From 11d5e301f39149910b5cd1dfa21ef082af40add1 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Sun, 24 May 2020 17:44:29 +0200
Subject: [PATCH] xtc format support + build tweaks
---
src/mol-model-formats/structure/xtc.ts | 34 +++++++++++++++++++++++
src/mol-plugin-state/formats/structure.ts | 15 ++++++++++
src/mol-plugin-state/transforms/model.ts | 20 +++++++++++++
webpack.config.common.js | 5 ++--
webpack.config.js | 3 +-
5 files changed, 73 insertions(+), 4 deletions(-)
create mode 100644 src/mol-model-formats/structure/xtc.ts
diff --git a/src/mol-model-formats/structure/xtc.ts b/src/mol-model-formats/structure/xtc.ts
new file mode 100644
index 000000000..759e38bc5
--- /dev/null
+++ b/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);
+ });
+}
diff --git a/src/mol-plugin-state/formats/structure.ts b/src/mol-plugin-state/formats/structure.ts
index 7a6f24d40..cffea9967 100644
--- a/src/mol-plugin-state/formats/structure.ts
+++ b/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]
\ No newline at end of file
diff --git a/src/mol-plugin-state/transforms/model.ts b/src/mol-plugin-state/transforms/model.ts
index 1a8ff6355..415072b22 100644
--- a/src/mol-plugin-state/transforms/model.ts
+++ b/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',
diff --git a/webpack.config.common.js b/webpack.config.common.js
index a2e035dae..ff2aba48d 100644
--- a/webpack.config.common.js
+++ b/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')
})
],
diff --git a/webpack.config.js b/webpack.config.js
index 1289b72ed..16765f511 100644
--- a/webpack.config.js
+++ b/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)
]
\ No newline at end of file
--
GitLab