diff --git a/CHANGELOG.md b/CHANGELOG.md
index cf1cf6f6e57212f6c45cf10cd5af7e2d216e060a..0ad012ff055382bca558992c62db278128e636e2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
- Fix handling of mmcif with empty ``label_*`` fields
+- Add LoadTrajectory action
## [v3.3.1] - 2022-02-27
diff --git a/src/mol-plugin-state/actions/structure.ts b/src/mol-plugin-state/actions/structure.ts
index 6bdd89273e92c5346ecfaf5d8a10299285079ee4..171824c15a2f69e6f7d9b66b4df19d1954e2bb93 100644
--- a/src/mol-plugin-state/actions/structure.ts
+++ b/src/mol-plugin-state/actions/structure.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -10,12 +10,12 @@ import { StateAction, StateSelection, StateTransformer } from '../../mol-state';
import { Task } from '../../mol-task';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../builder/structure/representation-preset';
-import { BuiltInTrajectoryFormat, BuiltInTrajectoryFormats } from '../formats/trajectory';
+import { BuiltInTrajectoryFormat, BuiltInTrajectoryFormats, TrajectoryFormatCategory } from '../formats/trajectory';
import { RootStructureDefinition } from '../helpers/root-structure';
import { PluginStateObject } from '../objects';
import { StateTransforms } from '../transforms';
import { Download } from '../transforms/data';
-import { CustomModelProperties, CustomStructureProperties, TrajectoryFromModelAndCoordinates } from '../transforms/model';
+import { CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, TrajectoryFromModelAndCoordinates } from '../transforms/model';
import { Asset } from '../../mol-util/assets';
import { PluginConfig } from '../../mol-plugin/config';
import { getFileInfo } from '../../mol-util/file-info';
@@ -311,4 +311,122 @@ export const AddTrajectory = StateAction.build({
const structure = await ctx.builders.structure.createStructure(model.selector);
await ctx.builders.structure.representation.applyPreset(structure, 'auto');
}).runInContext(taskCtx);
+}));
+
+export const LoadTrajectory = StateAction.build({
+ display: { name: 'Load Trajectory', description: 'Load trajectory of model/topology and coordinates from URL or file.' },
+ from: PluginStateObject.Root,
+ params(a, ctx: PluginContext) {
+ const { options } = ctx.dataFormats;
+ const modelOptions = options.filter(o => o[2] === TrajectoryFormatCategory || o[0] === 'psf');
+ const coordinatesOptions = options.filter(o => o[0] === 'dcd' || o[0] === 'xtc');
+
+ const modelExtensions: string[] = [];
+ for (const { name, provider } of ctx.dataFormats.list) {
+ if (provider.category === TrajectoryFormatCategory || name === 'psf') {
+ if (provider.binaryExtensions) modelExtensions.push(...provider.binaryExtensions);
+ if (provider.stringExtensions) modelExtensions.push(...provider.stringExtensions);
+ }
+ }
+
+ return {
+ source: PD.MappedStatic('file', {
+ url: PD.Group({
+ model: PD.Group({
+ url: PD.Url(''),
+ format: PD.Select(modelOptions[0][0], modelOptions),
+ isBinary: PD.Boolean(false),
+ }, { isExpanded: true }),
+ coordinates: PD.Group({
+ url: PD.Url(''),
+ format: PD.Select(coordinatesOptions[0][0], coordinatesOptions),
+ }, { isExpanded: true })
+ }, { isFlat: true }),
+ file: PD.Group({
+ model: PD.File({ accept: modelExtensions.map(e => `.${e}`).join(','), label: 'Model' }),
+ coordinates: PD.File({ accept: '.dcd,.xtc', label: 'Coordinates' }),
+ }, { isFlat: true }),
+ }, { options: [['url', 'URL'], ['file', 'File']] })
+ };
+ }
+})(({ params, state }, ctx: PluginContext) => Task.create('Load Trajectory', taskCtx => {
+ return state.transaction(async () => {
+ const s = params.source;
+
+ if (s.name === 'file' && (s.params.model === null || s.params.coordinates === null)) {
+ ctx.log.error('No file(s) selected');
+ return;
+ }
+
+ if (s.name === 'url' && (!s.params.model || !s.params.coordinates)) {
+ ctx.log.error('No URL(s) given');
+ return;
+ }
+
+ const processUrl = async (url: string | Asset.Url, format: string, isBinary: boolean) => {
+ const data = await ctx.builders.data.download({ url, isBinary });
+ const provider = ctx.dataFormats.get(format);
+
+ if (!provider) {
+ ctx.log.warn(`LoadTrajectory: could not find data provider for '${format}'`);
+ return;
+ }
+
+ return provider.parse(ctx, data);
+ };
+
+ const processFile = async (file: Asset.File | null) => {
+ if (!file) throw new Error('No file selected');
+
+ const info = getFileInfo(file.file!);
+ const isBinary = ctx.dataFormats.binaryExtensions.has(info.ext);
+ const { data } = await ctx.builders.data.readFile({ file, isBinary });
+ const provider = ctx.dataFormats.auto(info, data.cell?.obj!);
+
+ if (!provider) {
+ ctx.log.warn(`LoadTrajectory: could not find data provider for '${info.name}.${info.ext}'`);
+ return;
+ }
+
+ return provider.parse(ctx, data);
+ };
+
+ try {
+ const modelParsed = s.name === 'url'
+ ? await processUrl(s.params.model.url, s.params.model.format, s.params.model.isBinary)
+ : await processFile(s.params.model);
+
+ let model;
+ if ('trajectory' in modelParsed) {
+ model = await state.build().to(modelParsed.trajectory)
+ .apply(ModelFromTrajectory, { modelIndex: 0 })
+ .commit();
+ } else {
+ model = modelParsed.topology;
+ }
+
+ //
+
+ const coordinates = s.name === 'url'
+ ? await processUrl(s.params.coordinates.url, s.params.coordinates.format, true)
+ : await processFile(s.params.coordinates);
+
+ //
+
+ const dependsOn = [model.ref, coordinates.ref];
+ const traj = state.build().toRoot()
+ .apply(TrajectoryFromModelAndCoordinates, {
+ modelRef: model.ref,
+ coordinatesRef: coordinates.ref
+ }, { dependsOn })
+ .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 });
+
+ await state.updateTree(traj).runInContext(taskCtx);
+ const structure = await ctx.builders.structure.createStructure(traj.selector);
+ await ctx.builders.structure.representation.applyPreset(structure, 'auto');
+ } catch (e) {
+ console.error(e);
+ ctx.log.error(`Error loading trajectory`);
+ }
+ }).runInContext(taskCtx);
}));
\ No newline at end of file
diff --git a/src/mol-plugin-state/formats/registry.ts b/src/mol-plugin-state/formats/registry.ts
index 45e328dace350682327c4ddc641800970a8bed98..d4385d4dfbc9787d29d68ea89aa966c6de6c614b 100644
--- a/src/mol-plugin-state/formats/registry.ts
+++ b/src/mol-plugin-state/formats/registry.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -18,10 +18,10 @@ export class DataFormatRegistry {
private _map = new Map<string, DataFormatProvider>();
private _extensions: Set<string> | undefined = undefined;
private _binaryExtensions: Set<string> | undefined = undefined;
- private _options: [string, string, string][] | undefined = undefined;
+ private _options: [name: string, label: string, category: string][] | undefined = undefined;
- get types(): [string, string][] {
- return this._list.map(e => [e.name, e.provider.label] as [string, string]);
+ get types(): [name: string, label: string][] {
+ return this._list.map(e => [e.name, e.provider.label] as [name: string, label: string]);
}
get extensions() {
@@ -45,7 +45,7 @@ export class DataFormatRegistry {
get options() {
if (this._options) return this._options;
- const options: [string, string, string][] = [];
+ const options: [name: string, label: string, category: string][] = [];
this._list.forEach(({ name, provider }) => options.push([name, provider.label, provider.category || '']));
this._options = options;
return options;
diff --git a/src/mol-plugin-state/formats/structure.ts b/src/mol-plugin-state/formats/structure.ts
index 567f6ebb2e378970f8d40877f7f17139ebfd5671..7ec62dc06aecccc762cd6b00c3e1e23e1b57ac3a 100644
--- a/src/mol-plugin-state/formats/structure.ts
+++ b/src/mol-plugin-state/formats/structure.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -10,7 +10,10 @@ import { DataFormatProvider } from './provider';
export const StructureFormatCategory = 'Structure';
-export const PsfProvider = DataFormatProvider({
+//
+
+export { PsfProvider };
+const PsfProvider = DataFormatProvider({
label: 'PSF',
description: 'PSF',
category: StructureFormatCategory,
@@ -26,8 +29,14 @@ export const PsfProvider = DataFormatProvider({
return { format: format.selector, topology: topology.selector };
}
});
+type PsfProvider = typeof PsfProvider;
+
+export type TopologyProvider = PsfProvider;
+
+//
-export const DcdProvider = DataFormatProvider({
+export { DcdProvider };
+const DcdProvider = DataFormatProvider({
label: 'DCD',
description: 'DCD',
category: StructureFormatCategory,
@@ -40,8 +49,10 @@ export const DcdProvider = DataFormatProvider({
return coordinates.commit();
}
});
+type DcdProvider = typeof DcdProvider;
-export const XtcProvider = DataFormatProvider({
+export { XtcProvider };
+const XtcProvider = DataFormatProvider({
label: 'XTC',
description: 'XTC',
category: StructureFormatCategory,
@@ -54,6 +65,11 @@ export const XtcProvider = DataFormatProvider({
return coordinates.commit();
}
});
+type XtcProvider = typeof XtcProvider;
+
+export type CoordinatesProvider = DcdProvider | XtcProvider;
+
+//
export const BuiltInStructureFormats = [
['psf', PsfProvider] as const,
diff --git a/src/mol-plugin/spec.ts b/src/mol-plugin/spec.ts
index b2a50f37bfa5c5c2f51cd31a9eb8f9deec6bd36b..48f3c3fabfcd02942150caf224fafe0b696e3e4b 100644
--- a/src/mol-plugin/spec.ts
+++ b/src/mol-plugin/spec.ts
@@ -64,10 +64,10 @@ namespace PluginSpec {
export const DefaultPluginSpec = (): PluginSpec => ({
actions: [
PluginSpec.Action(StateActions.Structure.DownloadStructure),
- PluginSpec.Action(StateActions.Structure.AddTrajectory),
PluginSpec.Action(StateActions.Volume.DownloadDensity),
PluginSpec.Action(StateActions.DataFormat.DownloadFile),
PluginSpec.Action(StateActions.DataFormat.OpenFiles),
+ PluginSpec.Action(StateActions.Structure.LoadTrajectory),
PluginSpec.Action(StateActions.Structure.EnableModelCustomProps),
PluginSpec.Action(StateActions.Structure.EnableStructureCustomProps),