2.0.7

- handle pre-multiplied alpha
- don't clear draw target unless written to

CHANGELOG.md

@@ -3,8 +3,16 @@ All notable changes to this project will be documented in this file, following t
 
 Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
 
+
 ## [Unreleased]
 
+
+## [v2.0.7] - 2021-06-23
+
+- Add ability to specify ``volumeIndex`` in ``Viewer.loadVolumeFromUrl`` to better support Volume Server inputs.
+- Support in-place reordering for trajectory ``Frame.x/y/z`` arrays for better memory efficiency.
+- Fixed text CIF encoder edge cases (most notably single whitespace not being escaped).
+
 ## [v2.0.6] - 2021-06-01
 
 - Add glTF (GLB) and STL support to ``geo-export`` extension.

package-lock.json

@@ -1,11 +1,11 @@
 {
   "name": "molstar",
-  "version": "2.0.6",
+  "version": "2.0.7",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
-      "version": "2.0.6",
+      "version": "2.0.7",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^1.0.38",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.6",
+  "version": "2.0.7",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/apps/viewer/embedded.html

@@ -38,19 +38,6 @@
             viewer.loadPdb('7bv2');
             viewer.loadEmdb('EMD-30210', { detail: 6 });
 
-            // viewer.loadVolumeFromUrl({
-            //     url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
-            //     format: 'dscif',
-            //     isBinary: true 
-            // }, [{
-            //     type: 'relative',
-            //     value: 1,
-            //     color: 0x3377aa
-            // }], {
-            //     entryId: 'EMD-30210',
-            //     isLazy: true
-            // });
-
             // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
         </script>
     </body>

src/apps/viewer/index.ts

@@ -243,7 +243,46 @@ export class Viewer {
         }));
     }
 
-    async loadVolumeFromUrl({ url, format, isBinary }: { url: string, format: BuildInVolumeFormat, isBinary: boolean }, isovalues: VolumeIsovalueInfo[], options?: { entryId?: string, isLazy?: boolean }) {
+    /**
+     * @example Load X-ray density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1.5,
+            color: 0x3362B2
+        }, {
+            type: 'relative',
+            value: 3,
+            color: 0x33BB33,
+            volumeIndex: 1
+        }, {
+            type: 'relative',
+            value: -3,
+            color: 0xBB3333,
+            volumeIndex: 1
+        }], {
+            entryId: ['2FO-FC', 'FO-FC'],
+            isLazy: true
+        });
+     * *********************
+     * @example Load EM density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1,
+            color: 0x3377aa
+        }], {
+            entryId: 'EMD-30210',
+            isLazy: true
+        });
+     */
+    async loadVolumeFromUrl({ url, format, isBinary }: { url: string, format: BuildInVolumeFormat, isBinary: boolean }, isovalues: VolumeIsovalueInfo[], options?: { entryId?: string | string[], isLazy?: boolean }) {
         const plugin = this.plugin;
 
         if (!plugin.dataFormats.get(format)) {
@@ -257,26 +296,28 @@ export class Viewer {
                 format,
                 entryId: options?.entryId,
                 isBinary,
-                isovalues: isovalues.map(v => ({ alpha: 1, ...v }))
+                isovalues: isovalues.map(v => ({ alpha: 1, volumeIndex: 0, ...v }))
             });
             return update.commit();
         }
 
         return plugin.dataTransaction(async () => {
-            const data = await plugin.builders.data.download({ url, isBinary, label: options?.entryId }, { state: { isGhost: true } });
+            const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
 
             const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId: options?.entryId });
-            const volume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
-            if (!volume?.isOk) throw new Error('Failed to parse any volume.');
+            const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
+            if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
 
-            const repr = plugin.build().to(volume);
+            const repr = plugin.build();
             for (const iso of isovalues) {
-                repr.apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, volume.data!, {
-                    type: 'isosurface',
-                    typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
-                    color: 'uniform',
-                    colorParams: { value: iso.color }
-                }));
+                repr
+                    .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume)
+                    .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
+                        type: 'isosurface',
+                        typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                        color: 'uniform',
+                        colorParams: { value: iso.color }
+                    }));
             }
 
             await repr.commit();
@@ -296,5 +337,6 @@ export interface VolumeIsovalueInfo {
     type: 'absolute' | 'relative',
     value: number,
     color: Color,
-    alpha?: number
+    alpha?: number,
+    volumeIndex?: number
 }

src/extensions/dnatco/confal-pyramids/color.ts

@@ -181,6 +181,6 @@ export const ConfalPyramidsColorThemeProvider: ColorTheme.Provider<ConfalPyramid
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => ConfalPyramids.isApplicable(m)),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ConfalPyramidsProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ConfalPyramidsProvider.descriptor, false)
+        detach: (data) => data.structure && ConfalPyramidsProvider.ref(data.structure.models[0], false)
     }
 };

src/extensions/geo-export/controls.ts

@@ -5,6 +5,7 @@
  */
 
 import { getStyle } from '../../mol-gl/renderer';
+import { Box3D } from '../../mol-math/geometry';
 import { PluginComponent } from '../../mol-plugin-state/component';
 import { PluginContext } from '../../mol-plugin/context';
 import { Task } from '../../mol-task';
@@ -43,17 +44,18 @@ export class GeometryControls extends PluginComponent {
                 const renderObjects = this.plugin.canvas3d?.getRenderObjects()!;
                 const filename = this.getFilename();
 
-                let renderObjectExporter: ObjExporter | GlbExporter | StlExporter;
+                const boundingBox = Box3D.fromSphere3D(Box3D(), this.plugin.canvas3d?.boundingSphereVisible!);
+                let renderObjectExporter: GlbExporter | ObjExporter | StlExporter;
                 switch (this.behaviors.params.value.format) {
-                    case 'obj':
-                        renderObjectExporter = new ObjExporter(filename);
-                        break;
                     case 'glb':
                         const style = getStyle(this.plugin.canvas3d?.props.renderer.style!);
-                        renderObjectExporter = new GlbExporter(style);
+                        renderObjectExporter = new GlbExporter(style, boundingBox);
+                        break;
+                    case 'obj':
+                        renderObjectExporter = new ObjExporter(filename, boundingBox);
                         break;
                     case 'stl':
-                        renderObjectExporter = new StlExporter();
+                        renderObjectExporter = new StlExporter(boundingBox);
                         break;
                     default: throw new Error('Unsupported format.');
                 }

src/extensions/geo-export/glb-exporter.ts

@@ -8,6 +8,7 @@ import { BaseValues } from '../../mol-gl/renderable/schema';
 import { Style } from '../../mol-gl/renderer';
 import { asciiWrite } from '../../mol-io/common/ascii';
 import { IsNativeEndianLittle, flipByteOrder } from '../../mol-io/common/binary';
+import { Box3D } from '../../mol-math/geometry';
 import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
 import { PLUGIN_VERSION } from '../../mol-plugin/version';
 import { RuntimeContext } from '../../mol-task';
@@ -41,6 +42,7 @@ export class GlbExporter extends MeshExporter<GlbData> {
     private bufferViews: Record<string, any>[] = [];
     private binaryBuffer: ArrayBuffer[] = [];
     private byteOffset = 0;
+    private centerTransform: Mat4;
 
     private static vec3MinMax(a: NumberArray) {
         const min: number[] = [Infinity, Infinity, Infinity];
@@ -252,11 +254,12 @@ export class GlbExporter extends MeshExporter<GlbData> {
             }
 
             // node
-            const node: Record<string, any> = {
-                mesh: meshIndex!
-            };
             Mat4.fromArray(t, aTransform, instanceIndex * 16);
-            if (!Mat4.isIdentity(t)) node.matrix = t.slice();
+            Mat4.mul(t, this.centerTransform, t);
+            const node: Record<string, any> = {
+                mesh: meshIndex!,
+                matrix: t.slice()
+            };
             this.nodes.push(node);
         }
     }
@@ -334,7 +337,11 @@ export class GlbExporter extends MeshExporter<GlbData> {
         return new Blob([this.getData().glb], { type: 'model/gltf-binary' });
     }
 
-    constructor(private style: Style) {
+    constructor(private style: Style, boundingBox: Box3D) {
         super();
+        const tmpV = Vec3();
+        Vec3.add(tmpV, boundingBox.min, boundingBox.max);
+        Vec3.scale(tmpV, tmpV, -0.5);
+        this.centerTransform = Mat4.fromTranslation(Mat4(), tmpV);
     }
 }

src/extensions/geo-export/obj-exporter.ts

@@ -6,6 +6,7 @@
 
 import { sort, arraySwap } from '../../mol-data/util';
 import { asciiWrite } from '../../mol-io/common/ascii';
+import { Box3D } from '../../mol-math/geometry';
 import { Vec3, Mat3, Mat4 } from '../../mol-math/linear-algebra';
 import { RuntimeContext } from '../../mol-task';
 import { StringBuilder } from '../../mol-util';
@@ -35,6 +36,7 @@ export class ObjExporter extends MeshExporter<ObjData> {
     private currentColor: Color | undefined;
     private currentAlpha: number | undefined;
     private materialSet = new Set<string>();
+    private centerTransform: Mat4;
 
     private updateMaterial(color: Color, alpha: number) {
         if (this.currentColor === color && this.currentAlpha === alpha) return;
@@ -163,6 +165,7 @@ export class ObjExporter extends MeshExporter<ObjData> {
             const { vertices, normals, indices, groups, vertexCount, drawCount } = ObjExporter.getInstance(input, instanceIndex);
 
             Mat4.fromArray(t, aTransform, instanceIndex * 16);
+            Mat4.mul(t, this.centerTransform, t);
             mat3directionTransform(n, t);
 
             // position
@@ -273,8 +276,12 @@ export class ObjExporter extends MeshExporter<ObjData> {
         return new Blob([await zip(ctx, zipDataObj)], { type: 'application/zip' });
     }
 
-    constructor(private filename: string) {
+    constructor(private filename: string, boundingBox: Box3D) {
         super();
         StringBuilder.writeSafe(this.obj, `mtllib ${filename}.mtl\n`);
+        const tmpV = Vec3();
+        Vec3.add(tmpV, boundingBox.min, boundingBox.max);
+        Vec3.scale(tmpV, tmpV, -0.5);
+        this.centerTransform = Mat4.fromTranslation(Mat4(), tmpV);
     }
 }

src/extensions/geo-export/stl-exporter.ts

@@ -5,6 +5,7 @@
  */
 
 import { asciiWrite } from '../../mol-io/common/ascii';
+import { Box3D } from '../../mol-math/geometry';
 import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
 import { PLUGIN_VERSION } from '../../mol-plugin/version';
 import { RuntimeContext } from '../../mol-task';
@@ -26,6 +27,7 @@ export class StlExporter extends MeshExporter<StlData> {
     readonly fileExtension = 'stl';
     private triangleBuffers: ArrayBuffer[] = [];
     private triangleCount = 0;
+    private centerTransform: Mat4;
 
     protected async addMeshWithColors(input: AddMeshInput) {
         const { values, isGeoTexture, ctx } = input;
@@ -46,6 +48,7 @@ export class StlExporter extends MeshExporter<StlData> {
             const { vertices, indices, vertexCount, drawCount } = StlExporter.getInstance(input, instanceIndex);
 
             Mat4.fromArray(t, aTransform, instanceIndex * 16);
+            Mat4.mul(t, this.centerTransform, t);
 
             // position
             const vertexArray = new Float32Array(vertexCount * 3);
@@ -105,4 +108,12 @@ export class StlExporter extends MeshExporter<StlData> {
     async getBlob(ctx: RuntimeContext) {
         return new Blob([this.getData().stl], { type: 'model/stl' });
     }
+
+    constructor(boundingBox: Box3D) {
+        super();
+        const tmpV = Vec3();
+        Vec3.add(tmpV, boundingBox.min, boundingBox.max);
+        Vec3.scale(tmpV, tmpV, -0.5);
+        this.centerTransform = Mat4.fromTranslation(Mat4(), tmpV);
+    }
 }

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

@@ -115,6 +115,6 @@ export const StructureQualityReportColorThemeProvider: ColorTheme.Provider<Param
     isApplicable: (ctx: ThemeDataContext) => StructureQualityReport.isApplicable(ctx.structure?.models[0]),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? StructureQualityReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(StructureQualityReportProvider.descriptor, false)
+        detach: (data) => data.structure && StructureQualityReportProvider.ref(data.structure.models[0], false)
     }
 };

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

@@ -109,6 +109,6 @@ export const AssemblySymmetryClusterColorThemeProvider: ColorTheme.Provider<Asse
     isApplicable: (ctx: ThemeDataContext) => AssemblySymmetry.isApplicable(ctx.structure),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? AssemblySymmetryProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(AssemblySymmetryProvider.descriptor, false)
+        detach: (data) => data.structure && AssemblySymmetryProvider.ref(data.structure, false)
     }
 };

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

@@ -77,6 +77,6 @@ export const DensityFitColorThemeProvider: ColorTheme.Provider<{}, ValidationRep
     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)
+        detach: (data) => data.structure && ValidationReportProvider.ref(data.structure.models[0], false)
     }
 };

src/extensions/rcsb/validation-report/color/geometry-quality.ts

@@ -115,6 +115,6 @@ export const GeometryQualityColorThemeProvider: ColorTheme.Provider<GeometricQua
     isApplicable: (ctx: ThemeDataContext) => ValidationReport.isApplicable(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)
+        detach: (data) => data.structure && ValidationReportProvider.ref(data.structure.models[0], false)
     }
 };

src/extensions/rcsb/validation-report/color/random-coil-index.ts

@@ -68,6 +68,6 @@ export const RandomCoilIndexColorThemeProvider: ColorTheme.Provider<{}, Validati
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.isFromNmr(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)
+        detach: (data) => data.structure && ValidationReportProvider.ref(data.structure.models[0], false)
     }
 };

src/mol-canvas3d/canvas3d.ts

@@ -242,6 +242,7 @@ interface Canvas3D {
     requestCameraReset(options?: { durationMs?: number, snapshot?: Camera.SnapshotProvider }): void
     readonly camera: Camera
     readonly boundingSphere: Readonly<Sphere3D>
+    readonly boundingSphereVisible: Readonly<Sphere3D>
     setProps(props: PartialCanvas3DProps | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void), doNotRequestDraw?: boolean /* = false */): void
     getImagePass(props: Partial<ImageProps>): ImagePass
     getRenderObjects(): GraphicsRenderObject[]
@@ -717,6 +718,7 @@ namespace Canvas3D {
             },
             camera,
             boundingSphere: scene.boundingSphere,
+            boundingSphereVisible: scene.boundingSphereVisible,
             get notifyDidDraw() { return notifyDidDraw; },
             set notifyDidDraw(v: boolean) { notifyDidDraw = v; },
             didDraw,

src/mol-canvas3d/passes/draw.ts

@@ -290,7 +290,7 @@ export class DrawPass {
         renderer.setViewport(x, y, width, height);
         renderer.update(camera);
 
-        if (transparentBackground) {
+        if (transparentBackground && !antialiasingEnabled && toDrawingBuffer) {
             this.drawTarget.bind();
             renderer.clear(false);
         }

src/mol-canvas3d/passes/image.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -103,7 +103,9 @@ export class ImagePass {
         } else {
             this.webgl.readPixels(viewport.x, height - viewport.y - viewport.height, w, h, array);
         }
-        PixelData.flipY({ array, width: w, height: h });
+        const pixelData = PixelData.create(array, w, h);
+        PixelData.flipY(pixelData);
+        PixelData.divideByAlpha(pixelData);
         return new ImageData(new Uint8ClampedArray(array), w, h);
     }
 }

src/mol-io/writer/_spec/cif.spec.ts

@@ -3,7 +3,10 @@ import { CifWriter } from '../cif';
 import { decodeMsgPack } from '../../common/msgpack/decode';
 import { EncodedFile, EncodedCategory } from '../../common/binary-cif';
 import { Field } from '../../reader/cif/binary/field';
+import { TextEncoder } from '../cif/encoder/text';
 import * as C from '../cif/encoder';
+import { Column, Database, Table } from '../../../mol-data/db';
+import { parseCifText } from '../../reader/cif/text/parser';
 
 const cartn_x = Data.CifField.ofNumbers([1.001, 1.002, 1.003, 1.004, 1.005, 1.006, 1.007, 1.008, 1.009]);
 const cartn_y = Data.CifField.ofNumbers([-3.0, -2.666, -2.3333, -2.0, -1.666, -1.333, -1.0, -0.666, -0.333]);
@@ -38,6 +41,30 @@ const encoding_aware_encoder = CifWriter.createEncoder({
     ])
 });
 
+test('cif writer value escaping', async () => {
+    const values = ['1', ' ', '  ', ` ' `, `a'`, `b"`, `"`, '  a  ', `"'"`, `'"`, `\na`];
+    const table = Table.ofArrays({ values: Column.Schema.str }, { values });
+
+    const encoder = new TextEncoder();
+    C.Encoder.writeDatabase(encoder, 'test', Database.ofTables('test', { test: table._schema }, { test: table }));
+    encoder.encode();
+    const data = encoder.getData();
+
+    const result = await parseCifText(data).run();
+    if (result.isError) {
+        expect(false).toBe(true);
+        return;
+    }
+
+    const cat = result.result.blocks[0].categories['test'];
+    const parsed = cat.getField('values')?.toStringArray();
+
+    expect(values.length).toBe(parsed?.length);
+    for (let i = 0; i < values.length; i++) {
+        expect(values[i]).toBe(parsed?.[i]);
+    }
+});
+
 describe('encoding-config', () => {
     const decoded = process(encoding_aware_encoder);
 

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * Adapted from CIFTools.js (https://github.com/dsehnal/CIFTools.js)
  *
@@ -208,55 +208,61 @@ function writeChecked(builder: StringBuilder, val: string) {
         return false;
     }
 
-    let escape = val.charCodeAt(0) === 95 /* _ */, escapeCharStart = '\'', escapeCharEnd = '\' ';
-    let hasWhitespace = false;
-    let hasSingle = false;
-    let hasDouble = false;
-    for (let i = 0, _l = val.length - 1; i < _l; i++) {
+    const fst = val.charCodeAt(0);
+    let escape = false;
+    let escapeKind = 0; // 0 => ', 1 => "
+    let hasSingleQuote = false, hasDoubleQuote = false;
+    for (let i = 0, _l = val.length - 1; i <= _l; i++) {
         const c = val.charCodeAt(i);
 
         switch (c) {
-            case 9: hasWhitespace = true; break; // \t
+            case 9: // \t
+                escape = true;
+                break;
             case 10: // \n
                 writeMultiline(builder, val);
                 return true;
-            case 32: hasWhitespace = true; break; // ' '
+            case 32: // ' '
+                escape = true;
+                break;
             case 34: // "
-                if (hasSingle) {
+                // no need to escape quote if it's the last char and the length is > 1
+                if (i && i === _l) break;
+
+                if (hasSingleQuote) {
+                    // the string already has a " => use multiline value
                     writeMultiline(builder, val);
                     return true;
                 }
 
-                hasDouble = true;
+                hasDoubleQuote = true;
                 escape = true;
-                escapeCharStart = '\'';
-                escapeCharEnd = '\' ';
+                escapeKind = 0;
                 break;
             case 39: // '
-                if (hasDouble) {
+                // no need to escape quote if it's the last char and the length is > 1
+                if (i && i === _l) break;
+
+                if (hasDoubleQuote) {
                     writeMultiline(builder, val);
                     return true;
                 }
 
+                hasSingleQuote = true;
                 escape = true;
-                hasSingle = true;
-                escapeCharStart = '"';
-                escapeCharEnd = '" ';
+                escapeKind = 1;
                 break;
         }
     }
 
-    const fst = val.charCodeAt(0);
-    if (!escape && (fst === 35 /* # */|| fst === 36 /* $ */ || fst === 59 /* ; */ || fst === 91 /* [ */ || fst === 93 /* ] */ || hasWhitespace)) {
-        escapeCharStart = '\'';
-        escapeCharEnd = '\' ';
+    if (!escape && (fst === 35 /* # */ || fst === 36 /* $ */ || fst === 59 /* ; */ || fst === 91 /* [ */ || fst === 93 /* ] */ || fst === 95 /* _ */)) {
         escape = true;
     }
 
     if (escape) {
-        StringBuilder.writeSafe(builder, escapeCharStart);
+        StringBuilder.writeSafe(builder, escapeKind ? '"' : '\'');
         StringBuilder.writeSafe(builder, val);
-        StringBuilder.writeSafe(builder, escapeCharEnd);
+        StringBuilder.writeSafe(builder, escapeKind ? '" ' : '\' ');
     } else {
         StringBuilder.writeSafe(builder, val);
         StringBuilder.writeSafe(builder, ' ');

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

@@ -38,6 +38,8 @@ export function coordinatesFromDcd(dcdFile: DcdFile): Task<Coordinates> {
                 x: dcdFrame.x,
                 y: dcdFrame.y,
                 z: dcdFrame.z,
+
+                xyzOrdering: { isIdentity: true }
             };
 
             if (dcdFrame.cell) {

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

@@ -30,6 +30,7 @@ export function coordinatesFromXtc(file: XtcFile): Task<Coordinates> {
                 x: file.frames[i].x,
                 y: file.frames[i].y,
                 z: file.frames[i].z,
+                xyzOrdering: { isIdentity: true },
                 time: Time(offsetTime.value + deltaTime.value * i, deltaTime.unit)
             });
         }

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

@@ -83,6 +83,6 @@ export const AccessibleSurfaceAreaColorThemeProvider: ColorTheme.Provider<Access
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure,
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? AccessibleSurfaceAreaProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(AccessibleSurfaceAreaProvider.descriptor, false)
+        detach: (data) => data.structure && AccessibleSurfaceAreaProvider.ref(data.structure, false)
     }
 };

src/mol-model-props/computed/themes/interaction-type.ts

@@ -117,6 +117,6 @@ export const InteractionTypeColorThemeProvider: ColorTheme.Provider<InteractionT
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure,
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? InteractionsProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(InteractionsProvider.descriptor, false)
+        detach: (data) => data.structure && InteractionsProvider.ref(data.structure, false)
     }
 };

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

@@ -70,6 +70,6 @@ export const CrossLinkColorThemeProvider: ColorTheme.Provider<CrossLinkColorThem
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && CrossLinkRestraint.isApplicable(ctx.structure),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? CrossLinkRestraintProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(CrossLinkRestraintProvider.descriptor, false)
+        detach: (data) => data.structure && CrossLinkRestraintProvider.ref(data.structure, false)
     }
 };

src/mol-model-props/sequence/best-database-mapping.ts

@@ -29,7 +29,7 @@ namespace BestDatabaseSequenceMapping {
         type: 'static',
         defaultParams: {},
         getParams: () => ({}),
-        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site.fieldNames.indexOf('db_name') >= 0,
+        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('db_name') >= 0,
         obtain: async (ctx, data) => {
             return { value: fromCif(data) };
         }
@@ -92,4 +92,4 @@ namespace BestDatabaseSequenceMapping {
 
         return { dbName, accession, num, residue };
     }
-}
+}

src/mol-model-props/sequence/themes/best-database-mapping.ts

@@ -98,7 +98,7 @@ export const BestDatabaseSequenceMappingColorThemeProvider: ColorTheme.Provider<
         detach: (data) => {
             if (!data.structure) return;
             for (const m of data.structure.models) {
-                m.customProperties.reference(BestDatabaseSequenceMapping.Provider.descriptor, false);
+                BestDatabaseSequenceMapping.Provider.ref(m, false);
             }
         }
     }

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

@@ -1,10 +1,11 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { UUID } from '../../../mol-util';
+import { arrayEqual, UUID } from '../../../mol-util';
 import { Cell } from '../../../mol-math/geometry/spacegroup/cell';
 import { AtomicConformation } from '../model/properties/atomic';
 import { Column } from '../../../mol-data/db';
@@ -34,6 +35,12 @@ export interface Frame {
         readonly fy: ArrayLike<number>
         readonly fz: ArrayLike<number>
     }
+
+    readonly xyzOrdering: {
+        isIdentity: boolean,
+        frozen?: boolean,
+        index?: ArrayLike<number>,
+    }
 }
 
 //
@@ -85,41 +92,106 @@ namespace Coordinates {
             hasVelocities,
             hasForces,
             deltaTime,
-            timeOffset
+            timeOffset,
         };
     }
 
-    export function getAtomicConformation(frame: Frame, atomId: Column<number>): AtomicConformation {
+    /**
+     * Only use ordering if it's not identity.
+     */
+    export function getAtomicConformation(frame: Frame, atomId: Column<number>, ordering?: ArrayLike<number>): AtomicConformation {
+        let { x, y, z } = frame;
+
+        if (frame.xyzOrdering.frozen) {
+            if (ordering) {
+                if (frame.xyzOrdering.isIdentity) {
+                    // simple list reordering
+                    x = getOrderedCoords(x, ordering);
+                    y = getOrderedCoords(y, ordering);
+                    z = getOrderedCoords(z, ordering);
+                } else if (!arrayEqual(frame.xyzOrdering.index! as any, ordering as any)) {
+                    x = getSourceOrderedCoords(x, frame.xyzOrdering.index!, ordering);
+                    y = getSourceOrderedCoords(y, frame.xyzOrdering.index!, ordering);
+                    z = getSourceOrderedCoords(z, frame.xyzOrdering.index!, ordering);
+                }
+            } else if (!frame.xyzOrdering.isIdentity) {
+                x = getInvertedCoords(x, frame.xyzOrdering.index!);
+                y = getInvertedCoords(y, frame.xyzOrdering.index!);
+                z = getInvertedCoords(z, frame.xyzOrdering.index!);
+            }
+        } else if (ordering) {
+            if (frame.xyzOrdering.isIdentity) {
+                frame.xyzOrdering.isIdentity = false;
+                frame.xyzOrdering.index = ordering;
+                reorderCoordsInPlace(x as unknown as number[], ordering);
+                reorderCoordsInPlace(y as unknown as number[], ordering);
+                reorderCoordsInPlace(z as unknown as number[], ordering);
+            } else {
+                // is current ordering is not the same as requested?
+                //   => copy the conformations into a new array
+                if (!arrayEqual(frame.xyzOrdering.index! as any, ordering as any)) {
+                    x = getSourceOrderedCoords(x, frame.xyzOrdering.index!, ordering);
+                    y = getSourceOrderedCoords(y, frame.xyzOrdering.index!, ordering);
+                    z = getSourceOrderedCoords(z, frame.xyzOrdering.index!, ordering);
+                }
+            }
+        }
+
+        // once the conformation has been accessed at least once, freeze it.
+        //   => any other request to the frame with different ordering will result in a copy.
+        frame.xyzOrdering.frozen = true;
+
         return {
             id: UUID.create22(),
             atomId,
             occupancy: Column.ofConst(1, frame.elementCount, Column.Schema.int),
             B_iso_or_equiv: Column.ofConst(0, frame.elementCount, Column.Schema.float),
             xyzDefined: true,
-            x: frame.x,
-            y: frame.y,
-            z: frame.z,
+            x,
+            y,
+            z,
         };
     }
 
-    function reorderCoords(xs: ArrayLike<number>, index: ArrayLike<number>) {
-        const ret = new Float32Array(xs.length);
+    const _reorderBuffer = [0.123];
+    function reorderCoordsInPlace(xs: number[], index: ArrayLike<number>) {
+        const buffer = _reorderBuffer;
+
         for (let i = 0, _i = xs.length; i < _i; i++) {
-            ret[i] = xs[index[i]];
+            buffer[i] = xs[index[i]];
         }
+        for (let i = 0, _i = xs.length; i < _i; i++) {
+            xs[i] = buffer[i];
+        }
+    }
+
+    function getSourceOrderedCoords(xs: ArrayLike<number>, srcIndex: ArrayLike<number>, index: ArrayLike<number>) {
+        const ret = new Float32Array(xs.length);
+
+        for (let i = 0, _i = xs.length; i < _i; i++) {
+            ret[i] = xs[srcIndex[index[i]]];
+        }
+
         return ret;
     }
 
-    export function getAtomicConformationReordered(frame: Frame, atomId: Column<number>, srcIndex: ArrayLike<number>): AtomicConformation {
-        return {
-            id: UUID.create22(),
-            atomId,
-            occupancy: Column.ofConst(1, frame.elementCount, Column.Schema.int),
-            B_iso_or_equiv: Column.ofConst(0, frame.elementCount, Column.Schema.float),
-            xyzDefined: true,
-            x: reorderCoords(frame.x, srcIndex),
-            y: reorderCoords(frame.y, srcIndex),
-            z: reorderCoords(frame.z, srcIndex)
-        };
+    function getOrderedCoords(xs: ArrayLike<number>, index: ArrayLike<number>) {
+        const ret = new Float32Array(xs.length);
+
+        for (let i = 0, _i = xs.length; i < _i; i++) {
+            ret[i] = xs[index[i]];
+        }
+
+        return ret;
+    }
+
+    function getInvertedCoords(xs: ArrayLike<number>, index: ArrayLike<number>) {
+        const ret = new Float32Array(xs.length);
+
+        for (let i = 0, _i = xs.length; i < _i; i++) {
+            ret[index[i]] = xs[i];
+        }
+
+        return ret;
     }
 }

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

@@ -105,9 +105,7 @@ export namespace Model {
                 ...model,
                 id: UUID.create22(),
                 modelNum: i,
-                atomicConformation: isIdentity
-                    ? Coordinates.getAtomicConformation(f, model.atomicConformation.atomId)
-                    : Coordinates.getAtomicConformationReordered(f, model.atomicConformation.atomId, srcIndexArray!),
+                atomicConformation: Coordinates.getAtomicConformation(f, model.atomicConformation.atomId, srcIndexArray),
                 // TODO: add support for supplying sphere and gaussian coordinates in addition to atomic coordinates?
                 // coarseConformation: coarse.conformation,
                 customProperties: new CustomProperties(),

src/mol-model/structure/query/queries/filters.ts

@@ -278,7 +278,7 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
 
             for (let li = 0; li < buCount; li++) {
                 const lu = bondedUnits[li];
-                const bUnit = structure.unitMap.get(lu.unitB) as Unit.Atomic;
+                const bUnit = input.unitMap.get(lu.unitB) as Unit.Atomic;
                 const bElements = bUnit.elements;
                 const bonds = lu.getEdges(inputIndex);
                 for (let bi = 0, _bi = bonds.length; bi < _bi; bi++) {

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

@@ -191,6 +191,9 @@ export const CubeProvider = DataFormatProvider({
     }
 });
 
+
+type DsCifParams = { entryId?: string | string[] };
+
 export const DscifProvider = DataFormatProvider({
     label: 'DensityServer CIF',
     description: 'DensityServer CIF',
@@ -200,7 +203,7 @@ export const DscifProvider = DataFormatProvider({
     isApplicable: (info, data) => {
         return guessCifVariant(info, data) === 'dscif' ? true : false;
     },
-    parse: async (plugin, data, params?: Params) => {
+    parse: async (plugin, data, params?: DsCifParams) => {
         const cifCell = await plugin.build().to(data).apply(StateTransforms.Data.ParseCif).commit();
         const b = plugin.build().to(cifCell);
         const blocks = cifCell.obj!.data.blocks.slice(1); // zero block contains query meta-data
@@ -208,8 +211,11 @@ export const DscifProvider = DataFormatProvider({
         if (blocks.length !== 1 && blocks.length !== 2) throw new Error('unknown number of blocks');
 
         const volumes: StateObjectSelector<PluginStateObject.Volume.Data>[] = [];
+        let i = 0;
         for (const block of blocks) {
-            volumes.push(b.apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: block.header, entryId: params?.entryId }).selector);
+            const entryId = Array.isArray(params?.entryId) ? params?.entryId[i] : params?.entryId;
+            volumes.push(b.apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: block.header, entryId }).selector);
+            i++;
         }
 
         await b.commit();

src/mol-plugin-state/objects.ts

@@ -125,12 +125,13 @@ export namespace PluginStateObject {
             url: string | Asset.Url,
             isBinary: boolean,
             format: string,
-            entryId?: string,
+            entryId?: string | string[],
             isovalues: {
                 type: 'absolute' | 'relative',
                 value: number,
                 color: Color,
-                alpha?: number
+                alpha?: number,
+                volumeIndex?: number,
             }[]
         }
 

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

@@ -455,18 +455,20 @@ const LazyVolume = PluginStateTransform.BuiltIn({
         url: PD.Url(''),
         isBinary: PD.Boolean(false),
         format: PD.Text('ccp4'), // TODO: use Select based on available formats
-        entryId: PD.Text(''),
+        entryId: PD.Value<string | string[]>('', { isHidden: true }),
         isovalues: PD.ObjectList({
             type: PD.Text<'absolute' | 'relative'>('relative'), // TODO: Select
             value: PD.Numeric(0),
             color: PD.Color(ColorNames.black),
-            alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 })
+            alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+            volumeIndex: PD.Numeric(0),
         }, e => `${e.type} ${e.value}`)
     }
 })({
     apply({ a, params }) {
         return Task.create('Lazy Volume', async ctx => {
-            return new SO.Volume.Lazy(params, { label: `${params.entryId || params.url}`, description: 'Lazy Volume' });
+            const entryId = Array.isArray(params.entryId) ? params.entryId.join(', ') : params.entryId;
+            return new SO.Volume.Lazy(params, { label: `${entryId || params.url}`, description: 'Lazy Volume' });
         });
     }
 });

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

@@ -205,19 +205,21 @@ export class VolumeSourceControls extends CollapsableControls<{}, VolumeSourceCo
         try {
             const plugin = this.plugin;
             await plugin.dataTransaction(async () => {
-                const data = await plugin.builders.data.download({ url, isBinary, label: entryId }, { state: { isGhost: true } });
+                const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
                 const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId });
-                const volume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
-                if (!volume?.isOk) throw new Error('Failed to parse any volume.');
+                const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
+                if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
 
-                const repr = plugin.build().to(volume);
+                const repr = plugin.build();
                 for (const iso of isovalues) {
-                    repr.apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, volume.data!, {
-                        type: 'isosurface',
-                        typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
-                        color: 'uniform',
-                        colorParams: { value: iso.color }
-                    }));
+                    repr
+                        .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume)
+                        .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
+                            type: 'isosurface',
+                            typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                            color: 'uniform',
+                            colorParams: { value: iso.color }
+                        }));
                 }
 
                 await repr.commit();

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

@@ -276,10 +276,12 @@ const VolumeStreamingVisual = PluginStateTransform.BuiltIn({
         // TODO: is this correct behavior?
         if (!channel) return StateTransformer.UpdateResult.Unchanged;
 
+        const visible = b.data.repr.state.visible;
         const params = createVolumeProps(a.data, newParams.channel);
         const props = { ...b.data.repr.props, ...params.type.params };
         b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: channel.data }, params));
         await b.data.repr.createOrUpdate(props, channel.data).runInContext(ctx);
+        b.data.repr.setState({ visible });
         b.data.sourceData = channel.data;
 
         // TODO: set the transform here as well in case the structure moves?

src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts

@@ -205,6 +205,7 @@ export function InterUnitBondCylinderImpostorVisual(materialId: number): Complex
         eachLocation: eachInterBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<InterUnitBondCylinderParams>, currentProps: PD.Values<InterUnitBondCylinderParams>) => {
             state.createGeometry = (
+                newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||

src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts

@@ -187,6 +187,7 @@ export function IntraUnitBondCylinderImpostorVisual(materialId: number): UnitsVi
         eachLocation: eachIntraBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<IntraUnitBondCylinderParams>, currentProps: PD.Values<IntraUnitBondCylinderParams>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
             state.createGeometry = (
+                newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||

src/mol-theme/color/secondary-structure.ts

@@ -123,6 +123,6 @@ export const SecondaryStructureColorThemeProvider: ColorTheme.Provider<Secondary
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure,
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? SecondaryStructureProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(SecondaryStructureProvider.descriptor, false)
+        detach: (data) => data.structure && SecondaryStructureProvider.ref(data.structure, false)
     }
 };

src/mol-util/image.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -32,4 +32,16 @@ namespace PixelData {
         }
         return pixelData;
     }
+
+    /** to undo pre-multiplied alpha */
+    export function divideByAlpha(pixelData: PixelData): PixelData {
+        const { array } = pixelData;
+        for (let i = 0, il = array.length; i < il; i += 4) {
+            const a = array[i + 3] / 255;
+            array[i] /= a;
+            array[i + 1] /= a;
+            array[i + 2] /= a;
+        }
+        return pixelData;
+    }
 }