From a0d919c8db41d98f4a1132b72eb73ce72841455d Mon Sep 17 00:00:00 2001
From: dsehnal <david.sehnal@gmail.com>
Date: Tue, 9 Nov 2021 21:12:24 +0100
Subject: [PATCH] Viewer.loadTrajectory
---
src/apps/viewer/embedded.html | 9 ++++-
src/apps/viewer/index.ts | 71 ++++++++++++++++++++++++++++++++++-
2 files changed, 77 insertions(+), 3 deletions(-)
diff --git a/src/apps/viewer/embedded.html b/src/apps/viewer/embedded.html
index a5869d4e0..80271e1dc 100644
--- a/src/apps/viewer/embedded.html
+++ b/src/apps/viewer/embedded.html
@@ -35,8 +35,13 @@
pdbProvider: 'rcsb',
emdbProvider: 'rcsb',
});
- viewer.loadPdb('7bv2');
- viewer.loadEmdb('EMD-30210', { detail: 6 });
+ // viewer.loadPdb('7bv2');
+ // viewer.loadEmdb('EMD-30210', { detail: 6 });
+
+ viewer.loadTrajectory({
+ model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },
+ coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true }
+ });
// viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
</script>
diff --git a/src/apps/viewer/index.ts b/src/apps/viewer/index.ts
index 84fb6dae8..83d3f5d8a 100644
--- a/src/apps/viewer/index.ts
+++ b/src/apps/viewer/index.ts
@@ -30,7 +30,7 @@ import { PluginCommands } from '../../mol-plugin/commands';
import { PluginConfig } from '../../mol-plugin/config';
import { PluginSpec } from '../../mol-plugin/spec';
import { PluginState } from '../../mol-plugin/state';
-import { StateObjectSelector } from '../../mol-state';
+import { StateObjectSelector, StateTransformer } from '../../mol-state';
import { Asset } from '../../mol-util/assets';
import { Color } from '../../mol-util/color';
import '../../mol-util/polyfill';
@@ -38,6 +38,13 @@ import { ObjectKeys } from '../../mol-util/type-helpers';
import './embedded.html';
import './favicon.ico';
import './index.html';
+import { ParamDefinition } from '../../mol-util/param-definition';
+import { Task } from '../../mol-task';
+import { Coordinates, Time } from '../../mol-model/structure';
+import { PluginContext } from '../../mol-plugin/context';
+import { TrajectoryFromModelAndCoordinates } from '../../mol-plugin-state/transforms/model';
+import { BuildInStructureFormat } from '../../mol-plugin-state/formats/structure';
+import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
require('mol-plugin-ui/skin/light.scss');
@@ -328,6 +335,56 @@ export class Viewer {
});
}
+ /**
+ * @example
+ * viewer.loadTrajectory({
+ * model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },
+ * coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true },
+ * preset: 'all-models' // or 'default'
+ * });
+ */
+ async loadTrajectory(params: LoadTrajectoryParams) {
+ const plugin = this.plugin;
+
+ let model: StateObjectSelector, coords: StateObjectSelector;
+
+ if (params.model.kind === 'model-data' || params.model.kind === 'model-url') {
+ const data = params.model.kind === 'model-data'
+ ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
+ : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
+
+ const trajectory = await plugin.builders.structure.parseTrajectory(data, params.model.format ?? 'mmcif');
+ model = await plugin.builders.structure.createModel(trajectory);
+ } else {
+ const data = params.model.kind === 'topology-data'
+ ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
+ : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
+
+ const provider = plugin.dataFormats.get(params.model.format);
+ model = await provider!.parse(plugin, data);
+ }
+
+ {
+ const data = params.coordinates.kind === 'coordinates-data'
+ ? await plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })
+ : await plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel });
+
+ const provider = plugin.dataFormats.get(params.coordinates.format);
+ coords = await provider!.parse(plugin, data);
+ }
+
+ const trajectory = await plugin.build().toRoot()
+ .apply(TrajectoryFromModelAndCoordinates, {
+ modelRef: model.ref,
+ coordinatesRef: coords.ref
+ }, { dependsOn: [model.ref, coords.ref] })
+ .commit();
+
+ const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, params.preset ?? 'default');
+
+ return { model, coords, preset };
+ }
+
handleResize() {
this.plugin.layout.events.updated.next(void 0);
}
@@ -343,4 +400,16 @@ export interface VolumeIsovalueInfo {
color: Color,
alpha?: number,
volumeIndex?: number
+}
+
+export interface LoadTrajectoryParams {
+ model: { kind: 'model-url', url: string, format?: BuiltInTrajectoryFormat /* mmcif */, isBinary?: boolean }
+ | { kind: 'model-data', data: string | number[] | ArrayBuffer | Uint8Array, format?: BuiltInTrajectoryFormat /* mmcif */ }
+ | { kind: 'topology-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
+ | { kind: 'topology-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
+ modelLabel?: string,
+ coordinates: { kind: 'coordinates-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
+ | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
+ coordinatesLabel?: string,
+ preset?: keyof PresetTrajectoryHierarchy
}
\ No newline at end of file
--
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