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@@ -5,8 +5,6 @@
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*/
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import { PluginContext } from 'molstar/lib/mol-plugin/context';
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-import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
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-import { Expression } from 'molstar/lib/mol-script/language/expression';
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import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
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import { TrajectoryHierarchyPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/hierarchy-preset';
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import { ValidationReportGeometryQualityPreset } from 'molstar/lib/extensions/rcsb/validation-report/behavior';
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@@ -14,26 +12,17 @@ import { AssemblySymmetryPreset } from 'molstar/lib/extensions/rcsb/assembly-sym
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import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects';
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import { RootStructureDefinition } from 'molstar/lib/mol-plugin-state/helpers/root-structure';
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import { StructureRepresentationPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/representation-preset';
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-import {
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- Structure,
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- StructureSelection,
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- QueryContext,
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- StructureElement
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-} from 'molstar/lib/mol-model/structure';
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-import { compile } from 'molstar/lib/mol-script/runtime/query/compiler';
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+import { StructureElement } from 'molstar/lib/mol-model/structure';
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import { ViewerState } from '../types';
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import {
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StateSelection,
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StateObjectSelector,
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StateObject,
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- StateTransformer,
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- StateObjectRef
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+ StateTransformer
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} from 'molstar/lib/mol-state';
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import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
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import { CustomStructureProperties } from 'molstar/lib/mol-plugin-state/transforms/model';
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-import { FlexibleStructureFromModel as FlexibleStructureFromModel } from './superpose/flexible-structure';
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-import { StructureRepresentationRegistry } from 'molstar/lib/mol-repr/structure/registry';
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-import { StructureSelectionQueries as Q } from 'molstar/lib/mol-plugin-state/helpers/structure-selection-query';
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+import { FlexibleStructureFromModel } from './superpose/flexible-structure';
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import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
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import { InteractivityManager } from 'molstar/lib/mol-plugin-state/manager/interactivity';
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import { MembraneOrientationPreset } from 'molstar/lib/extensions/anvil/behavior';
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@@ -43,56 +32,16 @@ import {
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InitVolumeStreaming,
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VolumeStreamingVisual
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} from 'molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers';
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-
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-type Target = {
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- readonly auth_seq_id?: number
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- readonly label_seq_id?: number
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- readonly label_comp_id?: string
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- readonly label_asym_id?: string
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-}
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-
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-function targetToExpression(target: Target): Expression {
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- const residueTests: Expression[] = [];
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- const tests = Object.create(null);
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-
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- if (target.auth_seq_id) {
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- residueTests.push(MS.core.rel.eq([target.auth_seq_id, MS.ammp('auth_seq_id')]));
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- } else if (target.label_seq_id) {
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- residueTests.push(MS.core.rel.eq([target.label_seq_id, MS.ammp('label_seq_id')]));
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- }
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- if (target.label_comp_id) {
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- residueTests.push(MS.core.rel.eq([target.label_comp_id, MS.ammp('label_comp_id')]));
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- }
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- if (residueTests.length === 1) {
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- tests['residue-test'] = residueTests[0];
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- } else if (residueTests.length > 1) {
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- tests['residue-test'] = MS.core.logic.and(residueTests);
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- }
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-
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- if (target.label_asym_id) {
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- tests['chain-test'] = MS.core.rel.eq([target.label_asym_id, MS.ammp('label_asym_id')]);
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- }
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-
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- if (Object.keys(tests).length > 0) {
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- return MS.struct.modifier.union([
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- MS.struct.generator.atomGroups(tests)
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- ]);
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- } else {
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- return MS.struct.generator.empty;
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- }
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-}
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-
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-function targetToLoci(target: Target, structure: Structure): StructureElement.Loci {
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- const expression = targetToExpression(target);
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- const query = compile<StructureSelection>(expression);
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- const selection = query(new QueryContext(structure));
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- return StructureSelection.toLociWithSourceUnits(selection);
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-}
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-
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-type Range = {
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- label_asym_id: string
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- label_seq_id?: { beg: number, end?: number }
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-}
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+import {
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+ createSelectionExpressions,
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+ normalizeTargets,
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+ Range,
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+ SelectionExpression,
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+ Target,
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+ targetToLoci,
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+ toRange
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+} from './selection';
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+import { RcsbSuperpositionRepresentationPreset } from './superpose/preset';
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type BaseProps = {
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assemblyId?: string
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@@ -152,9 +101,17 @@ type FeatureDensityProps = {
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hiddenChannels?: string[]
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} & BaseProps
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-export type PresetProps = ValidationProps | StandardProps | SymmetryProps | FeatureProps | DensityProps | PropsetProps | MembraneProps | FeatureDensityProps | EmptyProps;
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+export type MotifProps = {
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+ kind: 'motif',
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+ label?: string,
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+ targets: Target[],
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+ color?: number
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+} & BaseProps
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+
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+export type PresetProps = ValidationProps | StandardProps | SymmetryProps | FeatureProps | DensityProps | PropsetProps |
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+MembraneProps | FeatureDensityProps | MotifProps | EmptyProps;
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-const RcsbParams = (a: PluginStateObject.Molecule.Trajectory | undefined, plugin: PluginContext) => ({
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+const RcsbParams = () => ({
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preset: PD.Value<PresetProps>({ kind: 'standard', assemblyId: '' }, { isHidden: true })
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});
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@@ -162,70 +119,10 @@ type StructureObject = StateObjectSelector<PluginStateObject.Molecule.Structure,
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const CommonParams = StructureRepresentationPresetProvider.CommonParams;
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-const reprBuilder = StructureRepresentationPresetProvider.reprBuilder;
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-const updateFocusRepr = StructureRepresentationPresetProvider.updateFocusRepr;
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-
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-type SelectionExpression = {
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- tag: string
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- type: StructureRepresentationRegistry.BuiltIn
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- label: string
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- expression: Expression
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-};
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-
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-export const RcsbSuperpositionRepresentationPreset = StructureRepresentationPresetProvider({
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- id: 'preset-superposition-representation-rcsb',
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- display: {
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- group: 'Superposition',
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- name: 'Alignment',
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- description: 'Show representations based on the structural alignment data.'
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- },
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- params: () => ({
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- ...CommonParams,
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- selectionExpressions: PD.Value<SelectionExpression[]>([])
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- }),
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- async apply(ref, params, plugin) {
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-
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- const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
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- if (!structureCell) return Object.create(null);
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-
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- const structure = structureCell.obj!.data;
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- const cartoonProps = {sizeFactor: structure.isCoarseGrained ? 0.8 : 0.2};
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-
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- let components = Object.create(null);
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- let representations = Object.create(null);
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- for (const expr of params.selectionExpressions) {
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-
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- const comp = await plugin.builders.structure.tryCreateComponentFromExpression(structureCell, expr.expression, expr.label, { label: expr.label });
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- Object.assign(components, {[expr.label]: comp});
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-
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- const { update, builder, typeParams, color } = reprBuilder(plugin, params);
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-
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- let typeProps = {...typeParams};
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- if (expr.type === 'cartoon') {
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- Object.assign(typeProps, {...cartoonProps});
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- }
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-
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- Object.assign(representations, {
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- [expr.label]: builder.buildRepresentation(update, comp, {type: expr.type,
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- typeParams: typeProps, color: color as any}, { tag: expr.tag }),
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- });
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-
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- await update.commit({ revertOnError: false });
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-
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- }
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- // needed to apply same coloring scheme to focus representation
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- await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
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-
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- return representations;
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- }
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-});
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-
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export const RcsbPreset = TrajectoryHierarchyPresetProvider({
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id: 'preset-trajectory-rcsb',
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display: { name: 'RCSB' },
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- isApplicable: o => {
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- return true;
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- },
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+ isApplicable: () => true,
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params: RcsbParams,
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async apply(trajectory, params, plugin) {
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const builder = plugin.builders.structure;
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@@ -253,7 +150,11 @@ export const RcsbPreset = TrajectoryHierarchyPresetProvider({
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if (!allowsFlexTransform) {
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structure = await builder.createStructure(modelProperties || model, structureParams);
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structureProperties = await builder.insertStructureProperties(structure);
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- unitcell = await builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: true });
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+
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+ // hide unit cell when dealing with motifs
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+ if (p.kind !== 'motif') {
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+ unitcell = await builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: true });
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+ }
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}
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let representation: StructureRepresentationPresetProvider.Result | undefined = undefined;
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@@ -292,23 +193,39 @@ export const RcsbPreset = TrajectoryHierarchyPresetProvider({
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let selectionExpressions: SelectionExpression[] = [];
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if (p.selection) {
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for (const range of p.selection) {
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- selectionExpressions = selectionExpressions.concat(createSelectionExpression(entryId, range));
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+ selectionExpressions = selectionExpressions.concat(createSelectionExpressions(entryId, range));
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}
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} else {
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- selectionExpressions = selectionExpressions.concat(createSelectionExpression(entryId));
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+ selectionExpressions = selectionExpressions.concat(createSelectionExpressions(entryId));
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}
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const params = {
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ignoreHydrogens: CommonParams.ignoreHydrogens.defaultValue,
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quality: CommonParams.quality.defaultValue,
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- theme: { globalName: 'superpose' as any, focus: { name: 'superpose' } },
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+ theme: { globalName: 'superpose', focus: { name: 'superpose' } },
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selectionExpressions: selectionExpressions
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};
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- representation = await RcsbSuperpositionRepresentationPreset.apply(structure, params, plugin);
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+ representation = await plugin.builders.structure.representation.applyPreset<any>(structureProperties!, RcsbSuperpositionRepresentationPreset, params);
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+ } else if (p.kind === 'motif' && structure?.obj) {
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+ // let's force ASM_1 for motifs (as we use this contract in the rest of the stack)
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+ // TODO should ASM_1 be the default, seems like we'd run into problems when selecting ligands that are e.g. ambiguous with asym_id & seq_id alone?
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+ const targets = normalizeTargets(p.targets, structure!.obj.data);
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+ let selectionExpressions = createSelectionExpressions(p.label || model.data!.entryId, targets);
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+ const globalExpressions = createSelectionExpressions(p.label || model.data!.entryId); // global reps, to be hidden
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+ selectionExpressions = selectionExpressions.concat(globalExpressions.map(e => { return { ...e, isHidden: true }; }));
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+
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+ if (p.color) {
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+ selectionExpressions = selectionExpressions.map(e => { return { ...e, color: p.color }; });
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+ }
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+ const params = {
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+ ignoreHydrogens: true,
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+ quality: CommonParams.quality.defaultValue,
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+ selectionExpressions: selectionExpressions
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+ };
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+ representation = await plugin.builders.structure.representation.applyPreset<any>(structureProperties!, RcsbSuperpositionRepresentationPreset, params);
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} else if (p.kind === 'validation') {
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representation = await plugin.builders.structure.representation.applyPreset(structureProperties!, ValidationReportGeometryQualityPreset);
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-
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} else if (p.kind === 'symmetry') {
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representation = await plugin.builders.structure.representation.applyPreset<any>(structureProperties!, AssemblySymmetryPreset, { symmetryIndex: p.symmetryIndex });
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@@ -325,17 +242,17 @@ export const RcsbPreset = TrajectoryHierarchyPresetProvider({
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}
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if ((p.kind === 'feature' || p.kind === 'feature-density') && structure?.obj) {
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- let loci = targetToLoci(p.target, structure.obj.data);
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+ let loci = targetToLoci(p.target, structure!.obj.data);
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// if target is only defined by chain: then don't force first residue
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const chainMode = p.target.label_asym_id && !p.target.auth_seq_id && !p.target.label_seq_id && !p.target.label_comp_id;
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// HELP-16678: check for rare case where ligand is not present in requested assembly
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if (loci.elements.length === 0 && !!p.assemblyId) {
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- // switch to Model (a.k.a. show coordinate independent of assembly )
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+ // switch to Model (a.k.a. show coordinates independent of assembly)
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const { selection } = plugin.managers.structure.hierarchy;
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const s = selection.structures[0];
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await plugin.managers.structure.hierarchy.updateStructure(s, { ...params, preset: { ...params.preset, assemblyId: void 0 } });
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// update loci
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- loci = targetToLoci(p.target, structure.obj.data);
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+ loci = targetToLoci(p.target, structure!.obj.data);
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}
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const target = chainMode ? loci : StructureElement.Loci.firstResidue(loci);
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@@ -409,83 +326,3 @@ async function initVolumeStreaming(plugin: PluginContext, structure: StructureOb
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volume: false
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});
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}
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-
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-export function createSelectionExpression(entryId: string, range?: Range): SelectionExpression[] {
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- if (range) {
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- const residues: number[] = (range.label_seq_id) ? toRange(range.label_seq_id.beg, range.label_seq_id.end) : [];
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- const test = selectionTest(range.label_asym_id, residues);
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- const label = labelFromProps(entryId, range);
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- return [{
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- expression: MS.struct.generator.atomGroups(test),
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- label: `${label}`,
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- type: 'cartoon',
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- tag: 'polymer'
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- }];
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- } else {
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- return [
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- {
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- expression: Q.polymer.expression,
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- label: `${entryId} - Polymers`,
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- type: 'cartoon',
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- tag: 'polymer'
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- },
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- {
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- expression: Q.ligand.expression,
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- label: `${entryId} - Ligands`,
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- type: 'ball-and-stick',
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- tag: 'ligand'
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- },
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- {
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- expression: Q.ion.expression,
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- label: `${entryId} - Ions`,
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- type: 'ball-and-stick',
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- tag: 'ion'
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- },
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- {
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- expression: Q.branched.expression,
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- label: `${entryId} - Carbohydrates`,
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- type: 'carbohydrate',
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- tag: 'branched-snfg-3d'
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- },
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- {
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- expression: Q.lipid.expression,
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- label: `${entryId} - Lipids`,
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- type: 'ball-and-stick',
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- tag: 'lipid'
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- },
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- {
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- expression: Q.water.expression,
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- label: `${entryId} - Waters`,
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- type: 'ball-and-stick',
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- tag: 'water'
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- }
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- ];
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- }
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-}
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-
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-export const selectionTest = (asymId: string, residues: number[]) => {
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- if (residues.length > 0) {
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- return {
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- 'chain-test': MS.core.rel.eq([MS.ammp('label_asym_id'), asymId]),
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- 'residue-test': MS.core.set.has([MS.set(...residues), MS.ammp('label_seq_id')])
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- };
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- } else {
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- return { 'chain-test': MS.core.rel.eq([MS.ammp('label_asym_id'), asymId]) };
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- }
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-};
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-
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-export const toRange = (start: number, end?: number) => {
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- if (!end) return [start];
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- const b = start < end ? start : end;
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- const e = start < end ? end : start;
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- return [...Array(e - b + 1)].map((_, i) => b + i);
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-};
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-
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-const labelFromProps = (entryId: string, range: Range) => {
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-
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- const residues: number[] = (range.label_seq_id) ? toRange(range.label_seq_id.beg, range.label_seq_id.end) : [];
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- const label = entryId + (range.label_asym_id ? `.${range.label_asym_id}` : '') +
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- (residues && residues.length > 0 ? `:${residues[0]}` : '') +
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- (residues && residues.length > 1 ? `-${residues[residues.length - 1]}` : '');
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- return label;
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-};
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Sebastian Bittrich