getQualityProps(props: Partial<QualityProps>, data?: any) {
             break;
     }
 
+    if (props.alpha !== undefined && props.alpha < 1) {
+        doubleSided = false;
+    }
+
     return {
         detail,
         radialSegments,

src/mol-repr/volume/isosurface.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>
@@ -122,12 +122,12 @@ export async function createVolumeIsosurfaceMesh(ctx: VisualContext, volume: Vol
     const transform = VolumeData.getGridToCartesianTransform(volume);
     ctx.runtime.update({ message: 'Transforming mesh...' });
     Mesh.transform(surface, transform);
-    console.log(surface, Tensor.create(volume.data.space, Tensor.Data1(ids)));
     return surface;
 }
 
 export const IsosurfaceMeshParams = {
     ...Mesh.Params,
+    quality: { ...Mesh.Params.quality, isEssential: false },
     ...VolumeIsosurfaceParams
 };
 export type IsosurfaceMeshParams = typeof IsosurfaceMeshParams
@@ -167,6 +167,7 @@ export async function createVolumeIsosurfaceWireframe(ctx: VisualContext, volume
 
 export const IsosurfaceWireframeParams = {
     ...Lines.Params,
+    quality: { ...Lines.Params.quality, isEssential: false },
     sizeFactor: PD.Numeric(1.5, { min: 0, max: 10, step: 0.1 }),
     ...VolumeIsosurfaceParams
 };

src/mol-repr/volume/slice.ts

@@ -6,9 +6,8 @@
 
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Image } from '../../mol-geo/geometry/image/image';
-import { BaseGeometry } from '../../mol-geo/geometry/base';
 import { ThemeRegistryContext, Theme } from '../../mol-theme/theme';
-import { VolumeData } from '../../mol-model/volume';
+import { VolumeData, VolumeIsoValue } from '../../mol-model/volume';
 import { VolumeVisual, VolumeRepresentation, VolumeRepresentationProvider } from './representation';
 import { LocationIterator } from '../../mol-geo/util/location-iterator';
 import { VisualUpdateState } from '../util';
@@ -18,57 +17,118 @@ import { VisualContext } from '../visual';
 import { Volume } from '../../mol-model/volume/volume';
 import { PickingId } from '../../mol-geo/geometry/picking';
 import { EmptyLoci, Loci } from '../../mol-model/loci';
-import { Interval, OrderedSet } from '../../mol-data/int';
-import { fillSerial } from '../../mol-util/array';
+import { Interval, OrderedSet, SortedArray } from '../../mol-data/int';
+import { transformPositionArray } from '../../mol-geo/util';
+import { equalEps } from '../../mol-math/linear-algebra/3d/common';
+import { RenderableState } from '../../mol-gl/renderable';
+import { createIsoValueParam, IsoValueParam } from './isosurface';
+import { Color } from '../../mol-util/color';
+import { ColorTheme } from '../../mol-theme/color';
 
 export async function createImage(ctx: VisualContext, volume: VolumeData, theme: Theme, props: PD.Values<SliceParams>, image?: Image) {
-    const dim = parseInt(props.dimension.name.toString());
-    // const index = props.dimension.params;
+    const { dimension: { name: dim }, isoValue } = props;
 
-    const { space } = volume.data;
+    const { space, data: data } = volume.data;
+    const { min, max } = volume.dataStats;
+    const isoVal = VolumeIsoValue.toAbsolute(isoValue, volume.dataStats).absoluteValue;
 
-    let width: number, height: number;
-    if (dim === 0) {
-        width = space.dimensions[1];
-        height = space.dimensions[2];
-    } else if (dim === 1) {
-        width = space.dimensions[0];
-        height = space.dimensions[2];
-    } else {
-        width = space.dimensions[0];
-        height = space.dimensions[1];
+    // TODO more color themes
+    const color = theme.color.color(NullLocation, false);
+    const [r, g, b] = Color.toRgbNormalized(color);
+
+    const {
+        width, height,
+        x, y, z,
+        x0, y0, z0,
+        nx, ny, nz
+    } = getSliceInfo(volume, props);
+
+    const corners = new Float32Array(
+        dim === 'x' ? [x, 0, 0,  x, y, 0,  x, 0, z,  x, y, z] :
+            dim === 'y' ? [0, y, 0,  x, y, 0,  0, y, z,  x, y, z] :
+                [0, 0, z,  0, y, z,  x, 0, z,  x, y, z]
+    );
+
+    const imageArray = new Float32Array(width * height * 4);
+    const groupArray = getGroupArray(volume, props);
+
+    let i = 0;
+    for (let iy = y0; iy < ny; ++iy) {
+        for (let ix = x0; ix < nx; ++ix) {
+            for (let iz = z0; iz < nz; ++iz) {
+                const val = space.get(data, ix, iy, iz);
+                const normVal = (val - min) / (max - min);
+
+                imageArray[i] = r * normVal * 2;
+                imageArray[i + 1] = g * normVal * 2;
+                imageArray[i + 2] = b * normVal * 2;
+                imageArray[i + 3] = val >= isoVal ? 1 : 0;
+
+                i += 4;
+            }
+        }
     }
 
-    const n = width * height;
+    const imageTexture = { width, height, array: imageArray, flipY: true };
+    const groupTexture = { width, height, array: groupArray, flipY: true };
 
-    // TODO fill with volume data values
-    const imageTexture = { width, height, array: new Float32Array(n * 4) };
-
-    for (let i = 0, il = n * 4; i < il; i += 4) {
-        imageTexture.array[i] = 0;
-        imageTexture.array[i + 1] = Math.random();
-        imageTexture.array[i + 2] = Math.random();
-        imageTexture.array[i + 3] = 1;
-    }
-
-    // TODO fill with linearized index into volume
-    //      (to be used for picking which needs a volume location/loci)
-    const groupTexture = { width, height, array: fillSerial(new Float32Array(n)) };
-
-    // TODO four corners of a plane
-    const corners = new Float32Array([
-        0, 0, 0,
-        0, 50, 0,
-        0, 0, 50,
-        0, 50, 50
-    ]);
+    const transform = VolumeData.getGridToCartesianTransform(volume);
+    transformPositionArray(transform, corners, 0, 4);
 
     return Image.create(imageTexture, corners, groupTexture, image);
 }
 
+function getSliceInfo(volume: VolumeData, props: PD.Values<SliceParams>) {
+    const { dimension: { name: dim, params: index } } = props;
+    const { space } = volume.data;
+
+    let width, height;
+    let x, y, z;
+    let x0 = 0, y0 = 0, z0 = 0;
+    let [nx, ny, nz] = space.dimensions;
+
+    if (dim === 'x') {
+        x = index, y = ny - 1, z = nz - 1;
+        width = nz, height = ny;
+        x0 = x, nx = x0 + 1;
+    } else if (dim === 'y') {
+        x = nx - 1, y = index, z = nz - 1;
+        width = nz, height = nx;
+        y0 = y, ny = y0 + 1;
+    } else {
+        x = nx - 1, y = ny - 1, z = index;
+        width = nx, height = ny;
+        z0 = z, nz = z0 + 1;
+    }
+    return {
+        width, height,
+        x, y, z,
+        x0, y0, z0,
+        nx, ny, nz
+    };
+}
+
+function getGroupArray(volume: VolumeData, props: PD.Values<SliceParams>) {
+    const { space } = volume.data;
+    const { width, height, x0, y0, z0, nx, ny, nz } = getSliceInfo(volume, props);
+    const groupArray = new Float32Array(width * height);
+
+    let j = 0;
+    for (let iy = y0; iy < ny; ++iy) {
+        for (let ix = x0; ix < nx; ++ix) {
+            for (let iz = z0; iz < nz; ++iz) {
+                groupArray[j] = space.dataOffset(ix, iy, iz);
+                j += 1;
+            }
+        }
+    }
+    return groupArray;
+}
+
 function getLoci(volume: VolumeData, props: PD.Values<SliceParams>) {
-    // TODO only slice indices
-    return Volume.Loci(volume);
+    // TODO cache somehow?
+    const groupArray = getGroupArray(volume, props);
+    return Volume.Cell.Loci(volume, SortedArray.ofUnsortedArray(groupArray));
 }
 
 function getSliceLoci(pickingId: PickingId, volume: VolumeData, props: PD.Values<SliceParams>, id: number) {
@@ -86,8 +146,15 @@ function eachSlice(loci: Loci, volume: VolumeData, props: PD.Values<SliceParams>
         if (apply(Interval.ofLength(volume.data.data.length))) changed = true;
     } else if (Volume.Isosurface.isLoci(loci)) {
         if (!VolumeData.areEquivalent(loci.volume, volume)) return false;
-        // TODO check isoValue
-        if (apply(Interval.ofLength(volume.data.data.length))) changed = true;
+        // TODO find a cheaper way?
+        const { dataStats, data: { data } } = volume;
+        const eps = dataStats.sigma;
+        const v = VolumeIsoValue.toAbsolute(loci.isoValue, dataStats).absoluteValue;
+        for (let i = 0, il = data.length; i < il; ++i) {
+            if (equalEps(v, data[i], eps)) {
+                if (apply(Interval.ofSingleton(i))) changed = true;
+            }
+        }
     } else if (Volume.Cell.isLoci(loci)) {
         if (!VolumeData.areEquivalent(loci.volume, volume)) return false;
         if (Interval.is(loci.indices)) {
@@ -104,22 +171,25 @@ function eachSlice(loci: Loci, volume: VolumeData, props: PD.Values<SliceParams>
 //
 
 export const SliceParams = {
-    ...BaseGeometry.Params,
     ...Image.Params,
-    dimension: PD.MappedStatic(0, {
-        0: PD.Numeric(0, { min: 0, max: 0, step: 1 }),
-        1: PD.Numeric(0, { min: 0, max: 0, step: 1 }),
-        2: PD.Numeric(0, { min: 0, max: 0, step: 1 }),
+    quality: { ...Image.Params.quality, isEssential: false },
+    dimension: PD.MappedStatic('x', {
+        x: PD.Numeric(0, { min: 0, max: 0, step: 1 }),
+        y: PD.Numeric(0, { min: 0, max: 0, step: 1 }),
+        z: PD.Numeric(0, { min: 0, max: 0, step: 1 }),
     }, { isEssential: true }),
+    isoValue: IsoValueParam,
 };
 export type SliceParams = typeof SliceParams
 export function getSliceParams(ctx: ThemeRegistryContext, volume: VolumeData) {
     const p = PD.clone(SliceParams);
-    p.dimension = PD.MappedStatic(0, {
-        0: PD.Numeric(0, { min: 0, max: volume.data.space.dimensions[0], step: 1 }),
-        1: PD.Numeric(0, { min: 0, max: volume.data.space.dimensions[1], step: 1 }),
-        2: PD.Numeric(0, { min: 0, max: volume.data.space.dimensions[2], step: 1 }),
+    const dim = volume.data.space.dimensions;
+    p.dimension = PD.MappedStatic('x', {
+        x: PD.Numeric(0, { min: 0, max: dim[0] - 1, step: 1 }),
+        y: PD.Numeric(0, { min: 0, max: dim[1] - 1, step: 1 }),
+        z: PD.Numeric(0, { min: 0, max: dim[2] - 1, step: 1 }),
     }, { isEssential: true });
+    p.isoValue = createIsoValueParam(VolumeIsoValue.absolute(volume.dataStats.min), volume.dataStats);
     return p;
 }
 
@@ -130,16 +200,32 @@ export function SliceVisual(materialId: number): VolumeVisual<SliceParams> {
         createLocationIterator: (volume: VolumeData) => LocationIterator(volume.data.data.length, 1, () => NullLocation),
         getLoci: getSliceLoci,
         eachLocation: eachSlice,
-        setUpdateState: (state: VisualUpdateState, volume: VolumeData, newProps: PD.Values<SliceParams>, currentProps: PD.Values<SliceParams>) => {
+        setUpdateState: (state: VisualUpdateState, volume: VolumeData, newProps: PD.Values<SliceParams>, currentProps: PD.Values<SliceParams>, newTheme: Theme, currentTheme: Theme) => {
             state.createGeometry = (
                 newProps.dimension.name !== currentProps.dimension.name ||
-                newProps.dimension.params !== currentProps.dimension.params
+                newProps.dimension.params !== currentProps.dimension.params ||
+                !VolumeIsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.dataStats) ||
+                !ColorTheme.areEqual(newTheme.color, currentTheme.color)
             );
         },
-        geometryUtils: Image.Utils
+        geometryUtils: {
+            ...Image.Utils,
+            createRenderableState: (props: PD.Values<SliceParams>) => {
+                const state = Image.Utils.createRenderableState(props);
+                updateRenderableState(state, props);
+                return state;
+            },
+            updateRenderableState
+        }
     }, materialId);
 }
 
+function updateRenderableState(state: RenderableState, props: PD.Values<SliceParams>) {
+    Image.Utils.updateRenderableState(state, props);
+    state.opaque = false;
+    state.writeDepth = true;
+}
+
 export function SliceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<VolumeData, SliceParams>): VolumeRepresentation<SliceParams> {
     return VolumeRepresentation('Slice', ctx, getParams, SliceVisual, getLoci);
 }

src/mol-script/language/symbol-table/core.ts

@@ -145,7 +145,8 @@ const str = {
 
 const list = {
     '@header': 'Lists',
-    getAt: symbol(Arguments.Dictionary({ 0: Argument(Types.List()), 1: Argument(Type.Num) }), Types.AnyVar)
+    getAt: symbol(Arguments.Dictionary({ 0: Argument(Types.List()), 1: Argument(Type.Num) }), Types.AnyVar),
+    equal: symbol(Arguments.Dictionary({ 0: Argument(Types.List()), 1: Argument(Types.List()) }), Type.Bool)
 };
 
 const set = {

src/mol-script/language/symbol-table/structure-query.ts

@@ -308,6 +308,7 @@ const atomProperty = {
 
         entityType: atomProp(Types.EntityType, 'Type of the entity as defined in mmCIF (polymer, non-polymer, branched, water)'),
         entitySubtype: atomProp(Types.EntitySubtype, 'Subtype of the entity as defined in mmCIF _entity_poly.type and _pdbx_entity_branch.type (other, polypeptide(D), polypeptide(L), polydeoxyribonucleotide, polyribonucleotide, polydeoxyribonucleotide/polyribonucleotide hybrid, cyclic-pseudo-peptide, peptide nucleic acid, oligosaccharide)'),
+        entityDescription: atomProp(Core.Types.List(Type.Str)),
         objectPrimitive: atomProp(Types.ObjectPrimitive, 'Type of the primitive object used to model this segment as defined in mmCIF/IHM (atomistic, sphere, gaussian, other)'),
 
         secondaryStructureKey: atomProp(Type.AnyValue, 'Unique value for each secondary structure element.'),

src/mol-script/runtime/query/base.ts

@@ -11,9 +11,13 @@ import { MSymbol } from '../../language/symbol';
 export class QueryRuntimeTable {
     private map = new Map<string, QuerySymbolRuntime>();
 
+    removeSymbol(runtime: QuerySymbolRuntime) {
+        this.map.delete(runtime.symbol.id);
+    }
+
     addSymbol(runtime: QuerySymbolRuntime) {
         if (this.map.has(runtime.symbol.id)) {
-            throw new Error(`Symbol '${runtime.symbol.id}' already added.`);
+            console.warn(`Symbol '${runtime.symbol.id}' already added. Call removeSymbol/removeCustomProps re-adding the symbol.`);
         }
         this.map.set(runtime.symbol.id, runtime);
     }
@@ -26,6 +30,14 @@ export class QueryRuntimeTable {
         }
     }
 
+    removeCustomProp(desc: CustomPropertyDescriptor<any>) {
+        if (!desc.symbols) return;
+
+        for (const k of Object.keys(desc.symbols)) {
+            this.removeSymbol((desc.symbols as any)[k]);
+        }
+    }
+
     getRuntime(id: string) {
         return this.map.get(id);
     }

src/mol-script/runtime/query/table.ts

@@ -14,6 +14,7 @@ import { upperCaseAny } from '../../../mol-util/string';
 import { VdwRadius, AtomWeight, AtomNumber } from '../../../mol-model/structure/model/properties/atomic';
 import { cantorPairing } from '../../../mol-data/util';
 import { bundleElementImpl, bundleGenerator } from '../../../mol-model/structure/query/queries/internal';
+import { arrayEqual } from '../../../mol-util/array';
 
 const C = QuerySymbolRuntime.Const;
 const D = QuerySymbolRuntime.Dynamic;
@@ -151,6 +152,7 @@ const symbols = [
 
     // ============= LIST ================
     C(MolScript.core.list.getAt, (ctx, v) => v[0](ctx)[v[1](ctx)]),
+    C(MolScript.core.list.equal, (ctx, v) => arrayEqual(v[0](ctx), v[1](ctx))),
 
     // ============= SET ================
     C(MolScript.core.set.has, function core_set_has(ctx, v) { return v[0](ctx).has(v[1](ctx)); }),
@@ -334,6 +336,7 @@ const symbols = [
 
     D(MolScript.structureQuery.atomProperty.macromolecular.entityType, atomProp(StructureProperties.entity.type)),
     D(MolScript.structureQuery.atomProperty.macromolecular.entitySubtype, atomProp(StructureProperties.entity.subtype)),
+    D(MolScript.structureQuery.atomProperty.macromolecular.entityDescription, atomProp(StructureProperties.entity.pdbx_description)),
     D(MolScript.structureQuery.atomProperty.macromolecular.objectPrimitive, atomProp(StructureProperties.unit.object_primitive)),
 
     D(MolScript.structureQuery.atomProperty.macromolecular.isNonStandard, atomProp(StructureProperties.residue.isNonStandard)),

src/mol-script/script/mol-script/symbols.ts

@@ -234,6 +234,7 @@ export const SymbolTable = [
             Alias(MolScript.structureQuery.atomProperty.macromolecular.B_iso_or_equiv, 'atom.B_iso_or_equiv', 'atom.bfactor'),
             Alias(MolScript.structureQuery.atomProperty.macromolecular.entityType, 'atom.entity-type'),
             Alias(MolScript.structureQuery.atomProperty.macromolecular.entitySubtype, 'atom.entity-subtype'),
+            Alias(MolScript.structureQuery.atomProperty.macromolecular.entityDescription, 'atom.entity-description'),
             Alias(MolScript.structureQuery.atomProperty.macromolecular.objectPrimitive, 'atom.object-primitive'),
             Alias(MolScript.structureQuery.atomProperty.macromolecular.chemCompType, 'atom.chem-comp-type'),
 

src/mol-theme/label.ts

@@ -56,10 +56,16 @@ export function lociLabel(loci: Loci, options: Partial<LabelOptions> = {}): stri
         case 'cell-loci':
             const size = OrderedSet.size(loci.indices);
             const start = OrderedSet.start(loci.indices);
-            return [
+            const absVal = VolumeIsoValue.absolute(loci.volume.data.data[start]);
+            const relVal = VolumeIsoValue.toRelative(absVal, loci.volume.dataStats);
+            const label = [
                 `${loci.volume.label || 'Volume'}`,
                 `${size === 1 ? `Cell #${start}` : `${size} Cells`}`
-            ].join(' | ');
+            ];
+            if (size === 1) {
+                label.push(`${VolumeIsoValue.toString(absVal)} (${VolumeIsoValue.toString(relVal)})`);
+            }
+            return label.join(' | ');
     }
 }
 

src/mol-util/array.ts

@@ -105,7 +105,7 @@ export function arraySetRemove<T>(xs: T[], x: T) {
     return true;
 }
 
-export function arrayEqual<T>(xs?: T[], ys?: T[]) {
+export function arrayEqual<T>(xs?: ArrayLike<T>, ys?: ArrayLike<T>) {
     if (!xs || xs.length === 0) return !ys || ys.length === 0;
     if (!ys) return false;
 

src/servers/volume/pack/format.ts

@@ -103,7 +103,7 @@ export function getProviderFromType(type: Type): Provider {
 export async function open(name: string, filename: string, type: Type): Promise<Context> {
     const provider = getProviderFromType(type);
     const descriptor = await File.openRead(filename);
-    const file = FileHandle.fromDescriptor(descriptor);
+    const file = FileHandle.fromDescriptor(descriptor, filename);
     const header = await provider.readHeader(name, file);
     const data = { header, file, slices: void 0 as any };
     return { data, provider };

src/servers/volume/pack/sampling.ts

@@ -32,7 +32,7 @@ export async function createContext(filename: string, channels: Format.Context[]
     }
 
     const ctx: Data.Context = {
-        file: FileHandle.fromDescriptor(await File.createFile(filename)),
+        file: FileHandle.fromDescriptor(await File.createFile(filename), filename),
         isPeriodic,
         channels,
         valueType,

src/servers/volume/server/api.ts

@@ -66,7 +66,7 @@ async function readHeader(filename: string | undefined, sourceId: string) {
     let file: FileHandle | undefined;
     try {
         if (!filename) return void 0;
-        file = FileHandle.fromDescriptor(await File.openRead(filename));
+        file = FileHandle.fromDescriptor(await File.openRead(filename), filename);
         const header = await DataFormat.readHeader(file);
         return header.header;
     } catch (e) {

src/servers/volume/server/query/execute.ts

@@ -34,7 +34,7 @@ export default async function execute(params: Data.QueryParams, outputProvider:
 
     let sourceFile: FileHandle | undefined;
     try {
-        sourceFile = FileHandle.fromDescriptor(await File.openRead(params.sourceFilename));
+        sourceFile = FileHandle.fromDescriptor(await File.openRead(params.sourceFilename), params.sourceFilename);
         await _execute(sourceFile, params, guid, outputProvider);
         return true;
     } catch (e) {

webpack.config.common.js

@@ -2,6 +2,7 @@ const path = require('path');
 const webpack = require('webpack');
 const ExtraWatchWebpackPlugin = require('extra-watch-webpack-plugin');
 const MiniCssExtractPlugin = require('mini-css-extract-plugin');
+const VersionFile = require('webpack-version-file-plugin');
 // const CircularDependencyPlugin = require('circular-dependency-plugin');
 
 const sharedConfig = {
@@ -38,11 +39,17 @@ const sharedConfig = {
             ],
         }),
         new webpack.DefinePlugin({
-            __VERSION__: webpack.DefinePlugin.runtimeValue(() => JSON.stringify(require('./package.json').version), true),
-            __VERSION_TIMESTAMP__: webpack.DefinePlugin.runtimeValue(() => `${new Date().valueOf()}`, true),
+            // __VERSION__: webpack.DefinePlugin.runtimeValue(() => JSON.stringify(require('./package.json').version), true),
+            // __VERSION_TIMESTAMP__: webpack.DefinePlugin.runtimeValue(() => `${new Date().valueOf()}`, true),
             'process.env.DEBUG': JSON.stringify(process.env.DEBUG)
         }),
-        new MiniCssExtractPlugin({ filename: 'app.css' })
+        new MiniCssExtractPlugin({ filename: 'app.css' }),
+        new VersionFile({
+            extras: { timestamp: `${new Date().valueOf()}` },
+            packageFile: path.resolve(__dirname, 'package.json'),
+            templateString: `export const PLUGIN_VERSION = '<%= package.version %>';\nexport const PLUGIN_VERSION_DATE = new Date(<%= extras.timestamp %>);`,
+            outputFile: path.resolve(__dirname, 'lib/mol-plugin/version.js')
+        })
     ],
     resolve: {
         modules: [