2.0.2

.npmignore

@@ -1 +1 @@
-tsconfig.commonjs.buildinfo
+tsconfig.commonjs.tsbuildinfo

package-lock.json

@@ -1,11 +1,11 @@
 {
   "name": "molstar",
-  "version": "2.0.0-dev.13",
+  "version": "2.0.2",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
-      "version": "2.0.0-dev.13",
+      "version": "2.0.2",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^1.0.38",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.0-dev.13",
+  "version": "2.0.2",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -14,6 +14,7 @@
     "lint": "eslint .",
     "lint-fix": "eslint . --fix",
     "test": "npm run lint && jest",
+    "jest": "jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
     "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
     "build-tsc": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.json --incremental\"",

src/examples/alpha-orbitals/index.ts

@@ -174,7 +174,8 @@ export class AlphaOrbitalsExample {
             kind,
             relativeIsovalue: this.state.value.isoValue,
             pickable: false,
-            xrayShaded: true
+            xrayShaded: true,
+            tryUseGpu: false
         };
     }
 

src/extensions/alpha-orbitals/transforms.ts

@@ -172,7 +172,8 @@ export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
         color: PD.Color(ColorNames.blue),
         alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
         xrayShaded: PD.Boolean(false),
-        pickable: PD.Boolean(true)
+        pickable: PD.Boolean(true),
+        tryUseGpu: PD.Boolean(true)
     }
 })({
     canAutoUpdate() {
@@ -230,7 +231,7 @@ function volumeParams(plugin: PluginContext, volume: PluginStateObject.Volume.Da
         colorParams: { value: params.color }
     } : {
         type: 'isosurface',
-        typeParams: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, alpha: params.alpha, xrayShaded: params.xrayShaded },
+        typeParams: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, alpha: params.alpha, xrayShaded: params.xrayShaded, tryUseGpu: params.tryUseGpu },
         color: 'uniform',
         colorParams: { value: params.color }
     });

src/mol-canvas3d/canvas3d.ts

@@ -234,6 +234,7 @@ interface Canvas3D {
     readonly boundingSphere: Readonly<Sphere3D>
     setProps(props: PartialCanvas3DProps | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void), doNotRequestDraw?: boolean /* = false */): void
     getImagePass(props: Partial<ImageProps>): ImagePass
+    getRenderObjects(): GraphicsRenderObject[]
 
     /** Returns a copy of the current Canvas3D instance props */
     readonly props: Readonly<Canvas3DProps>
@@ -769,6 +770,11 @@ namespace Canvas3D {
             getImagePass: (props: Partial<ImageProps> = {}) => {
                 return new ImagePass(webgl, renderer, scene, camera, helper, passes.draw.wboitEnabled, props);
             },
+            getRenderObjects(): GraphicsRenderObject[] {
+                const renderObjects: GraphicsRenderObject[] = [];
+                scene.forEach((_, ro) => renderObjects.push(ro));
+                return renderObjects;
+            },
 
             get props() {
                 return getProps();

src/mol-gl/compute/marching-cubes/isosurface.ts

@@ -32,6 +32,7 @@ const IsosurfaceSchema = {
     uSize: UniformSpec('f'),
     uLevels: UniformSpec('f'),
     uCount: UniformSpec('f'),
+    uInvert: UniformSpec('b'),
 
     uGridDim: UniformSpec('v3'),
     uGridTexDim: UniformSpec('v3'),
@@ -44,7 +45,7 @@ type IsosurfaceValues = Values<typeof IsosurfaceSchema>
 
 const IsosurfaceName = 'isosurface';
 
-function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, packedGroup: boolean): ComputeRenderable<IsosurfaceValues> {
+function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, invert: boolean, packedGroup: boolean): ComputeRenderable<IsosurfaceValues> {
     if (ctx.namedComputeRenderables[IsosurfaceName]) {
         const v = ctx.namedComputeRenderables[IsosurfaceName].values as IsosurfaceValues;
 
@@ -56,6 +57,7 @@ function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture
         ValueCell.updateIfChanged(v.uSize, Math.pow(2, levels));
         ValueCell.updateIfChanged(v.uLevels, levels);
         ValueCell.updateIfChanged(v.uCount, count);
+        ValueCell.updateIfChanged(v.uInvert, invert);
 
         ValueCell.update(v.uGridDim, gridDim);
         ValueCell.update(v.uGridTexDim, gridTexDim);
@@ -66,12 +68,12 @@ function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture
 
         ctx.namedComputeRenderables[IsosurfaceName].update();
     } else {
-        ctx.namedComputeRenderables[IsosurfaceName] = createIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, packedGroup);
+        ctx.namedComputeRenderables[IsosurfaceName] = createIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup);
     }
     return ctx.namedComputeRenderables[IsosurfaceName];
 }
 
-function createIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, packedGroup: boolean) {
+function createIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, invert: boolean, packedGroup: boolean) {
     // console.log('uSize', Math.pow(2, levels))
     const values: IsosurfaceValues = {
         ...QuadValues,
@@ -85,6 +87,7 @@ function createIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Text
         uSize: ValueCell.create(Math.pow(2, levels)),
         uLevels: ValueCell.create(levels),
         uCount: ValueCell.create(count),
+        uInvert: ValueCell.create(invert),
 
         uGridDim: ValueCell.create(gridDim),
         uGridTexDim: ValueCell.create(gridTexDim),
@@ -112,7 +115,7 @@ function setRenderingDefaults(ctx: WebGLContext) {
     state.clearColor(0, 0, 0, 0);
 }
 
-export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Texture, volumeData: Texture, histogramPyramid: HistogramPyramid, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
+export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Texture, volumeData: Texture, histogramPyramid: HistogramPyramid, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, invert: boolean, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
     const { gl, resources, extensions } = ctx;
     const { pyramidTex, height, levels, scale, count } = histogramPyramid;
     const width = pyramidTex.getWidth();
@@ -167,7 +170,7 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
     groupTexture.attachFramebuffer(framebuffer, 1);
     normalTexture.attachFramebuffer(framebuffer, 2);
 
-    const renderable = getIsosurfaceRenderable(ctx, pyramidTex, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, packedGroup);
+    const renderable = getIsosurfaceRenderable(ctx, pyramidTex, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup);
     ctx.state.currentRenderItemId = -1;
 
     const { drawBuffers } = ctx.extensions;
@@ -201,7 +204,7 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
  *
  * Implementation based on http://www.miaumiau.cat/2016/10/stream-compaction-in-webgl/
  */
-export function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, gridTexScale: Vec2, transform: Mat4, isoValue: number, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
+export function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, gridTexScale: Vec2, transform: Mat4, isoValue: number, invert: boolean, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
     // console.time('calcActiveVoxels');
     const activeVoxelsTex = calcActiveVoxels(ctx, volumeData, gridDim, gridTexDim, isoValue, gridTexScale);
     // ctx.waitForGpuCommandsCompleteSync();
@@ -213,7 +216,7 @@ export function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDi
     // console.timeEnd('createHistogramPyramid');
 
     // console.time('createIsosurfaceBuffers');
-    const gv = createIsosurfaceBuffers(ctx, activeVoxelsTex, volumeData, compacted, gridDim, gridTexDim, transform, isoValue, packedGroup, vertexTexture, groupTexture, normalTexture);
+    const gv = createIsosurfaceBuffers(ctx, activeVoxelsTex, volumeData, compacted, gridDim, gridTexDim, transform, isoValue, invert, packedGroup, vertexTexture, groupTexture, normalTexture);
     // ctx.waitForGpuCommandsCompleteSync();
     // console.timeEnd('createIsosurfaceBuffers');
 

src/mol-gl/shader/marching-cubes/isosurface.frag.ts

@@ -18,6 +18,7 @@ uniform float uIsoValue;
 uniform float uLevels;
 uniform float uSize;
 uniform float uCount;
+uniform bool uInvert;
 
 uniform vec3 uGridDim;
 uniform vec3 uGridTexDim;
@@ -163,6 +164,13 @@ void main(void) {
     // current vertex for the up to 15 MC cases
     int currentVertex = vI - idot4(m, starts);
 
+    // ensure winding-order is the same for negative and positive iso-levels
+    if (uInvert) {
+        int v = imod(currentVertex + 1, 3);
+        if (v == 1) currentVertex += 2;
+        else if (v == 0) currentVertex -= 2;
+    }
+
     // get index into triIndices table
     int mcIndex = 16 * int(edgeIndex) + currentVertex;
     vec4 mcData = texture2D(tTriIndices, vec2(imod(mcIndex, 64), mcIndex / 64) / 64.);
@@ -273,11 +281,18 @@ void main(void) {
         voxelPadded(b1 - c3).a - voxelPadded(b1 + c3).a,
         voxelPadded(b1 - c4).a - voxelPadded(b1 + c4).a
     ));
-    mat3 normalMatrix = transpose3(inverse3(mat3(uGridTransform)));
-    gl_FragData[2].xyz = normalMatrix * -vec3(
+    gl_FragData[2].xyz = -vec3(
         n0.x + t * (n0.x - n1.x),
         n0.y + t * (n0.y - n1.y),
         n0.z + t * (n0.z - n1.z)
     );
+
+    // ensure normal-direction is the same for negative and positive iso-levels
+    if (uInvert) {
+        gl_FragData[2].xyz *= -1.0;
+    }
+
+    // apply normal matrix
+    gl_FragData[2].xyz *= transpose3(inverse3(mat3(uGridTransform)));
 }
 `;

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

@@ -17,7 +17,7 @@ const SdfString = `
 M  CHG  3   1  -1   3  -1   5  -1
 M  END
 > <DATABASE_ID>
-DB14523
+0
 
 > <DATABASE_NAME>
 drugbank
@@ -112,7 +112,24 @@ Phosphate ion
 > <SYNONYMS>
 Orthophosphate; Phosphate
 
-$$$$`;
+$$$$
+
+Comp 2
+
+5  4  0  0  0  0            999 V2000
+  0.0000    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
+ -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  0.0000   -0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
+  0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
+  0.8250    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
+4  1  1  0  0  0  0
+4  2  2  0  0  0  0
+4  3  1  0  0  0  0
+4  5  1  0  0  0  0
+M  CHG  3   1  -1   3  -1   5  -1
+M  END
+> <DATABASE_ID>
+1`;
 
 describe('sdf reader', () => {
     it('basic', async () => {
@@ -120,14 +137,20 @@ describe('sdf reader', () => {
         if (parsed.isError) {
             throw new Error(parsed.message);
         }
-        const compound = parsed.result.compounds[0];
-        const { molFile, dataItems } = compound;
+        const compound1 = parsed.result.compounds[0];
+        const compound2 = parsed.result.compounds[1];
+        const { molFile, dataItems } = compound1;
         const { atoms, bonds } = molFile;
 
+        expect(parsed.result.compounds.length).toBe(2);
+
         // number of structures
         expect(atoms.count).toBe(5);
         expect(bonds.count).toBe(4);
 
+        expect(compound2.molFile.atoms.count).toBe(5);
+        expect(compound2.molFile.bonds.count).toBe(4);
+
         expect(atoms.x.value(0)).toBeCloseTo(0, 0.001);
         expect(atoms.y.value(0)).toBeCloseTo(0.8250, 0.0001);
         expect(atoms.z.value(0)).toBeCloseTo(0, 0.0001);
@@ -138,12 +161,15 @@ describe('sdf reader', () => {
         expect(bonds.order.value(3)).toBe(1);
 
         expect(dataItems.dataHeader.value(0)).toBe('DATABASE_ID');
-        expect(dataItems.data.value(0)).toBe('DB14523');
+        expect(dataItems.data.value(0)).toBe('0');
 
         expect(dataItems.dataHeader.value(1)).toBe('DATABASE_NAME');
         expect(dataItems.data.value(1)).toBe('drugbank');
 
         expect(dataItems.dataHeader.value(31)).toBe('SYNONYMS');
         expect(dataItems.data.value(31)).toBe('Orthophosphate; Phosphate');
+
+        expect(compound1.dataItems.data.value(0)).toBe('0');
+        expect(compound2.dataItems.data.value(0)).toBe('1');
     });
 });

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

@@ -22,6 +22,7 @@ export interface SdfFile {
     }[]
 }
 
+const delimiter = '$$$$';
 function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, data: Column<string> } {
     const dataHeader = TokenBuilder.create(tokenizer.data, 32);
     const data = TokenBuilder.create(tokenizer.data, 32);
@@ -29,6 +30,7 @@ function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, da
     let sawHeaderToken = false;
     while (tokenizer.position < tokenizer.length) {
         const line = Tokenizer.readLine(tokenizer);
+        if (line.startsWith(delimiter)) break;
         if (!!line) {
             if (line.startsWith('> <')) {
                 TokenBuilder.add(dataHeader, tokenizer.tokenStart + 3, tokenizer.tokenEnd - 1);
@@ -49,9 +51,7 @@ function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, da
     };
 }
 
-function handleMolFile(data: string) {
-    const tokenizer = Tokenizer(data);
-
+function handleMolFile(tokenizer: Tokenizer) {
     const title = Tokenizer.readLine(tokenizer).trim();
     const program = Tokenizer.readLine(tokenizer).trim();
     const comment = Tokenizer.readLine(tokenizer).trim();
@@ -60,6 +60,15 @@ function handleMolFile(data: string) {
 
     const atomCount = +counts.substr(0, 3), bondCount = +counts.substr(3, 3);
 
+    if (Number.isNaN(atomCount) || Number.isNaN(bondCount)) {
+        // try to skip to next molecule
+        while (tokenizer.position < tokenizer.length) {
+            const line = Tokenizer.readLine(tokenizer);
+            if (line.startsWith(delimiter)) break;
+        }
+        return;
+    }
+
     const atoms = handleAtoms(tokenizer, atomCount);
     const bonds = handleBonds(tokenizer, bondCount);
     const dataItems = handleDataItems(tokenizer);
@@ -70,10 +79,16 @@ function handleMolFile(data: string) {
     };
 }
 
-const delimiter = '$$$$';
 function parseInternal(data: string): Result<SdfFile> {
-    const result: SdfFile = { compounds: data.split(delimiter).map(d => handleMolFile(d)) };
-    return Result.success(result);
+    const tokenizer = Tokenizer(data);
+
+    const compounds: SdfFile['compounds'] = [];
+    while (tokenizer.position < tokenizer.length) {
+        const c = handleMolFile(tokenizer);
+        if (c) compounds.push(c);
+    }
+
+    return Result.success({ compounds });
 }
 
 export function parseSdf(data: string) {

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

@@ -54,6 +54,12 @@ const StandardComponents = (function() {
         { id: 'SEC', name: 'SELENOCYSTEINE', type: 'L-peptide linking' },
         { id: 'PYL', name: 'PYRROLYSINE', type: 'L-peptide linking' },
 
+        { id: 'MSE', name: 'SELENOMETHIONINE', type: 'L-peptide linking' },
+        { id: 'SEP', name: 'PHOSPHOSERINE', type: 'L-peptide linking' },
+        { id: 'TPO', name: 'PHOSPHOTHREONINE', type: 'L-peptide linking' },
+        { id: 'PTR', name: 'O-PHOSPHOTYROSINE', type: 'L-peptide linking' },
+        { id: 'PCA', name: 'PYROGLUTAMIC ACID', type: 'L-peptide linking' },
+
         { id: 'A', name: 'ADENOSINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
         { id: 'C', name: 'CYTIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
         { id: 'T', name: 'THYMIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },

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

@@ -245,7 +245,9 @@ export const WaterNames = new Set([
 export const AminoAcidNamesL = new Set([
     'HIS', 'ARG', 'LYS', 'ILE', 'PHE', 'LEU', 'TRP', 'ALA', 'MET', 'PRO', 'CYS',
     'ASN', 'VAL', 'GLY', 'SER', 'GLN', 'TYR', 'ASP', 'GLU', 'THR', 'SEC', 'PYL',
-    'UNK' // unknown amino acid from CCD
+    'UNK', // unknown amino acid from CCD
+    'MSE', 'SEP', 'TPO', 'PTR', 'PCA' // common
+
 ]);
 export const AminoAcidNamesD = new Set([
     'DAL', // D-ALANINE

src/mol-plugin-state/animation/built-in/state-interpolation.ts

@@ -6,12 +6,13 @@
 
 import { PluginCommands } from '../../../mol-plugin/commands';
 import { StateTransform } from '../../../mol-state';
+import { shallowEqual } from '../../../mol-util';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginStateAnimation } from '../model';
 
 export const AnimateStateInterpolation = PluginStateAnimation.create({
     name: 'built-in.animate-state-interpolation',
-    display: { name: 'Animate State Interpolation' },
+    display: { name: 'Animate State (experimental)' },
     params: () => ({
         transtionDurationInMs: PD.Numeric(2000, { min: 100, max: 30000, step: 10 })
     }),
@@ -42,15 +43,25 @@ export const AnimateStateInterpolation = PluginStateAnimation.create({
 
         for (const s of src) {
             for (const t of tar) {
+                // TODO: better than quadratic alg.
+                // TODO: support for adding/removing nodes
                 if (t.ref !== s.ref) continue;
                 if (t.version === s.version) continue;
 
                 const e = StateTransform.fromJSON(s), f = StateTransform.fromJSON(t);
 
+                const oldState = state.cells.get(s.ref);
+                if (!oldState) continue;
+
+                let newState;
                 if (!e.transformer.definition.interpolate) {
-                    update.to(s.ref).update(currentT <= 0.5 ? e.params : f.params);
+                    newState = currentT <= 0.5 ? e.params : f.params;
                 } else {
-                    update.to(s.ref).update(e.transformer.definition.interpolate(e.params, f.params, currentT, ctx.plugin));
+                    newState = e.transformer.definition.interpolate(e.params, f.params, currentT, ctx.plugin);
+                }
+
+                if (!shallowEqual(oldState, newState)) {
+                    update.to(s.ref).update(newState);
                 }
             }
         }

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

@@ -123,14 +123,23 @@ export const GroProvider: TrajectoryFormatProvider = {
 };
 
 export const MolProvider: TrajectoryFormatProvider = {
-    label: 'MOL/SDF',
-    description: 'MOL/SDF',
+    label: 'MOL',
+    description: 'MOL',
     category: TrajectoryFormatCategory,
-    stringExtensions: ['mol', 'sdf', 'sd'],
+    stringExtensions: ['mol'],
     parse: directTrajectory(StateTransforms.Model.TrajectoryFromMOL),
     visuals: defaultVisuals
 };
 
+export const SdfProvider: TrajectoryFormatProvider = {
+    label: 'SDF',
+    description: 'SDF',
+    category: TrajectoryFormatCategory,
+    stringExtensions: ['sdf', 'sd'],
+    parse: directTrajectory(StateTransforms.Model.TrajectoryFromSDF),
+    visuals: defaultVisuals
+};
+
 export const Mol2Provider: TrajectoryFormatProvider = {
     label: 'MOL2',
     description: 'MOL2',
@@ -148,6 +157,7 @@ export const BuiltInTrajectoryFormats = [
     ['gro', GroProvider] as const,
     ['xyz', XyzProvider] as const,
     ['mol', MolProvider] as const,
+    ['sdf', SdfProvider] as const,
     ['mol2', Mol2Provider] as const,
 ] as const;
 

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

@@ -39,6 +39,7 @@ import { parseXtc } from '../../mol-io/reader/xtc/parser';
 import { coordinatesFromXtc } from '../../mol-model-formats/structure/xtc';
 import { parseXyz } from '../../mol-io/reader/xyz/parser';
 import { trajectoryFromXyz } from '../../mol-model-formats/structure/xyz';
+import { parseSdf } from '../../mol-io/reader/sdf/parser';
 
 export { CoordinatesFromDcd };
 export { CoordinatesFromXtc };
@@ -50,6 +51,7 @@ export { TrajectoryFromPDB };
 export { TrajectoryFromGRO };
 export { TrajectoryFromXYZ };
 export { TrajectoryFromMOL };
+export { TrajectoryFromSDF };
 export { TrajectoryFromMOL2 };
 export { TrajectoryFromCube };
 export { TrajectoryFromCifCore };
@@ -292,6 +294,36 @@ const TrajectoryFromMOL = PluginStateTransform.BuiltIn({
     }
 });
 
+type TrajectoryFromSDF = typeof TrajectoryFromSDF
+const TrajectoryFromSDF = PluginStateTransform.BuiltIn({
+    name: 'trajectory-from-sdf',
+    display: { name: 'Parse SDF', description: 'Parse SDF string and create trajectory.' },
+    from: [SO.Data.String],
+    to: SO.Molecule.Trajectory
+})({
+    apply({ a }) {
+        return Task.create('Parse SDF', async ctx => {
+            const parsed = await parseSdf(a.data).runInContext(ctx);
+            if (parsed.isError) throw new Error(parsed.message);
+
+            const models: Model[] = [];
+
+            for (const { molFile } of parsed.result.compounds) {
+                const traj = await trajectoryFromMol(molFile).runInContext(ctx);
+                for (let i = 0; i < traj.frameCount; i++) {
+                    models.push(await Task.resolveInContext(traj.getFrameAtIndex(i), ctx));
+                }
+            }
+
+            const traj = new ArrayTrajectory(models);
+
+            const props = trajectoryProps(traj);
+            return new SO.Molecule.Trajectory(traj, props);
+        });
+    }
+});
+
+
 type TrajectoryFromMOL2 = typeof TrajectoryFromMOL
 const TrajectoryFromMOL2 = PluginStateTransform.BuiltIn({
     name: 'trajectory-from-mol2',
@@ -382,6 +414,10 @@ const ModelFromTrajectory = PluginStateTransform.BuiltIn({
             return new SO.Molecule.Model(model, { label, description });
         });
     },
+    interpolate(a, b, t) {
+        const modelIndex = t >= 1 ? b.modelIndex : a.modelIndex + Math.floor((b.modelIndex - a.modelIndex + 1) * t);
+        return { modelIndex };
+    },
     dispose({ b }) {
         b?.data.customProperties.dispose();
     }

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

@@ -151,7 +151,7 @@ const VolumeFromDensityServerCif = PluginStateTransform.BuiltIn({
             const densityServerCif = CIF.schema.densityServer(block);
             const volume = await volumeFromDensityServerData(densityServerCif, { entryId: params.entryId }).runInContext(ctx);
             const [x, y, z] = volume.grid.cells.space.dimensions;
-            const props = { label: densityServerCif.volume_data_3d_info.name.value(0), description: `Volume ${x}\u00D7${y}\u00D7${z}` };
+            const props = { label: params.entryId ?? densityServerCif.volume_data_3d_info.name.value(0), description: `Volume ${x}\u00D7${y}\u00D7${z}` };
             return new SO.Volume.Data(volume, props);
         });
     },

src/mol-plugin/spec.ts

@@ -21,6 +21,7 @@ import { StateActions } from '../mol-plugin-state/actions';
 import { AssignColorVolume } from '../mol-plugin-state/actions/volume';
 import { StateTransforms } from '../mol-plugin-state/transforms';
 import { BoxifyVolumeStreaming, CreateVolumeStreamingBehavior, InitVolumeStreaming } from '../mol-plugin/behavior/dynamic/volume-streaming/transformers';
+import { AnimateStateInterpolation } from '../mol-plugin-state/animation/built-in/state-interpolation';
 
 export { PluginSpec };
 
@@ -126,6 +127,7 @@ export const DefaultPluginSpec = (): PluginSpec => ({
         AnimateModelIndex,
         AnimateCameraSpin,
         AnimateStateSnapshots,
-        AnimateAssemblyUnwind
+        AnimateAssemblyUnwind,
+        AnimateStateInterpolation
     ]
 });

src/mol-repr/structure/visual/gaussian-surface-mesh.ts

@@ -182,7 +182,7 @@ async function createGaussianSurfaceTextureMesh(ctx: VisualContext, unit: Unit,
     const isoLevel = Math.exp(-props.smoothness) / densityTextureData.radiusFactor;
 
     const buffer = textureMesh?.doubleBuffer.get();
-    const gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, true, buffer?.vertex, buffer?.group, buffer?.normal);
+    const gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, buffer?.vertex, buffer?.group, buffer?.normal);
 
     const boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
     const surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
@@ -241,7 +241,7 @@ async function createStructureGaussianSurfaceTextureMesh(ctx: VisualContext, str
     const isoLevel = Math.exp(-props.smoothness) / densityTextureData.radiusFactor;
 
     const buffer = textureMesh?.doubleBuffer.get();
-    const gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, true, buffer?.vertex, buffer?.group, buffer?.normal);
+    const gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, buffer?.vertex, buffer?.group, buffer?.normal);
 
     const boundingSphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
     const surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);

src/mol-repr/volume/isosurface.ts

@@ -176,7 +176,7 @@ async function createVolumeIsosurfaceTextureMesh(ctx: VisualContext, volume: Vol
     const { texture, gridDimension, gridTexDim, gridTexScale, transform } = VolumeIsosurfaceTexture.get(volume, ctx.webgl);
 
     const buffer = textureMesh?.doubleBuffer.get();
-    const gv = extractIsosurface(ctx.webgl, texture, gridDimension, gridTexDim, gridTexScale, transform, isoLevel, false, buffer?.vertex, buffer?.group, buffer?.normal);
+    const gv = extractIsosurface(ctx.webgl, texture, gridDimension, gridTexDim, gridTexScale, transform, isoLevel, value < 0, false, buffer?.vertex, buffer?.group, buffer?.normal);
 
     const surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, Volume.getBoundingSphere(volume), textureMesh);
 

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

@@ -11,7 +11,7 @@ import { MolScriptSymbolTable as MolScript } from '../../language/symbol-table';
 import { Type } from '../../language/type';
 import { Types as StructureQueryTypes } from '../../language/symbol-table/structure-query';
 import { MolScriptBuilder as B } from '../../language/builder';
-import { getPositionalArgs, tryGetArg } from './macro';
+import { getPositionalArgs, tryGetArg } from './script-macro';
 
 export type MolScriptSymbol =
     | { kind: 'alias', aliases: string[], symbol: MSymbol }

src/tests/browser/marching-cubes.ts

@@ -73,7 +73,7 @@ async function init() {
         console.timeEnd('gpu mc pyramid2');
 
         console.time('gpu mc vert2');
-        createIsosurfaceBuffers(webgl, activeVoxelsTex2, densityTextureData2.texture, compacted2, densityTextureData2.gridDim, densityTextureData2.gridTexDim, densityTextureData2.transform, isoValue, true);
+        createIsosurfaceBuffers(webgl, activeVoxelsTex2, densityTextureData2.texture, compacted2, densityTextureData2.gridDim, densityTextureData2.gridTexDim, densityTextureData2.transform, isoValue, false, true);
         webgl.waitForGpuCommandsCompleteSync();
         console.timeEnd('gpu mc vert2');
         console.timeEnd('gpu mc2');
@@ -96,7 +96,7 @@ async function init() {
     console.timeEnd('gpu mc pyramid');
 
     console.time('gpu mc vert');
-    const gv = createIsosurfaceBuffers(webgl, activeVoxelsTex, densityTextureData.texture, compacted, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.transform, isoValue, true);
+    const gv = createIsosurfaceBuffers(webgl, activeVoxelsTex, densityTextureData.texture, compacted, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.transform, isoValue, false, true);
     webgl.waitForGpuCommandsCompleteSync();
     console.timeEnd('gpu mc vert');
     console.timeEnd('gpu mc');