diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
index 44d2743edacb14fdba7884afe469dd500696fb44..27c9cd543282d1d76a194cbf8f6ff793e9599af3 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
@@ -2,6 +2,7 @@
* Copyright (c) 2019 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>
*/
import { PluginStateObject as SO, PluginStateTransform } from '../../../state/objects';
@@ -13,38 +14,39 @@ import { urlCombine } from '../../../../mol-util/url';
import { createIsoValueParam } from '../../../../mol-repr/volume/isosurface';
import { VolumeIsoValue } from '../../../../mol-model/volume';
import { StateAction, StateObject, StateTransformer } from '../../../../mol-state';
-import { getStreamingMethod, getEmdbIdAndContourLevel } from './util';
+import { getStreamingMethod, getId, getContourLevel, getEmdbId } from './util';
import { VolumeStreaming } from './behavior';
import { VolumeRepresentation3DHelpers } from '../../../../mol-plugin/state/transforms/representation';
import { BuiltInVolumeRepresentations } from '../../../../mol-repr/volume/registry';
import { createTheme } from '../../../../mol-theme/theme';
import { Box3D } from '../../../../mol-math/geometry';
import { Vec3 } from '../../../../mol-math/linear-algebra';
-// import { PluginContext } from '../../../../mol-plugin/context';
export const InitVolumeStreaming = StateAction.build({
display: { name: 'Volume Streaming' },
from: SO.Molecule.Structure,
params(a) {
const method = getStreamingMethod(a && a.data);
+ const id = getId(a && a.data);
return {
method: PD.Select<VolumeServerInfo.Kind>(method, [['em', 'EM'], ['x-ray', 'X-Ray']]),
- id: PD.Text((a && a.data.models.length > 0 && a.data.models[0].entry) || ''),
+ id: PD.Text(id),
serverUrl: PD.Text('https://ds.litemol.org'),
defaultView: PD.Text<VolumeStreaming.ViewTypes>(method === 'em' ? 'cell' : 'selection-box'),
- behaviorRef: PD.Text('', { isHidden: true })
+ behaviorRef: PD.Text('', { isHidden: true }),
+ emContourProvider: PD.Select<'wwpdb' | 'pdbe'>('wwpdb', [['wwpdb', 'wwPDB'], ['pdbe', 'PDBe']], { isHidden: true }),
};
},
isApplicable: (a) => a.data.models.length === 1
})(({ ref, state, params }, plugin: PluginContext) => Task.create('Volume Streaming', async taskCtx => {
- // TODO: custom react view for this and the VolumeStreamingBehavior transformer
-
let dataId = params.id.toLowerCase(), emDefaultContourLevel: number | undefined;
if (params.method === 'em') {
await taskCtx.update('Getting EMDB info...');
- const emInfo = await getEmdbIdAndContourLevel(plugin, taskCtx, dataId);
- dataId = emInfo.emdbId;
- emDefaultContourLevel = emInfo.contour;
+ if (!dataId.toUpperCase().startsWith('EMD')) {
+ dataId = await getEmdbId(plugin, taskCtx, dataId)
+ }
+ const contourLevel = await getContourLevel(params.emContourProvider, plugin, taskCtx, dataId);
+ emDefaultContourLevel = contourLevel || 0;
}
const infoTree = state.build().to(ref)
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
index 21b343e84869c3a9e3a4d8097e80ab9cd5584d5d..2e1c5aa4963a47ff49e16f360b34809e802bb144 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
@@ -2,12 +2,14 @@
* Copyright (c) 2019 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>
*/
import { Structure } from '../../../../mol-model/structure';
import { VolumeServerInfo } from './model';
import { PluginContext } from '../../../../mol-plugin/context';
import { RuntimeContext } from '../../../../mol-task';
+import { getXMLNodeByName, XMLDocument } from '../../../../mol-util/xml-parser';
export function getStreamingMethod(s?: Structure, defaultKind: VolumeServerInfo.Kind = 'x-ray'): VolumeServerInfo.Kind {
if (!s) return defaultKind;
@@ -23,7 +25,53 @@ export function getStreamingMethod(s?: Structure, defaultKind: VolumeServerInfo.
return 'x-ray';
}
-export async function getEmdbIdAndContourLevel(plugin: PluginContext, taskCtx: RuntimeContext, pdbId: string) {
+export function getId(s?: Structure): string {
+ if (!s) return ''
+
+ const model = s.models[0]
+ if (model.sourceData.kind !== 'mmCIF') return ''
+
+ const d = model.sourceData.data
+ for (let i = 0, il = d.pdbx_database_related._rowCount; i < il; ++i) {
+ if (d.pdbx_database_related.db_name.value(i).toUpperCase() === 'EMDB') {
+ return d.pdbx_database_related.db_id.value(i)
+ }
+ }
+
+ return s.models.length > 0 ? s.models[0].entryId : ''
+}
+
+export async function getContourLevel(provider: 'wwpdb' | 'pdbe', plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
+ switch (provider) {
+ case 'wwpdb': return getContourLevelWwpdb(plugin, taskCtx, emdbId)
+ case 'pdbe': return getContourLevelPdbe(plugin, taskCtx, emdbId)
+ }
+}
+
+export async function getContourLevelWwpdb(plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
+ // TODO: parametrize to a differnt URL? in plugin settings perhaps
+ const header = await plugin.fetch<XMLDocument>({ url: `https://ftp.wwpdb.org/pub/emdb/structures/${emdbId.toUpperCase()}/header/${emdbId.toLowerCase()}.xml`, type: 'xml' }).runInContext(taskCtx);
+
+ const map = getXMLNodeByName('map', header!.root!.children!)!
+ const contourLevel = parseFloat(getXMLNodeByName('contourLevel', map.children!)!.content!)
+
+ return contourLevel;
+}
+
+export async function getContourLevelPdbe(plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
+ emdbId = emdbId.toUpperCase()
+ // TODO: parametrize to a differnt URL? in plugin settings perhaps
+ const header = await plugin.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/emdb/entry/map/${emdbId}`, type: 'json' }).runInContext(taskCtx);
+ const emdbEntry = header && header[emdbId];
+ let contourLevel: number | undefined = void 0;
+ if (emdbEntry && emdbEntry[0] && emdbEntry[0].map && emdbEntry[0].map.contour_level && emdbEntry[0].map.contour_level.value !== void 0) {
+ contourLevel = +emdbEntry[0].map.contour_level.value;
+ }
+
+ return contourLevel;
+}
+
+export async function getEmdbId(plugin: PluginContext, taskCtx: RuntimeContext, pdbId: string) {
// TODO: parametrize to a differnt URL? in plugin settings perhaps
const summary = await plugin.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/${pdbId}`, type: 'json' }).runInContext(taskCtx);
@@ -39,13 +87,5 @@ export async function getEmdbIdAndContourLevel(plugin: PluginContext, taskCtx: R
throw new Error(`No related EMDB entry found for '${pdbId}'.`);
}
- // TODO: parametrize to a differnt URL? in plugin settings perhaps
- const emdb = await plugin.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/emdb/entry/map/${emdbId}`, type: 'json' }).runInContext(taskCtx);
- const emdbEntry = emdb && emdb[emdbId];
- let contour: number | undefined = void 0;
- if (emdbEntry && emdbEntry[0] && emdbEntry[0].map && emdbEntry[0].map.contour_level && emdbEntry[0].map.contour_level.value !== void 0) {
- contour = +emdbEntry[0].map.contour_level.value;
- }
-
- return { emdbId, contour };
+ return emdbId
}
\ No newline at end of file