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Commit 242d2959 authored by David Sehnal's avatar David Sehnal
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Structure lookup 3D

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src/mol-model/structure/structure/element.ts
+ 2
− 2
View file @ 242d2959
......@@ -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;
}
......
src/mol-model/structure/structure/structure.ts
+ 8
− 2
View file @ 242d2959
......@@ -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>) {
......
src/mol-model/structure/structure/util/lookup3d.ts
+ 59
− 67
View file @ 242d2959
......@@ -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);
}
}
......
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