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",
+  "version": "2.0.2",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
-      "version": "2.0.0",
+      "version": "2.0.2",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^1.0.38",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.0",
+  "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/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-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
@@ -127,7 +127,9 @@ Comp 2
 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`;
+M  END
+> <DATABASE_ID>
+1`;
 
 describe('sdf reader', () => {
     it('basic', async () => {
@@ -159,12 +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-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/transforms/model.ts

@@ -414,6 +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
     ]
 });