From 118daa2b2537ef27004a002326ef812c076a7e59 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Sat, 2 Mar 2019 14:07:56 +0100
Subject: [PATCH] StructureElement.Loci.toScriptExpression, mol-script fixes
---
.../structure/query/queries/modifiers.ts | 3 +-
src/mol-model/structure/structure/element.ts | 41 +++++++++++++++----
.../dynamic/volume-streaming/behavior.ts | 25 +++++------
.../language/symbol-table/structure-query.ts | 4 ++
src/mol-script/runtime/query/table.ts | 13 ++++++
5 files changed, 65 insertions(+), 21 deletions(-)
diff --git a/src/mol-model/structure/query/queries/modifiers.ts b/src/mol-model/structure/query/queries/modifiers.ts
index 0b0904515..f85855d26 100644
--- a/src/mol-model/structure/query/queries/modifiers.ts
+++ b/src/mol-model/structure/query/queries/modifiers.ts
@@ -279,11 +279,10 @@ export function expandProperty(query: StructureQuery, property: QueryFn): Struct
ctx.element.element = elements[i];
const p = property(ctx);
if (!propertyToStructureIndexMap.has(p)) continue;
-
const indices = propertyToStructureIndexMap.get(p)!.array;
for (let _sI = 0, __sI = indices.length; _sI < __sI; _sI++) {
- builders[indices[i]].addToUnit(unit.id, elements[i]);
+ builders[indices[_sI]].addToUnit(unit.id, elements[i]);
}
}
}
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index 1bd19cde9..db379cf93 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -4,14 +4,17 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { OrderedSet, SortedArray } from 'mol-data/int'
-import Unit from './unit'
+import { UniqueArray } from 'mol-data/generic';
+import { OrderedSet, SortedArray } from 'mol-data/int';
+import { BoundaryHelper } from 'mol-math/geometry/boundary-helper';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { MolScriptBuilder as MS } from 'mol-script/language/builder';
import { ElementIndex } from '../model';
-import { ResidueIndex, ChainIndex } from '../model/indexing';
+import { ChainIndex, ResidueIndex } from '../model/indexing';
import Structure from './structure';
+import Unit from './unit';
import { Boundary } from './util/boundary';
-import { BoundaryHelper } from 'mol-math/geometry/boundary-helper';
-import { Vec3 } from 'mol-math/linear-algebra';
+import { StructureProperties } from '../structure';
interface StructureElement<U = Unit> {
readonly kind: 'element-location',
@@ -38,11 +41,11 @@ namespace StructureElement {
function _wrongUnitKind(kind: string) { throw new Error(`Property only available for ${kind} models.`); }
export function atomicProperty<T>(p: (location: StructureElement<Unit.Atomic>) => T) {
- return property(l => Unit.isAtomic(l.unit) ? p(l as StructureElement<Unit.Atomic>) : _wrongUnitKind('atomic') );
+ return property(l => Unit.isAtomic(l.unit) ? p(l as StructureElement<Unit.Atomic>) : _wrongUnitKind('atomic'));
}
export function coarseProperty<T>(p: (location: StructureElement<Unit.Spheres | Unit.Gaussians>) => T) {
- return property(l => Unit.isCoarse(l.unit) ? p(l as StructureElement<Unit.Spheres | Unit.Gaussians>) : _wrongUnitKind('coarse') );
+ return property(l => Unit.isCoarse(l.unit) ? p(l as StructureElement<Unit.Spheres | Unit.Gaussians>) : _wrongUnitKind('coarse'));
}
/** Represents multiple element index locations */
@@ -240,6 +243,30 @@ namespace StructureElement {
return { box: boundaryHelper.getBox(), sphere: boundaryHelper.getSphere() };
}
+
+ export function toScriptExpression(loci: Loci) {
+ if (loci.structure.models.length > 1) {
+ console.warn('toScriptExpression is only supported for Structure with single model, returning empty expression.');
+ return MS.struct.generator.empty();
+ }
+ const sourceIndices = UniqueArray.create<number, number>();
+ const el = StructureElement.create(), p = StructureProperties.atom.sourceIndex;
+ for (const e of loci.elements) {
+ const { indices } = e;
+ const { elements } = e.unit;
+
+ el.unit = e.unit;
+ for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
+ el.element = elements[OrderedSet.getAt(indices, i)];
+ const idx = p(el);
+ UniqueArray.add(sourceIndices, idx, idx);
+ }
+ }
+ return MS.struct.generator.atomGroups({
+ 'atom-test': MS.core.set.has([MS.set.apply(null, sourceIndices.array), MS.struct.atomProperty.core.sourceIndex()]),
+ 'group-by': 0
+ });
+ }
}
}
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
index d39eda8b0..86476d4b9 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
@@ -4,22 +4,23 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
+import CIF from 'mol-io/reader/cif';
+import { Box3D } from 'mol-math/geometry';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { volumeFromDensityServerData } from 'mol-model-formats/volume/density-server';
+import { StructureElement } from 'mol-model/structure';
+import { VolumeData, VolumeIsoValue } from 'mol-model/volume';
import { PluginBehavior } from 'mol-plugin/behavior';
+import { PluginContext } from 'mol-plugin/context';
import { PluginStateObject } from 'mol-plugin/state/objects';
-import { ParamDefinition as PD } from 'mol-util/param-definition';
-import { VolumeServerInfo, VolumeServerHeader } from './model';
import { createIsoValueParam } from 'mol-repr/volume/isosurface';
-import { VolumeIsoValue, VolumeData } from 'mol-model/volume';
import { Color } from 'mol-util/color';
-import { Vec3 } from 'mol-math/linear-algebra';
-import { PluginContext } from 'mol-plugin/context';
import { LRUCache } from 'mol-util/lru-cache';
-import CIF from 'mol-io/reader/cif';
-import { Box3D } from 'mol-math/geometry';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
import { urlCombine } from 'mol-util/url';
-import { volumeFromDensityServerData } from 'mol-model-formats/volume/density-server';
-import { StructureElement } from 'mol-model/structure';
+import { VolumeServerHeader, VolumeServerInfo } from './model';
import { CreateVolumeStreamingBehavior } from './transformers';
+import { ButtonsType } from 'mol-util/input/input-observer';
export class VolumeStreaming extends PluginStateObject.CreateBehavior<VolumeStreaming.Behavior>({ name: 'Volume Streaming' }) { }
@@ -147,8 +148,8 @@ export namespace VolumeStreaming {
register(ref: string): void {
// this.ref = ref;
- this.subscribeObservable(this.plugin.events.canvas3d.click, ({ current }) => {
- if (this.params.view.name !== 'selection-box') return;
+ this.subscribeObservable(this.plugin.events.canvas3d.click, ({ current, buttons }) => {
+ if (buttons !== ButtonsType.Flag.Secondary || this.params.view.name !== 'selection-box') return;
// TODO: support link loci as well?
// Perhaps structure loci too?
if (!StructureElement.isLoci(current.loci)) return;
@@ -198,7 +199,7 @@ export namespace VolumeStreaming {
break;
}
- const data = emptyData ? { } : await this.queryData(box);
+ const data = emptyData ? {} : await this.queryData(box);
if (!data) return false;
diff --git a/src/mol-script/language/symbol-table/structure-query.ts b/src/mol-script/language/symbol-table/structure-query.ts
index 6e345445a..1d87ccf8a 100644
--- a/src/mol-script/language/symbol-table/structure-query.ts
+++ b/src/mol-script/language/symbol-table/structure-query.ts
@@ -150,6 +150,10 @@ const modifier = {
'as-whole-residues': Argument(Type.Bool, { isOptional: true })
}), Types.ElementSelectionQuery, 'Pick all atom sets that are connected to the target.'),
+ wholeResidues: symbol(Arguments.Dictionary({
+ 0: Argument(Types.ElementSelectionQuery),
+ }), Types.ElementSelectionQuery, 'Expand the selection to whole residues.'),
+
expandProperty: symbol(Arguments.Dictionary({
0: Argument(Types.ElementSelectionQuery),
property: Argument(Type.AnyValue)
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index 2b6b45dcf..bbe87566e 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -195,6 +195,19 @@ const symbols = [
groupBy: xs['group-by']
})(ctx)),
+ D(MolScript.structureQuery.generator.all, (ctx) => Queries.generators.all(ctx)),
+ D(MolScript.structureQuery.generator.empty, (ctx) => Queries.generators.none(ctx)),
+
+ // ============= MODIFIERS ================
+
+ D(MolScript.structureQuery.modifier.includeSurroundings, (ctx, xs) => Queries.modifiers.includeSurroundings(xs[0] as any, {
+ radius: xs['radius'](ctx),
+ wholeResidues: !!(xs['as-whole-residues'] && xs['as-whole-residues'](ctx)),
+ elementRadius: xs['atom-radius']
+ })(ctx)),
+ D(MolScript.structureQuery.modifier.wholeResidues, (ctx, xs) => Queries.modifiers.wholeResidues(xs[0] as any)(ctx)),
+ D(MolScript.structureQuery.modifier.expandProperty, (ctx, xs) => Queries.modifiers.expandProperty(xs[0] as any, xs['property'])(ctx)),
+
// ============= ATOM PROPERTIES ================
// ~~~ CORE ~~~
--
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