ability to load more PDB ids at once (as separate structures), various tweaks

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

@@ -28,10 +28,11 @@ export const InitVolumeStreaming = StateAction.build({
     params(a) {
         return {
             method: PD.Select<VolumeServerInfo.Kind>(getStreamingMethod(a && a.data), [['em', 'EM'], ['x-ray', 'X-Ray']]),
-            id: PD.Text((a && a.data.models[0].label) || ''),
+            id: PD.Text((a && a.data.models.length > 0 && a.data.models[0].label) || ''),
             serverUrl: PD.Text('https://webchem.ncbr.muni.cz/DensityServer')
         };
-    }
+    },
+    isApplicable: (a) => a.data.models.length === 1
 })(({ ref, state, params }, plugin: PluginContext) => Task.create('Volume Streaming', async taskCtx => {
     // TODO: custom react view for this and the VolumeStreamingBehavior transformer
 

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

@@ -105,29 +105,41 @@ const DownloadStructure = StateAction.build({
 })(({ params, state }, ctx: PluginContext) => {
     const b = state.build();
     const src = params.source;
-    let downloadParams: StateTransformer.Params<Download>;
+    let downloadParams: StateTransformer.Params<Download>[];
 
     switch (src.name) {
         case 'url':
-            downloadParams = { url: src.params.url, isBinary: src.params.isBinary };
+            downloadParams = [{ url: src.params.url, isBinary: src.params.isBinary }];
             break;
         case 'pdbe-updated':
-            downloadParams = { url: `https://www.ebi.ac.uk/pdbe/static/entry/${src.params.id.toLowerCase()}_updated.cif`, isBinary: false, label: `PDBe: ${src.params.id}` };
+            downloadParams = getDownloadParams(src.params.id, id => `https://www.ebi.ac.uk/pdbe/static/entry/${id.toLowerCase()}_updated.cif`, id => `PDBe: ${id}`, false);
             break;
         case 'rcsb':
-            downloadParams = { url: `https://files.rcsb.org/download/${src.params.id.toUpperCase()}.cif`, isBinary: false, label: `RCSB: ${src.params.id}` };
+            downloadParams = getDownloadParams(src.params.id, id => `https://files.rcsb.org/download/${id.toUpperCase()}.cif`, id => `RCSB: ${id}`, false);
             break;
         case 'bcif-static':
-            downloadParams = { url: `https://webchem.ncbr.muni.cz/ModelServer/static/bcif/${src.params.id.toLowerCase()}`, isBinary: true, label: `BinaryCIF: ${src.params.id}` };
+            downloadParams = getDownloadParams(src.params.id, id => `https://webchem.ncbr.muni.cz/ModelServer/static/bcif/${id.toLowerCase()}`, id => `BinaryCIF: ${id}`, true);
             break;
         default: throw new Error(`${(src as any).name} not supported.`);
     }
 
-    const data = b.toRoot().apply(StateTransforms.Data.Download, downloadParams, { props: { isGhost: true }});
-    const traj = createModelTree(data, src.name === 'url' ? src.params.format : 'cif');
-    return state.updateTree(createStructureTree(ctx, traj, params.source.params.supportProps));
+    for (const download of downloadParams) {
+        const data = b.toRoot().apply(StateTransforms.Data.Download, download, { props: { isGhost: true }});
+        const traj = createModelTree(data, src.name === 'url' ? src.params.format : 'cif');
+        createStructureTree(ctx, traj, params.source.params.supportProps)
+    }
+    return state.updateTree(b);
 });
 
+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);
+    const ret: StateTransformer.Params<Download>[] = [];
+    for (const id of ids) {
+        ret.push({ url: url(id), isBinary, label: label(id) })
+    }
+    return ret;
+}
+
 function createModelTree(b: StateBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, format: 'pdb' | 'cif' | 'gro' = 'cif') {
     let parsed: StateBuilder.To<PluginStateObject.Molecule.Trajectory>
     switch (format) {

src/mol-plugin/state/snapshots.ts

@@ -178,7 +178,7 @@ class PluginStateSnapshotManager extends PluginComponent<{
         const snapshot = this.setCurrent(next)!;
         await this.plugin.state.setSnapshot(snapshot);
         const delay = typeof snapshot.durationInMs !== 'undefined' ? snapshot.durationInMs : this.state.nextSnapshotDelayInMs;
-        this.timeoutHandle = setTimeout(this.next, delay);
+        if (this.state.isPlaying) this.timeoutHandle = setTimeout(this.next, delay);
     };
 
     play() {

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

@@ -266,7 +266,6 @@ const UserStructureSelection = PluginStateTransform.BuiltIn({
         const compiled = compile<Sel>(query);
         const result = compiled(new QueryContext(a.data));
         const s = Sel.unionStructure(result);
-        if (s.elementCount === 0) return StateObject.Null;
         const props = { label: `${params.label || 'Selection'}`, description: structureDesc(s) };
         return new SO.Molecule.Structure(s, props);
     }

src/mol-script/language/parser.ts

@@ -163,7 +163,7 @@ namespace Language {
     }
 
     function isNumber(value: string) {
-        return /-?(0|[1-9][0-9]*)([.][0-9]+)?([eE][+-]?[0-9]+)?/.test(value);
+        return /-?(0|[1-9][0-9]*)([.][0-9]+)?([eE][+-]?[0-9]+)?/.test(value) && !isNaN(+value);
     }
 
     export function parse(input: string): Expression[] {