0.7.1-dev.2

- so the build contains the correct version number

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.20",
+  "version": "0.7.1-dev.2",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.20",
+  "version": "0.7.1-dev.2",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -34,7 +34,8 @@
     "model-server-watch": "nodemon --watch lib lib/servers/servers/model/server.js",
     "volume-server-test": "node lib/servers/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
     "plugin-state": "node lib/servers/servers/plugin-state/index.js",
-    "preversion": "npm run test && npm run build",
+    "preversion": "npm run test",
+    "version": "npm run build",
     "postversion": "git push && git push --tags"
   },
   "files": [

src/apps/viewer/index.html

@@ -45,6 +45,9 @@
                 return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
             }
 
+            var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
+            if (debugMode) molstar.setDebugMode(debugMode);
+
             var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
             var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
             var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
@@ -59,7 +62,7 @@
             if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
 
             var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
-            var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim();
+            var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
             if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
 
             var structureUrl = getParam('structure-url', '[^&]+').trim();

src/apps/viewer/index.ts

@@ -23,8 +23,12 @@ import { ObjectKeys } from '../../mol-util/type-helpers';
 import { PluginState } from '../../mol-plugin/state';
 import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
 import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+
 require('mol-plugin-ui/skin/light.scss');
 
+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
+export { setProductionMode, setDebugMode } from '../../mol-util/debug';
+
 const Extensions = {
     'cellpack': PluginSpec.Behavior(CellPack),
     'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),

src/mol-canvas3d/canvas3d.ts

@@ -362,10 +362,19 @@ namespace Canvas3D {
 
             camera.setState({ radiusMax: scene.boundingSphere.radius }, 0);
             reprCount.next(reprRenderObjects.size);
+            if (isDebugMode) consoleStats();
 
             return true;
         }
 
+        function consoleStats() {
+            console.table(scene.renderables.map(r => ({
+                drawCount: r.values.drawCount.ref.value,
+                instanceCount: r.values.instanceCount.ref.value,
+                materialId: r.materialId,
+            })));
+        }
+
         function add(repr: Representation.Any) {
             registerAutoUpdate(repr);
 
@@ -384,6 +393,7 @@ namespace Canvas3D {
             reprRenderObjects.set(repr, newRO);
 
             scene.update(repr.renderObjects, false);
+            if (isDebugMode) consoleStats();
         }
 
         function remove(repr: Representation.Any) {
@@ -394,6 +404,7 @@ namespace Canvas3D {
                 renderObjects.forEach(o => scene.remove(o));
                 reprRenderObjects.delete(repr);
                 scene.update(repr.renderObjects, false, true);
+                if (isDebugMode) consoleStats();
             }
         }
 

src/mol-model/sequence/alignment/sequence.ts

@@ -24,16 +24,26 @@ namespace AlignSequences {
 
     function createSeqIdIndicesMap(element: StructureElement.Loci.Element) {
         const seqIds = new Map<number, StructureElement.UnitIndex[]>();
-        if (!Unit.isAtomic(element.unit)) return seqIds;
-
-        const { label_seq_id } = element.unit.model.atomicHierarchy.residues;
-        const { residueIndex } = element.unit;
-        for (let i = 0, il = OrderedSet.size(element.indices); i < il; ++i) {
-            const uI = OrderedSet.getAt(element.indices, i);
-            const eI = element.unit.elements[uI];
-            const seqId = label_seq_id.value(residueIndex[eI]);
-            if (seqIds.has(seqId)) seqIds.get(seqId)!.push(uI);
-            else seqIds.set(seqId, [uI]);
+        if (Unit.isAtomic(element.unit)) {
+            const { label_seq_id } = element.unit.model.atomicHierarchy.residues;
+            const { residueIndex } = element.unit;
+            for (let i = 0, il = OrderedSet.size(element.indices); i < il; ++i) {
+                const uI = OrderedSet.getAt(element.indices, i);
+                const eI = element.unit.elements[uI];
+                const seqId = label_seq_id.value(residueIndex[eI]);
+                if (seqIds.has(seqId)) seqIds.get(seqId)!.push(uI);
+                else seqIds.set(seqId, [uI]);
+            }
+        } else if (Unit.isCoarse(element.unit)) {
+            const { seq_id_begin } = Unit.isSpheres(element.unit)
+                ? element.unit.model.coarseHierarchy.spheres
+                : element.unit.model.coarseHierarchy.gaussians;
+            for (let i = 0, il = OrderedSet.size(element.indices); i < il; ++i) {
+                const uI = OrderedSet.getAt(element.indices, i);
+                const eI = element.unit.elements[uI];
+                const seqId = seq_id_begin.value(eI);
+                seqIds.set(seqId, [uI]);
+            }
         }
         return seqIds;
     }

src/mol-plugin-state/manager/snapshots.ts

@@ -231,6 +231,8 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
 
                 if (PluginStateSnapshotManager.isStateSnapshot(snapshot)) {
                     return this.setStateSnapshot(snapshot);
+                } else if (PluginStateSnapshotManager.isStateSnapshot(snapshot.data)) {
+                    return this.setStateSnapshot(snapshot.data);
                 } else {
                     this.plugin.state.setSnapshot(snapshot);
                 }
@@ -330,7 +332,7 @@ namespace PluginStateSnapshotManager {
         snapshot: PluginState.Snapshot
     }
 
-    export function Entry(snapshot: PluginState.Snapshot, params: {name?: string, description?: string }): Entry {
+    export function Entry(snapshot: PluginState.Snapshot, params: { name?: string, description?: string }): Entry {
         return { timestamp: +new Date(), snapshot, ...params };
     }
 

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

@@ -42,7 +42,7 @@ 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.data.name || a.label }).runInContext(ctx);
-            const props = { label: volume.label || 'Volume', description: 'Volume' };
+            const props = { label: volume.label || 'Volume', description: `Volume ${a.data.header.NX}\u00D7${a.data.header.NX}\u00D7${a.data.header.NX}` };
             return new SO.Volume.Data(volume, props);
         });
     }
@@ -63,7 +63,7 @@ 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.data.name || a.label }).runInContext(ctx);
-            const props = { label: volume.label || 'Volume', description: 'Volume' };
+            const props = { label: volume.label || 'Volume', description: `Volume ${a.data.header.xExtent}\u00D7${a.data.header.yExtent}\u00D7${a.data.header.zExtent}` };
             return new SO.Volume.Data(volume, props);
         });
     }
@@ -85,7 +85,7 @@ 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.data.name || a.label }).runInContext(ctx);
-            const props = { label: volume.label || 'Volume', description: 'Volume' };
+            const props = { label: volume.label || 'Volume', description: `Volume ${a.data.header.dim[0]}\u00D7${a.data.header.dim[1]}\u00D7${a.data.header.dim[2]}` };
             return new SO.Volume.Data(volume, props);
         });
     }
@@ -102,8 +102,7 @@ const VolumeFromDx = PluginStateTransform.BuiltIn({
         return Task.create('Parse DX', async 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' };
+            const props = { label: volume.label || 'Volume', description: `Volume ${a.data.header.dim[0]}\u00D7${a.data.header.dim[1]}\u00D7${a.data.header.dim[2]}` };
             return new SO.Volume.Data(volume, props);
         });
     }
@@ -135,7 +134,8 @@ const VolumeFromDensityServerCif = PluginStateTransform.BuiltIn({
             if (!block) throw new Error(`Data block '${[header]}' not found.`);
             const densityServerCif = CIF.schema.densityServer(block);
             const volume = await volumeFromDensityServerData(densityServerCif).runInContext(ctx);
-            const props = { label: densityServerCif.volume_data_3d_info.name.value(0), description: `${densityServerCif.volume_data_3d_info.name.value(0)}` };
+            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}` };
             return new SO.Volume.Data(volume, props);
         });
     }

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

@@ -172,7 +172,7 @@ export class MeasurementControls extends PurePluginUIComponent<{}, { isBusy: boo
                 {entries}
             </div>}
             {entries.length === 0 && <div className='msp-control-offset msp-help-text'>
-                <div className='msp-help-description' style={{ padding: 0 }}><Icon svg={HelpOutline} inline />Add one or more selections <ToggleSelectionModeButton /></div>
+                <div className='msp-help-description'><Icon svg={HelpOutline} inline />Add one or more selections (toggle <ToggleSelectionModeButton inline /> mode)</div>
             </div>}
         </>;
     }

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

@@ -30,7 +30,7 @@ import Structure from '../../mol-model/structure/structure/structure';
 import { ViewportHelpContent, HelpGroup, HelpText } from '../viewport/help';
 
 
-export class ToggleSelectionModeButton extends PurePluginUIComponent {
+export class ToggleSelectionModeButton extends PurePluginUIComponent<{ inline?: boolean }> {
     componentDidMount() {
         this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
         this.subscribe(this.plugin.layout.events.updated, () => this.forceUpdate());
@@ -42,7 +42,10 @@ export class ToggleSelectionModeButton extends PurePluginUIComponent {
     }
 
     render() {
-        return <IconButton svg={CursorSvg} onClick={this._toggleSelMode} title={'Toggle Selection Mode'} style={{ background: 'transparent' }} toggleState={this.plugin.selectionMode} />;
+        const style = this.props.inline
+            ? { background: 'transparent', width: 'auto', height: 'auto', lineHeight: 'unset' }
+            : { background: 'transparent' };
+        return <IconButton svg={CursorSvg} onClick={this._toggleSelMode} title={'Toggle Selection Mode'} style={style} toggleState={this.plugin.selectionMode} />;
     }
 }
 

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

@@ -278,7 +278,7 @@ export class SuperpositionControls extends PurePluginUIComponent<{}, Superpositi
                 {entries.map((e, i) => this.lociEntry(e, i))}
             </div>}
             {entries.length < 2 && <div className='msp-control-offset msp-help-text'>
-                <div className='msp-help-description'><Icon svg={HelpOutline} inline />Add 2 or more selections <ToggleSelectionModeButton /> from separate structures. Selections must be limited to single polymer chains or residues therein.</div>
+                <div className='msp-help-description'><Icon svg={HelpOutline} inline />Add 2 or more selections (toggle <ToggleSelectionModeButton inline /> mode) from separate structures. Selections must be limited to single polymer chains or residues therein.</div>
             </div>}
             {entries.length > 1 && <Button title='Superpose structures by selected chains.' className='msp-btn-commit msp-btn-commit-on' onClick={this.superposeChains} style={{ marginTop: '1px' }}>
                 Superpose
@@ -293,7 +293,7 @@ export class SuperpositionControls extends PurePluginUIComponent<{}, Superpositi
                 {entries.map((e, i) => this.atomsLociEntry(e, i))}
             </div>}
             {entries.length < 2 && <div className='msp-control-offset msp-help-text'>
-                <div className='msp-help-description'><Icon svg={HelpOutline} inline />Add 1 or more selections <ToggleSelectionModeButton /> from
+                <div className='msp-help-description'><Icon svg={HelpOutline} inline />Add 1 or more selections (toggle <ToggleSelectionModeButton inline /> mode) from
                 separate structures. Selections must be limited to single atoms.</div>
             </div>}
             {entries.length > 1 && <Button title='Superpose structures by selected atoms.' className='msp-btn-commit msp-btn-commit-on' onClick={this.superposeAtoms} style={{ marginTop: '1px' }}>

src/mol-util/debug.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -16,13 +16,12 @@ let isProductionMode = process.env.NODE_ENV === 'production';
  */
 let isDebugMode = process.env.DEBUG === '*' || process.env.DEBUG === 'molstar';
 
-if (typeof window !== 'undefined' && !(window as any).setMolStarDebugMode) {
-    try {
-        (window as any).setMolStarDebugMode = function setMolStarDebugMode(isDebug?: boolean, isProduction?: boolean) {
-            if (typeof isDebug !== 'undefined') isDebugMode = isDebug;
-            if (typeof isProduction !== 'undefined') isProductionMode = isProduction;
-        };
-    } catch { }
+export { isProductionMode, isDebugMode };
+
+export function setProductionMode(value?: boolean) {
+    if (typeof value !== 'undefined') isProductionMode = value;
 }
 
-export { isProductionMode, isDebugMode };
+export function setDebugMode(value?: boolean) {
+    if (typeof value !== 'undefined') isDebugMode = value;
+}