diff --git a/src/mol-model/structure/query/modifiers.ts b/src/mol-model/structure/query/modifiers.ts
index e66bbab42bd731581fb9f1b64e415cdba17676cb..3b332ff7fcfc9d142ae080968375a3c54af0eedb 100644
--- a/src/mol-model/structure/query/modifiers.ts
+++ b/src/mol-model/structure/query/modifiers.ts
@@ -70,7 +70,6 @@ async function getIncludeSurroundings(ctx: RuntimeContext, source: Structure, st
const r = params.radius;
let progress = 0;
-
for (const unit of structure.units) {
const { x, y, z } = unit.conformation;
const elements = unit.elements;
@@ -78,19 +77,19 @@ async function getIncludeSurroundings(ctx: RuntimeContext, source: Structure, st
const e = elements[i];
lookup.findIntoBuilder(x(e), y(e), z(e), r, builder);
}
-
progress++;
if (progress % 2500 === 0 && ctx.shouldUpdate) await ctx.update({ message: 'Include Surroudnings', isIndeterminate: true });
}
- if (!!params.wholeResidues) return getWholeResidues(ctx, source, builder.getStructure())
- return builder.getStructure();
+ return !!params.wholeResidues ? getWholeResidues(ctx, source, builder.getStructure()) : builder.getStructure();
}
export function includeSurroundings(query: Query.Provider, params: IncludeSurroundingsParams): Query.Provider {
return async (structure, ctx) => {
const inner = await query(structure, ctx);
if (Selection.isSingleton(inner)) {
- return Selection.Singletons(structure, await getIncludeSurroundings(ctx, structure, inner.structure, params));
+ const surr = await getIncludeSurroundings(ctx, structure, inner.structure, params);
+ const ret = Selection.Singletons(structure, surr);
+ return ret;
} else {
const builder = new UniqueStructuresBuilder(structure);
for (const s of inner.structures) {
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 4ea70f014d413e7d14967ae769c2d500cb0cdf24..5c34fd555248e6b3c2cf752446930b7d47116f6e 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -11,6 +11,7 @@ import { SortedArray } from 'mol-data/int';
import { idFactory } from 'mol-util/id-factory';
import { IntraUnitBonds, computeIntraUnitBonds } from './unit/bonds'
import { CoarseElements, CoarseSphereConformation, CoarseGaussianConformation } from '../model/properties/coarse';
+import { ValueRef } from 'mol-util';
// A building block of a structure that corresponds to an atomic or a coarse grained representation
// 'conveniently grouped together'.
@@ -26,7 +27,7 @@ namespace Unit {
export function create(id: number, kind: Kind, model: Model, operator: SymmetryOperator, elements: SortedArray): Unit {
switch (kind) {
- case Kind.Atomic: return new Atomic(id, unitIdFactory(), model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation));
+ case Kind.Atomic: return new Atomic(id, unitIdFactory(), model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation), AtomicProperties());
case Kind.Spheres: return createCoarse(id, unitIdFactory(), model, Kind.Spheres, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres));
case Kind.Gaussians: return createCoarse(id, unitIdFactory(), model, Kind.Gaussians, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians));
}
@@ -71,32 +72,32 @@ namespace Unit {
readonly residueIndex: ArrayLike<number>;
readonly chainIndex: ArrayLike<number>;
+ private props: AtomicProperties;
+
getChild(elements: SortedArray): Unit {
if (elements.length === this.elements.length) return this;
- return new Atomic(this.id, this.invariantId, this.model, elements, this.conformation);
+ return new Atomic(this.id, this.invariantId, this.model, elements, this.conformation, AtomicProperties());
}
applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
- return new Atomic(id, this.invariantId, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation));
+ return new Atomic(id, this.invariantId, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation), this.props);
}
- private _lookup3d?: Lookup3D = void 0;
get lookup3d() {
- if (this._lookup3d) return this._lookup3d;
+ if (this.props.lookup3d.ref) return this.props.lookup3d.ref;
const { x, y, z } = this.model.atomicConformation;
- this._lookup3d = GridLookup3D({ x, y, z, indices: this.elements });
- return this._lookup3d;
+ this.props.lookup3d.ref = GridLookup3D({ x, y, z, indices: this.elements });
+ return this.props.lookup3d.ref;
}
- private _bonds?: IntraUnitBonds = void 0;
get bonds() {
- if (this._bonds) return this._bonds;
- this._bonds = computeIntraUnitBonds(this);
- return this._bonds;
+ if (this.props.bonds.ref) return this.props.bonds.ref;
+ this.props.bonds.ref = computeIntraUnitBonds(this);
+ return this.props.bonds.ref;
}
- constructor(id: number, invariantId: number, model: Model, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping) {
+ constructor(id: number, invariantId: number, model: Model, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping, props: AtomicProperties) {
this.id = id;
this.invariantId = invariantId;
this.model = model;
@@ -105,9 +106,19 @@ namespace Unit {
this.residueIndex = model.atomicHierarchy.residueSegments.segmentMap;
this.chainIndex = model.atomicHierarchy.chainSegments.segmentMap;
+ this.props = props;
}
}
+ interface AtomicProperties {
+ lookup3d: ValueRef<Lookup3D | undefined>,
+ bonds: ValueRef<IntraUnitBonds | undefined>,
+ }
+
+ function AtomicProperties() {
+ return { lookup3d: ValueRef.create(void 0), bonds: ValueRef.create(void 0) };
+ }
+
class Coarse<K extends Kind.Gaussians | Kind.Spheres, C extends CoarseSphereConformation | CoarseGaussianConformation> implements Base {
readonly kind: K;
@@ -127,16 +138,18 @@ namespace Unit {
applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
- return createCoarse(id, this.invariantId, this.model, this.kind, this.elements, SymmetryOperator.createMapping(op, this.getCoarseElements()));
+ const ret = createCoarse(id, this.invariantId, this.model, this.kind, this.elements, SymmetryOperator.createMapping(op, this.getCoarseElements()));
+ (ret as Coarse<K, C>)._lookup3d = this._lookup3d;
+ return ret;
}
- private _lookup3d?: Lookup3D = void 0;
+ private _lookup3d: ValueRef<Lookup3D | undefined> = ValueRef.create(void 0);
get lookup3d() {
- if (this._lookup3d) return this._lookup3d;
- const { x, y, z } = this.getCoarseElements();
+ if (this._lookup3d.ref) return this._lookup3d.ref;
// TODO: support sphere radius?
- this._lookup3d = GridLookup3D({ x, y, z, indices: this.elements });
- return this._lookup3d;
+ const { x, y, z } = this.getCoarseElements();
+ this._lookup3d.ref = GridLookup3D({ x, y, z, indices: this.elements });
+ return this._lookup3d.ref;
}
private getCoarseElements() {
diff --git a/src/mol-model/structure/structure/util/lookup3d.ts b/src/mol-model/structure/structure/util/lookup3d.ts
index bee1c7c03a9e2cca5f7f05959644a31877cc2ef9..beb7c150a40cc72668c78134543d78c80342d41a 100644
--- a/src/mol-model/structure/structure/util/lookup3d.ts
+++ b/src/mol-model/structure/structure/util/lookup3d.ts
@@ -81,7 +81,13 @@ export class StructureLookup3D implements Lookup3D<Element> {
return false;
}
- boundary: { box: Box3D; sphere: Sphere3D; };
+ _boundary: { box: Box3D; sphere: Sphere3D; } | undefined = void 0;
+
+ get boundary() {
+ if (this.boundary) return this._boundary!;
+ this._boundary = computeStructureBoundary(this.structure);
+ return this._boundary!;
+ }
constructor(private structure: Structure) {
const { units } = structure;
@@ -106,6 +112,5 @@ export class StructureLookup3D implements Lookup3D<Element> {
}
this.unitLookup = GridLookup3D({ x: xs, y: ys, z: zs, radius, indices: OrderedSet.ofBounds(0, unitCount) });
- this.boundary = computeStructureBoundary(structure);
}
}
\ No newline at end of file