|
|
@@ -11,22 +11,19 @@ import { PluginContext } from 'molstar/lib/mol-plugin/context';
|
|
|
import { PluginCommands } from 'molstar/lib/mol-plugin/command';
|
|
|
import { PluginBehaviors } from 'molstar/lib/mol-plugin/behavior';
|
|
|
import { StateTransforms } from 'molstar/lib/mol-plugin/state/transforms';
|
|
|
-import { StructureRepresentation3DHelpers } from 'molstar/lib/mol-plugin/state/transforms/representation';
|
|
|
-import { PluginStateObject as PSO, PluginStateObject } from 'molstar/lib/mol-plugin/state/objects';
|
|
|
+import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin/state/objects';
|
|
|
import { AnimateModelIndex } from 'molstar/lib/mol-plugin/state/animation/built-in';
|
|
|
-import { StateBuilder, StateObject, StateSelection } from 'molstar/lib/mol-state';
|
|
|
-import { LoadParams, SupportedFormats, RepresentationStyle, StateElements } from './helpers';
|
|
|
+import { StateBuilder, StateSelection } from 'molstar/lib/mol-state';
|
|
|
+import { LoadParams, SupportedFormats, StateElements } from './helpers';
|
|
|
import { ControlsWrapper } from './ui/controls';
|
|
|
import { Scheduler } from 'molstar/lib/mol-task';
|
|
|
-import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
|
|
|
-import { BuiltInStructureRepresentations } from 'molstar/lib/mol-repr/structure/registry';
|
|
|
-import { BuiltInColorThemes } from 'molstar/lib/mol-theme/color';
|
|
|
-import { BuiltInSizeThemes } from 'molstar/lib/mol-theme/size';
|
|
|
-import { ColorNames } from 'molstar/lib/mol-util/color/tables';
|
|
|
import { InitVolumeStreaming, CreateVolumeStreamingInfo } from 'molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers';
|
|
|
import { ParamDefinition } from 'molstar/lib/mol-util/param-definition';
|
|
|
import { PluginSpec } from 'molstar/lib/mol-plugin/spec';
|
|
|
import { StructureRepresentationInteraction } from 'molstar/lib/mol-plugin/behavior/dynamic/selection/structure-representation-interaction';
|
|
|
+import { StructureSelectionQueries as Q } from 'molstar/lib/mol-plugin/util/structure-selection-helper';
|
|
|
+import { Model } from 'molstar/lib/mol-model/structure';
|
|
|
+import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
|
|
|
require('molstar/lib/mol-plugin/skin/light.scss')
|
|
|
|
|
|
export class StructureViewer {
|
|
|
@@ -72,8 +69,8 @@ export class StructureViewer {
|
|
|
|
|
|
private model(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats, assemblyId: string) {
|
|
|
const parsed = format === 'cif'
|
|
|
- ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
|
|
|
- : b.apply(StateTransforms.Model.TrajectoryFromPDB);
|
|
|
+ ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif, {}, { ref: StateElements.Trajectory })
|
|
|
+ : b.apply(StateTransforms.Model.TrajectoryFromPDB, {}, { ref: StateElements.Trajectory });
|
|
|
|
|
|
return parsed
|
|
|
.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 }, { ref: StateElements.Model });
|
|
|
@@ -85,91 +82,15 @@ export class StructureViewer {
|
|
|
const s = model
|
|
|
.apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: StateElements.Assembly });
|
|
|
|
|
|
- s.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' }, { ref: StateElements.Sequence });
|
|
|
- s.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' }, { ref: StateElements.Het });
|
|
|
- s.apply(StateTransforms.Model.StructureComplexElement, { type: 'water' }, { ref: StateElements.Water });
|
|
|
-
|
|
|
return s;
|
|
|
}
|
|
|
|
|
|
- private visual(_style?: RepresentationStyle, partial?: boolean) {
|
|
|
- const structure = this.getObj<PluginStateObject.Molecule.Structure>(StateElements.Assembly);
|
|
|
- if (!structure) return;
|
|
|
-
|
|
|
- const style = _style || { };
|
|
|
-
|
|
|
- const update = this.state.build();
|
|
|
-
|
|
|
- if (!partial || (partial && style.sequence)) {
|
|
|
- const root = update.to(StateElements.Sequence);
|
|
|
- if (style.sequence && style.sequence.hide) {
|
|
|
- root.delete(StateElements.SequenceVisual);
|
|
|
- } else {
|
|
|
- root.applyOrUpdate(StateElements.SequenceVisual, StateTransforms.Representation.StructureRepresentation3D,
|
|
|
- StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
|
|
|
- (style.sequence && style.sequence.kind) || 'cartoon',
|
|
|
- (style.sequence && style.sequence.coloring) || 'unit-index', structure));
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- if (!partial || (partial && style.hetGroups)) {
|
|
|
- const root = update.to(StateElements.Het);
|
|
|
- if (style.hetGroups && style.hetGroups.hide) {
|
|
|
- root.delete(StateElements.HetVisual);
|
|
|
- } else {
|
|
|
- if (style.hetGroups && style.hetGroups.hide) {
|
|
|
- root.delete(StateElements.HetVisual);
|
|
|
- } else {
|
|
|
- root.applyOrUpdate(StateElements.HetVisual, StateTransforms.Representation.StructureRepresentation3D,
|
|
|
- StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
|
|
|
- (style.hetGroups && style.hetGroups.kind) || 'ball-and-stick',
|
|
|
- (style.hetGroups && style.hetGroups.coloring), structure));
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- if (!partial || (partial && style.carbs)) {
|
|
|
- const root = update.to(StateElements.Het);
|
|
|
- if (style.hetGroups && style.hetGroups.hide) {
|
|
|
- root.delete(StateElements.HetVisual);
|
|
|
- } else {
|
|
|
- if (style.carbs && style.carbs.hide) {
|
|
|
- root.delete(StateElements.HetCarbs);
|
|
|
- } else {
|
|
|
- root.applyOrUpdate(StateElements.HetCarbs, StateTransforms.Representation.StructureRepresentation3D,
|
|
|
- StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin, 'carbohydrate', void 0, structure));
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- if (!partial || (partial && style.water)) {
|
|
|
- const root = update.to(StateElements.Water);
|
|
|
- if (style.water && style.water.hide) {
|
|
|
- root.delete(StateElements.WaterVisual);
|
|
|
- } else {
|
|
|
- root.applyOrUpdate(StateElements.WaterVisual, StateTransforms.Representation.StructureRepresentation3D,
|
|
|
- StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
|
|
|
- (style.water && style.water.kind) || 'ball-and-stick',
|
|
|
- (style.water && style.water.coloring), structure, { alpha: 0.51 }));
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- return update;
|
|
|
- }
|
|
|
-
|
|
|
- private getObj<T extends StateObject>(ref: string): T['data'] {
|
|
|
- const state = this.state;
|
|
|
- const cell = state.select(ref)[0];
|
|
|
- if (!cell || !cell.obj) return void 0;
|
|
|
- return (cell.obj as T).data;
|
|
|
- }
|
|
|
-
|
|
|
private applyState(tree: StateBuilder) {
|
|
|
return PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
|
|
|
}
|
|
|
|
|
|
private loadedParams: LoadParams = { url: '', format: 'cif', assemblyId: '' };
|
|
|
- async load({ url, format = 'cif', assemblyId = '', representationStyle }: LoadParams) {
|
|
|
+ async load({ url, format = 'cif', assemblyId = '' }: LoadParams) {
|
|
|
let loadType: 'full' | 'update' = 'full';
|
|
|
|
|
|
const state = this.plugin.state.dataState;
|
|
|
@@ -192,7 +113,7 @@ export class StructureViewer {
|
|
|
await this.applyState(tree);
|
|
|
}
|
|
|
|
|
|
- await this.updateStyle(representationStyle);
|
|
|
+ await this.updateStyle();
|
|
|
|
|
|
this.loadedParams = { url, format, assemblyId };
|
|
|
Scheduler.setImmediate(() => PluginCommands.Camera.Reset.dispatch(this.plugin, { }));
|
|
|
@@ -200,19 +121,37 @@ export class StructureViewer {
|
|
|
this.experimentalData.init()
|
|
|
}
|
|
|
|
|
|
- async updateStyle(style?: RepresentationStyle, partial?: boolean) {
|
|
|
- const tree = this.visual(style, partial);
|
|
|
- if (!tree) return;
|
|
|
- await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
|
|
|
+ async updateStyle() {
|
|
|
+ const { structureRepresentation: rep } = this.plugin.helpers
|
|
|
+ await rep.setFromExpression('add', 'cartoon', Q.all)
|
|
|
+ await rep.setFromExpression('add', 'carbohydrate', Q.all)
|
|
|
+ await rep.setFromExpression('add', 'ball-and-stick', MS.struct.modifier.union([
|
|
|
+ MS.struct.combinator.merge([ Q.ligandsPlusConnected, Q.branchedConnectedOnly, Q.water ])
|
|
|
+ ]))
|
|
|
}
|
|
|
|
|
|
experimentalData = {
|
|
|
init: async () => {
|
|
|
- const asm = this.state.select(StateElements.Assembly)[0].obj!;
|
|
|
- const params = ParamDefinition.getDefaultValues(InitVolumeStreaming.definition.params!(asm, this.plugin));
|
|
|
- params.behaviorRef = StateElements.VolumeStreaming;
|
|
|
- params.defaultView = 'box';
|
|
|
- await this.plugin.runTask(this.state.applyAction(InitVolumeStreaming, params, StateElements.Assembly));
|
|
|
+ const model = this.state.select(StateElements.Model)[0].obj;
|
|
|
+ const asm = this.state.select(StateElements.Assembly)[0].obj;
|
|
|
+ if (!model || !asm) return
|
|
|
+
|
|
|
+ const m = model.data as Model
|
|
|
+ const hasXrayMap = m.sourceData.data.pdbx_database_status.status_code_sf.value(0) === 'REL'
|
|
|
+ let hasEmMap = false
|
|
|
+ for (let i = 0, il = m.sourceData.data.pdbx_database_related._rowCount; i < il; ++i) {
|
|
|
+ if (m.sourceData.data.pdbx_database_related.db_name.value(i).toUpperCase() === 'EMDB') {
|
|
|
+ hasEmMap = true
|
|
|
+ break
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ if (hasXrayMap || hasEmMap) {
|
|
|
+ const params = ParamDefinition.getDefaultValues(InitVolumeStreaming.definition.params!(asm, this.plugin));
|
|
|
+ params.behaviorRef = StateElements.VolumeStreaming;
|
|
|
+ params.defaultView = 'selection-box';
|
|
|
+ await this.plugin.runTask(this.state.applyAction(InitVolumeStreaming, params, StateElements.Assembly));
|
|
|
+ }
|
|
|
},
|
|
|
remove: () => {
|
|
|
const r = this.state.select(StateSelection.Generators.ofTransformer(CreateVolumeStreamingInfo))[0];
|
|
|
@@ -220,51 +159,4 @@ export class StructureViewer {
|
|
|
PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.state, ref: r.transform.ref });
|
|
|
}
|
|
|
}
|
|
|
-
|
|
|
- hetGroups = {
|
|
|
- reset: () => {
|
|
|
- const update = this.state.build().delete(StateElements.HetGroupFocus);
|
|
|
- PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
|
|
|
- PluginCommands.Camera.Reset.dispatch(this.plugin, { });
|
|
|
- },
|
|
|
- focusFirst: async (resn: string) => {
|
|
|
- if (!this.state.transforms.has(StateElements.Assembly)) return;
|
|
|
-
|
|
|
- const update = this.state.build();
|
|
|
-
|
|
|
- update.delete(StateElements.HetGroupFocus);
|
|
|
-
|
|
|
- const surroundings = MS.struct.modifier.includeSurroundings({
|
|
|
- 0: MS.struct.filter.first([
|
|
|
- MS.struct.generator.atomGroups({
|
|
|
- 'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), resn]),
|
|
|
- 'group-by': MS.struct.atomProperty.macromolecular.residueKey()
|
|
|
- })
|
|
|
- ]),
|
|
|
- radius: 5,
|
|
|
- 'as-whole-residues': true
|
|
|
- });
|
|
|
-
|
|
|
- const sel = update.to(StateElements.Assembly)
|
|
|
- .apply(StateTransforms.Model.StructureSelection, { label: resn, query: surroundings }, { ref: StateElements.HetGroupFocus });
|
|
|
-
|
|
|
- sel.apply(StateTransforms.Representation.StructureRepresentation3D, this.createSurVisualParams());
|
|
|
-
|
|
|
- await PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
|
|
|
-
|
|
|
- const focus = (this.state.select(StateElements.HetGroupFocus)[0].obj as PluginStateObject.Molecule.Structure).data;
|
|
|
- const sphere = focus.boundary.sphere;
|
|
|
- const snapshot = this.plugin.canvas3d.camera.getFocus(sphere.center, 0.75 * sphere.radius);
|
|
|
- PluginCommands.Camera.SetSnapshot.dispatch(this.plugin, { snapshot, durationMs: 250 });
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- private createSurVisualParams() {
|
|
|
- const asm = this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure;
|
|
|
- return StructureRepresentation3DHelpers.createParams(this.plugin, asm.data, {
|
|
|
- repr: BuiltInStructureRepresentations['ball-and-stick'],
|
|
|
- color: [BuiltInColorThemes.uniform, () => ({ value: ColorNames.gray })],
|
|
|
- size: [BuiltInSizeThemes.uniform, () => ({ value: 0.33 } )]
|
|
|
- });
|
|
|
- }
|
|
|
}
|
Alexander Rose