diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index 009950daf9f0c610641ea4690387e2d9484b3a5c..e62dcf1333a3585005a1075391a2314152e4f21d 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -16,7 +16,7 @@ namespace Element {
export const create: (unit: number, index: number) => Element = Tuple.create;
export const is: (x: any) => x is Element = Tuple.is;
export const unitId: (e: Element) => number = Tuple.fst;
- export const index: (e: Element) => number = Tuple.snd;
+ export const elementIndex: (e: Element) => number = Tuple.snd;
export const areEqual: (e: Element, b: Element) => boolean = Tuple.areEqual;
export const hashCode: (e: Element) => number = Tuple.hashCode;
@@ -30,7 +30,7 @@ namespace Element {
export function updateLocation(structure: Structure, l: Location, element: Element) {
l.unit = structure.units[unitId(element)];
- l.element = index(element);
+ l.element = elementIndex(element);
return l;
}
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 9a3cd5b2efd7f771a0715350dff5a4898b30ed74..8c7c500ab53c09b25d44b6f54c7705b018c59415 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -12,7 +12,6 @@ import { sortArray, sort, arraySwap, hash1 } from 'mol-data/util';
import Element from './element'
import Unit from './unit'
import { StructureLookup3D } from './util/lookup3d';
-import { computeStructureBoundary } from './util/boundary';
class Structure {
readonly unitMap: IntMap<Unit>;
@@ -48,7 +47,14 @@ class Structure {
}
get boundary() {
- return computeStructureBoundary(this);
+ return this.lookup3d.boundary;
+ }
+
+ private _lookup3d?: StructureLookup3D = void 0;
+ get lookup3d() {
+ if (this._lookup3d) return this._lookup3d;
+ this._lookup3d = StructureLookup3D.create(this);
+ return this._lookup3d;
}
constructor(units: ArrayLike<Unit>) {
diff --git a/src/mol-model/structure/structure/util/lookup3d.ts b/src/mol-model/structure/structure/util/lookup3d.ts
index 8c8fc57e39404b9bddbbae63702aa06cc6f31e36..f3056afdc74f2eaea0d8d1ead9f654774e7c4859 100644
--- a/src/mol-model/structure/structure/util/lookup3d.ts
+++ b/src/mol-model/structure/structure/util/lookup3d.ts
@@ -6,93 +6,85 @@
import Structure from '../structure'
import Element from '../element'
-import { Lookup3D, /*GridLookup3D,*/ Result, Box3D, Sphere3D } from 'mol-math/geometry';
-//import { ElementSet, Unit } from '../../structure';
-//import { Vec3 } from 'mol-math/linear-algebra';
-//import { OrderedSet } from 'mol-data/int';
-//import { computeStructureBoundary } from './boundary';
+import { Lookup3D, GridLookup3D, Result, Box3D, Sphere3D } from 'mol-math/geometry';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { computeStructureBoundary } from './boundary';
+import { OrderedSet } from 'mol-data/int';
interface StructureLookup3D extends Lookup3D<Element> {}
namespace StructureLookup3D {
class Impl implements StructureLookup3D {
- //private unitLookup: Lookup3D;
+ private unitLookup: Lookup3D;
private result = Result.create<Element>();
- //private pivot = Vec3.zero();
+ private pivot = Vec3.zero();
find(x: number, y: number, z: number, radius: number): Result<Element> {
Result.reset(this.result);
- // const { units, elements } = this.structure;
- // const closeUnits = this.unitLookup.find(x, y, z, radius);
- // if (closeUnits.count === 0) return this.result;
-
- // for (let t = 0, _t = closeUnits.count; t < _t; t++) {
- // const i = closeUnits.indices[t];
- // const unitId = ElementSet.groupUnitIndex(elements, i);
- // const group = ElementSet.groupAt(elements, i);
- // const unit = units[unitId];
- // Vec3.set(this.pivot, x, y, z);
- // if (!unit.operator.isIdentity) {
- // Vec3.transformMat4(this.pivot, this.pivot, unit.operator.inverse);
- // }
- // const groupLookup = Unit.getLookup3d(unit, group);
- // const groupResult = groupLookup.find(this.pivot[0], this.pivot[1], this.pivot[2], radius);
- // for (let j = 0, _j = groupResult.count; j < _j; j++) {
- // Result.add(this.result, Element.create(unitId, groupResult.indices[j]), groupResult.squaredDistances[j]);
- // }
- // }
+ const { units } = this.structure;
+ const closeUnits = this.unitLookup.find(x, y, z, radius);
+ if (closeUnits.count === 0) return this.result;
+
+ for (let t = 0, _t = closeUnits.count; t < _t; t++) {
+ const unit = units[closeUnits.indices[t]];
+ Vec3.set(this.pivot, x, y, z);
+ if (!unit.conformation.operator.isIdentity) {
+ Vec3.transformMat4(this.pivot, this.pivot, unit.conformation.operator.inverse);
+ }
+ const unitLookup = unit.lookup3d;
+ const groupResult = unitLookup.find(this.pivot[0], this.pivot[1], this.pivot[2], radius);
+ for (let j = 0, _j = groupResult.count; j < _j; j++) {
+ Result.add(this.result, Element.create(unit.id, groupResult.indices[j]), groupResult.squaredDistances[j]);
+ }
+ }
return this.result;
}
check(x: number, y: number, z: number, radius: number): boolean {
- // const { units, elements } = this.structure;
- // const closeUnits = this.unitLookup.find(x, y, z, radius);
- // if (closeUnits.count === 0) return false;
-
- // for (let t = 0, _t = closeUnits.count; t < _t; t++) {
- // const i = closeUnits.indices[t];
- // const unitId = ElementSet.groupUnitIndex(elements, i);
- // const group = ElementSet.groupAt(elements, i);
- // const unit = units[unitId];
- // Vec3.set(this.pivot, x, y, z);
- // if (!unit.operator.isIdentity) {
- // Vec3.transformMat4(this.pivot, this.pivot, unit.operator.inverse);
- // }
- // const groupLookup = Unit.getLookup3d(unit, group);
- // if (groupLookup.check(this.pivot[0], this.pivot[1], this.pivot[2], radius)) return true;
- // }
+ const { units } = this.structure;
+ const closeUnits = this.unitLookup.find(x, y, z, radius);
+ if (closeUnits.count === 0) return false;
+
+ for (let t = 0, _t = closeUnits.count; t < _t; t++) {
+ const unit = units[closeUnits.indices[t]];
+ Vec3.set(this.pivot, x, y, z);
+ if (!unit.conformation.operator.isIdentity) {
+ Vec3.transformMat4(this.pivot, this.pivot, unit.conformation.operator.inverse);
+ }
+ const groupLookup = unit.lookup3d;
+ if (groupLookup.check(this.pivot[0], this.pivot[1], this.pivot[2], radius)) return true;
+ }
return false;
}
boundary: { box: Box3D; sphere: Sphere3D; };
- constructor(structure: Structure) {
- // const { units, elements } = structure;
- // const unitCount = ElementSet.groupCount(elements);
- // const xs = new Float32Array(unitCount);
- // const ys = new Float32Array(unitCount);
- // const zs = new Float32Array(unitCount);
- // const radius = new Float32Array(unitCount);
-
- // const center = Vec3.zero();
- // for (let i = 0; i < unitCount; i++) {
- // const group = ElementSet.groupAt(elements, i);
- // const unit = units[ElementSet.groupUnitIndex(elements, i)];
- // const lookup = Unit.getLookup3d(unit, group);
- // const s = lookup.boundary.sphere;
-
- // Vec3.transformMat4(center, s.center, unit.operator.matrix);
-
- // xs[i] = center[0];
- // ys[i] = center[1];
- // zs[i] = center[2];
- // radius[i] = s.radius;
- // }
-
- // this.unitLookup = GridLookup3D({ x: xs, y: ys, z: zs, radius, indices: OrderedSet.ofBounds(0, unitCount) });
- // this.boundary = computeStructureBoundary(structure);
+ constructor(private structure: Structure) {
+ const { units } = structure;
+ const unitCount = units.length;
+ const xs = new Float32Array(unitCount);
+ const ys = new Float32Array(unitCount);
+ const zs = new Float32Array(unitCount);
+ const radius = new Float32Array(unitCount);
+
+ const center = Vec3.zero();
+ for (let i = 0; i < unitCount; i++) {
+ const unit = units[i];
+ const lookup = unit.lookup3d;
+ const s = lookup.boundary.sphere;
+
+ Vec3.transformMat4(center, s.center, unit.conformation.operator.matrix);
+
+ xs[i] = center[0];
+ ys[i] = center[1];
+ zs[i] = center[2];
+ radius[i] = s.radius;
+ }
+
+ this.unitLookup = GridLookup3D({ x: xs, y: ys, z: zs, radius, indices: OrderedSet.ofBounds(0, unitCount) });
+ this.boundary = computeStructureBoundary(structure);
}
}