diff --git a/src/mol-model/structure/query/context.ts b/src/mol-model/structure/query/context.ts
index 772fae563744ef4243990e06bfa840aaafae1674..245cd5b37d400a1f3272669ada830123f6423152 100644
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -4,8 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Structure, StructureElement } from '../structure';
+import { Structure, StructureElement, Unit } from '../structure';
import { now } from 'mol-task';
+import { ElementIndex } from '../model';
export interface QueryContextView {
readonly element: StructureElement;
@@ -26,6 +27,11 @@ export class QueryContext implements QueryContextView {
readonly element: StructureElement = StructureElement.create();
currentStructure: Structure = void 0 as any;
+ setElement(unit: Unit, e: ElementIndex) {
+ this.element.unit = unit;
+ this.element.element = e;
+ }
+
pushCurrentElement(): StructureElement {
this.currentElementStack[this.currentElementStack.length] = this.element;
(this.element as StructureElement) = StructureElement.create();
diff --git a/src/mol-model/structure/query/queries/filters.ts b/src/mol-model/structure/query/queries/filters.ts
index 06f8ce8a4a84e65a3b68bb40841af3066f72589e..699a774509424b044aa0b3aa18350e8feff172db 100644
--- a/src/mol-model/structure/query/queries/filters.ts
+++ b/src/mol-model/structure/query/queries/filters.ts
@@ -107,7 +107,7 @@ export interface WithinParams {
target: StructureQuery,
minRadius?: number,
maxRadius: number,
- atomRadius?: QueryFn<number>,
+ elementRadius?: QueryFn<number>,
invert?: boolean
}
@@ -120,12 +120,12 @@ export function within(params: WithinParams): StructureQuery {
selection: params.query(queryCtx),
target: params.target(queryCtx),
maxRadius: params.maxRadius,
- minRadius: params.minRadius ? params.minRadius : 0,
- atomRadius: params.atomRadius || _zeroRadius,
+ minRadius: params.minRadius ? Math.max(0, params.minRadius) : 0,
+ elementRadius: params.elementRadius!,
invert: !!params.invert,
}
- if (ctx.minRadius === 0 && ctx.atomRadius === _zeroRadius) {
+ if (ctx.minRadius === 0 && typeof params.minRadius === 'undefined') {
return withinMaxRadius(ctx);
} else {
// TODO
@@ -142,7 +142,7 @@ interface WithinContext {
minRadius: number,
maxRadius: number,
invert: boolean,
- atomRadius: QueryFn<number>
+ elementRadius: QueryFn<number>
}
function withinMaxRadius({ queryCtx, selection, target, maxRadius, invert }: WithinContext) {
const targetLookup = StructureSelection.unionStructure(target).lookup3d;
@@ -151,34 +151,18 @@ function withinMaxRadius({ queryCtx, selection, target, maxRadius, invert }: Wit
const pos = Vec3.zero();
StructureSelection.forEach(selection, (s, sI) => {
const { units } = s;
-
let withinRadius = false;
for (let i = 0, _i = units.length; i < _i; i++) {
const unit = units[i];
- const { elements, conformation } = unit;
-
- switch (unit.kind) {
- case Unit.Kind.Atomic:
- // TODO: assign radius to gaussian elements?
- case Unit.Kind.Gaussians:
- for (let i = 0, _i = elements.length; i < _i; i++) {
- conformation.position(elements[i], pos);
- if (targetLookup.check(pos[0], pos[1], pos[2], maxRadius)) {
- withinRadius = true;
- break;
- }
- }
- break;
- case Unit.Kind.Spheres:
- const radius = unit.coarseConformation.radius;
- for (let i = 0, _i = elements.length; i < _i; i++) {
- conformation.position(elements[i], pos);
- if (targetLookup.check(pos[0], pos[1], pos[2], maxRadius + radius[elements[i]])) {
- withinRadius = true;
- break;
- }
- }
+ const { elements, conformation: { position, r } } = unit;
+
+ for (let i = 0, _i = elements.length; i < _i; i++) {
+ const e = elements[i];
+ position(e, pos);
+ if (targetLookup.check(pos[0], pos[1], pos[2], maxRadius + r(e))) {
+ withinRadius = true;
break;
+ }
}
if (withinRadius) break;
}
diff --git a/src/mol-model/structure/query/utils/structure-distance.ts b/src/mol-model/structure/query/utils/structure-distance.ts
new file mode 100644
index 0000000000000000000000000000000000000000..315292b751137ce779e2b349e61cbdaf15adffa8
--- /dev/null
+++ b/src/mol-model/structure/query/utils/structure-distance.ts
@@ -0,0 +1,116 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Structure, Unit } from '../../structure'
+import { Vec3 } from 'mol-math/linear-algebra';
+import { QueryFn, QueryContext } from '../context';
+
+export function checkStructureMinMaxDistance(ctx: QueryContext, a: Structure, b: Structure, minDist: number, maxDist: number, elementRadius: QueryFn<number>) {
+ if (a.elementCount === 0 || b.elementCount === 0) return true;
+
+ if (a.elementCount <= b.elementCount) return MinMaxDist.check(ctx, a, b, minDist, maxDist, elementRadius);
+ return MinMaxDist.check(ctx, b, a, minDist, maxDist, elementRadius);
+}
+
+export function checkStructureMaxRadiusDistance(ctx: QueryContext, a: Structure, b: Structure, maxDist: number, elementRadius: QueryFn<number>) {
+ if (a.elementCount === 0 || b.elementCount === 0) return true;
+
+ if (a.elementCount <= b.elementCount) return MaxRadiusDist.check(ctx, a, b, maxDist, elementRadius);
+ return MaxRadiusDist.check(ctx, b, a, maxDist, elementRadius);
+}
+
+namespace MinMaxDist {
+ const enum Result {
+ BelowMin,
+ WithinMax,
+ Miss
+ }
+
+ const distVec = Vec3.zero();
+ function inUnit(ctx: QueryContext, unit: Unit, p: Vec3, eRadius: number, minDist: number, maxDist: number, elementRadius: QueryFn<number>) {
+ const { elements, conformation: { position } } = unit, dV = distVec;
+ ctx.element.unit = unit;
+ let withinRange = false;
+ for (let i = 0, _i = elements.length; i < _i; i++) {
+ const e = elements[i];
+ ctx.element.element = e;
+ const d = Math.max(0, Vec3.distance(p, position(e, dV)) - eRadius - elementRadius(ctx));
+ if (d < minDist) return Result.BelowMin;
+ if (d < maxDist) withinRange = true;
+ }
+ return withinRange ? Result.WithinMax : Result.Miss;
+ }
+
+ export function toPoint(ctx: QueryContext, s: Structure, point: Vec3, radius: number, minDist: number, maxDist: number, elementRadius: QueryFn<number>) {
+ const { units } = s;
+ let withinRange = false;
+ for (let i = 0, _i = units.length; i < _i; i++) {
+ const iu = inUnit(ctx, units[i], point, radius, minDist, maxDist, elementRadius);
+ if (iu === Result.BelowMin) return Result.BelowMin;
+ if (iu === Result.WithinMax) withinRange = true;
+ }
+ return withinRange ? Result.WithinMax : Result.Miss;
+ }
+
+ const distPivot = Vec3.zero();
+ export function check(ctx: QueryContext, a: Structure, b: Structure, minDist: number, maxDist: number, elementRadius: QueryFn<number>) {
+ if (a.elementCount === 0 || b.elementCount === 0) return 0;
+
+ const { units } = a;
+ let withinRange = false;
+ for (let i = 0, _i = units.length; i < _i; i++) {
+ const unit = units[i];
+ const { elements, conformation: { position } } = unit;
+ for (let i = 0, _i = elements.length; i < _i; i++) {
+ const e = elements[i];
+ ctx.setElement(unit, e);
+ const tp = toPoint(ctx, b, position(e, distPivot), elementRadius(ctx), minDist, maxDist, elementRadius);
+ if (tp === Result.BelowMin) return Result.BelowMin;
+ if (tp === Result.WithinMax) withinRange = true;
+ }
+ }
+ return withinRange;
+ }
+}
+
+namespace MaxRadiusDist {
+ const distVec = Vec3.zero();
+ function inUnit(ctx: QueryContext, unit: Unit, p: Vec3, eRadius: number, maxDist: number, elementRadius: QueryFn<number>) {
+ const { elements, conformation: { position } } = unit, dV = distVec;
+ ctx.element.unit = unit;
+ for (let i = 0, _i = elements.length; i < _i; i++) {
+ const e = elements[i];
+ ctx.element.element = e;
+ if (Math.max(0, Vec3.distance(p, position(e, dV)) - eRadius - elementRadius(ctx)) <= maxDist) return true;
+ }
+ return false;
+ }
+
+ export function toPoint(ctx: QueryContext, s: Structure, point: Vec3, radius: number, maxDist: number, elementRadius: QueryFn<number>) {
+ const { units } = s;
+ for (let i = 0, _i = units.length; i < _i; i++) {
+ if (inUnit(ctx, units[i], point, radius, maxDist, elementRadius)) return true;
+ }
+ return false;
+ }
+
+ const distPivot = Vec3.zero();
+ export function check(ctx: QueryContext, a: Structure, b: Structure, maxDist: number, elementRadius: QueryFn<number>) {
+ if (a.elementCount === 0 || b.elementCount === 0) return 0;
+
+ const { units } = a;
+ for (let i = 0, _i = units.length; i < _i; i++) {
+ const unit = units[i];
+ const { elements, conformation: { position } } = unit;
+ for (let i = 0, _i = elements.length; i < _i; i++) {
+ const e = elements[i];
+ ctx.setElement(unit, e);
+ if (toPoint(ctx, b, position(e, distPivot), elementRadius(ctx), maxDist, elementRadius)) return true;
+ }
+ }
+ return false;
+ }
+}
\ No newline at end of file