xtc format support

+ build tweaks

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

@@ -0,0 +1,34 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Task } from '../../mol-task';
+import { XtcFile } from '../../mol-io/reader/xtc/parser';
+import { Coordinates, Frame, Time } from '../../mol-model/structure/coordinates';
+import { Cell } from '../../mol-math/geometry/spacegroup/cell';
+
+export function coordinatesFromXtc(file: XtcFile): Task<Coordinates> {
+    return Task.create('Parse XTC', async ctx => {
+        await ctx.update('Converting to coordinates');
+
+        const deltaTime = Time(file.deltaTime, 'step');
+        const offsetTime = Time(file.timeOffset, deltaTime.unit);
+
+        const frames: Frame[] = [];
+        for (let i = 0, il = file.frames.length; i < il; ++i) {
+            frames.push({
+                elementCount: file.frames[i].count,
+                // TODO:
+                cell: Cell.empty(),
+                x: file.frames[i].x,
+                y: file.frames[i].y,
+                z: file.frames[i].z,
+                time: Time(offsetTime.value + deltaTime.value * i, deltaTime.unit)
+            });
+        }
+
+        return Coordinates.create(frames, deltaTime, offsetTime);
+    });
+}

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

@@ -41,9 +41,24 @@ export const DcdProvider = DataFormatProvider({
     }
 });
 
+export const XtcProvider = DataFormatProvider({
+    label: 'XTC',
+    description: 'XTC',
+    category: Category,
+    binaryExtensions: ['xtc'],
+    parse: (plugin, data) => {
+        const coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(StateTransforms.Model.CoordinatesFromXtc);
+
+        return coordinates.commit();
+    }
+});
+
 export const BuiltInStructureFormats = [
     ['psf', PsfProvider] as const,
     ['dcd', DcdProvider] as const,
+    ['xtc', XtcProvider] as const,
 ] as const;
 
 export type BuildInStructureFormat = (typeof BuiltInStructureFormats)[number][0]

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

@@ -37,8 +37,11 @@ import { trajectoryFromCifCore } from '../../mol-model-formats/structure/cif-cor
 import { trajectoryFromCube } from '../../mol-model-formats/structure/cube';
 import { parseMol2 } from '../../mol-io/reader/mol2/parser';
 import { trajectoryFromMol2 } from '../../mol-model-formats/structure/mol2';
+import { parseXtc } from '../../mol-io/reader/xtc/parser';
+import { coordinatesFromXtc } from '../../mol-model-formats/structure/xtc';
 
 export { CoordinatesFromDcd };
+export { CoordinatesFromXtc };
 export { TopologyFromPsf };
 export { TrajectoryFromModelAndCoordinates };
 export { TrajectoryFromBlob };
@@ -81,6 +84,23 @@ const CoordinatesFromDcd = PluginStateTransform.BuiltIn({
     }
 });
 
+type CoordinatesFromXtc = typeof CoordinatesFromDcd
+const CoordinatesFromXtc = PluginStateTransform.BuiltIn({
+    name: 'coordinates-from-xtc',
+    display: { name: 'Parse XTC', description: 'Parse XTC binary data.' },
+    from: [SO.Data.Binary],
+    to: SO.Molecule.Coordinates
+})({
+    apply({ a }) {
+        return Task.create('Parse XTC', async ctx => {
+            const parsed = await parseXtc(a.data).runInContext(ctx);
+            if (parsed.isError) throw new Error(parsed.message);
+            const coordinates = await coordinatesFromXtc(parsed.result).runInContext(ctx);
+            return new SO.Molecule.Coordinates(coordinates, { label: a.label, description: 'Coordinates' });
+        });
+    }
+});
+
 type TopologyFromPsf = typeof TopologyFromPsf
 const TopologyFromPsf = PluginStateTransform.BuiltIn({
     name: 'topology-from-psf',

webpack.config.common.js

@@ -32,13 +32,14 @@ const sharedConfig = {
             ],
         }),
         new webpack.DefinePlugin({
-            'process.env.DEBUG': JSON.stringify(process.env.DEBUG)
+            'process.env.DEBUG': JSON.stringify(process.env.DEBUG),
+            '__MOLSTAR_DEBUG_TIMESTAMP__': webpack.DefinePlugin.runtimeValue(() => `${new Date().valueOf()}`, true)
         }),
         new MiniCssExtractPlugin({ filename: 'molstar.css',  }),
         new VersionFile({
             extras: { timestamp: `${new Date().valueOf()}` },
             packageFile: path.resolve(__dirname, 'package.json'),
-            templateString: `export const PLUGIN_VERSION = '<%= package.version %>';\nexport const PLUGIN_VERSION_DATE = new Date(<%= extras.timestamp %>);`,
+            templateString: `export const PLUGIN_VERSION = '<%= package.version %>';\nexport const PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : <%= extras.timestamp %>);`,
             outputFile: path.resolve(__dirname, 'lib/mol-plugin/version.js')
         })
     ],

webpack.config.js

@@ -1,6 +1,5 @@
 const { createApp, createExample, createBrowserTest } = require('./webpack.config.common.js');
 
-const apps = ['viewer'];
 const examples = ['proteopedia-wrapper', 'basic-wrapper', 'lighting'];
 const tests = [
     'font-atlas',
@@ -10,7 +9,7 @@ const tests = [
 ];
 
 module.exports = [
-    ...apps.map(createApp),
+    createApp('viewer', 'molstar'),
     ...examples.map(createExample),
     ...tests.map(createBrowserTest)
 ]