diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index 890472d04e189235c56476dfe9af7f93746da1ef..aa575c77289110a74d22d197f439c239c0c37ec0 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -54,16 +54,17 @@ namespace SymmetryOperator {
readonly position: CoordinateMapper,
x(index: number): number,
y(index: number): number,
- z(index: number): number
+ z(index: number): number,
+ r(index: number): number
}
export interface Coordinates { x: ArrayLike<number>, y: ArrayLike<number>, z: ArrayLike<number> }
- export function createMapping(operator: SymmetryOperator, coords: Coordinates): ArrayMapping {
+ export function createMapping(operator: SymmetryOperator, coords: Coordinates, radius: ((index: number) => number) | undefined): ArrayMapping {
const invariantPosition = SymmetryOperator.createCoordinateMapper(SymmetryOperator.Default, coords);
const position = operator.isIdentity ? invariantPosition : SymmetryOperator.createCoordinateMapper(operator, coords);
const { x, y, z } = createProjections(operator, coords);
- return { operator, invariantPosition, position, x, y, z };
+ return { operator, invariantPosition, position, x, y, z, r: radius ? radius : _zeroRadius };
}
export function createCoordinateMapper(t: SymmetryOperator, coords: Coordinates): CoordinateMapper {
@@ -74,6 +75,8 @@ namespace SymmetryOperator {
export { SymmetryOperator }
+function _zeroRadius(i: number) { return 0; }
+
interface Projections { x(index: number): number, y(index: number): number, z(index: number): number }
function createProjections(t: SymmetryOperator, coords: SymmetryOperator.Coordinates): Projections {
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 32fc551caafadeeca2b6c04f66fc33bb1a12a685..7113f640bb74a5d5d72bc73fc10227c84e0959ca 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -324,22 +324,12 @@ namespace Structure {
}
const distVec = Vec3.zero();
- function atomicOrGaussianDistance(u: Unit.Atomic | Unit.Gaussians, p: Vec3, r: number) {
- const { elements, conformation } = u;
+ function unitElementMinDistance(unit: Unit, p: Vec3, eRadius: number) {
+ const { elements, conformation: { position, r } } = unit, dV = distVec;
let minD = Number.MAX_VALUE;
for (let i = 0, _i = elements.length; i < _i; i++) {
- const d = Vec3.distance(p, conformation.position(elements[i], distVec)) - r;
- if (d < minD) minD = d;
- }
- return minD;
- }
-
- function sphereDistance(u: Unit.Spheres, p: Vec3, r: number) {
- const { elements, conformation } = u;
- const radius = u.coarseConformation.radius;
- let minD = Number.MAX_VALUE;
- for (let i = 0, _i = elements.length; i < _i; i++) {
- const d = Vec3.distance(p, conformation.position(elements[i], distVec)) - r - radius[elements[i]];
+ const e = elements[i];
+ const d = Vec3.distance(p, position(e, dV)) - eRadius - r(e);
if (d < minD) minD = d;
}
return minD;
@@ -347,19 +337,10 @@ namespace Structure {
export function minDistanceToPoint(s: Structure, point: Vec3, radius: number) {
const { units } = s;
- let minD = Number.MAX_VALUE, d = 0;
+ let minD = Number.MAX_VALUE;
for (let i = 0, _i = units.length; i < _i; i++) {
const unit = units[i];
- switch (unit.kind) {
- case Unit.Kind.Atomic:
- // TODO: assign radius to gaussian elements?
- case Unit.Kind.Gaussians:
- d = atomicOrGaussianDistance(unit, point, radius);
- break;
- case Unit.Kind.Spheres:
- d = sphereDistance(unit, point, radius);
- break;
- }
+ const d = unitElementMinDistance(unit, point, radius);
if (d < minD) minD = d;
}
return minD;
@@ -370,30 +351,16 @@ namespace Structure {
if (a.elementCount === 0 || b.elementCount === 0) return 0;
const { units } = a;
- let minD = Number.MAX_VALUE, d = 0;
+ let minD = Number.MAX_VALUE;
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++) {
- const d = minDistanceToPoint(b, conformation.position(elements[i], distPivot), 0);
- if (d < minD) minD = d;
- }
- break;
- case Unit.Kind.Spheres:
- const radius = unit.coarseConformation.radius;
- for (let i = 0, _i = elements.length; i < _i; i++) {
- const d = minDistanceToPoint(b, conformation.position(elements[i], distPivot), radius[elements[i]]);
- if (d < minD) minD = d;
- }
- break;
+ const { elements, conformation: { position, r } } = unit;
+ for (let i = 0, _i = elements.length; i < _i; i++) {
+ const e = elements[i];
+ const d = minDistanceToPoint(b, position(e, distPivot), r(e));
+ if (d < minD) minD = d;
}
- if (d < minD) minD = d;
}
return minD;
}
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 8ec99349308a246bf74320c2b517233d85999e8b..3bb205123d1961beddc044f7add9ab6ea7b3bc6c 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -29,9 +29,9 @@ namespace Unit {
export function create(id: number, kind: Kind, model: Model, operator: SymmetryOperator, elements: StructureElement.Set): Unit {
switch (kind) {
- 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));
+ case Kind.Atomic: return new Atomic(id, unitIdFactory(), model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation, void 0), AtomicProperties());
+ case Kind.Spheres: return createCoarse(id, unitIdFactory(), model, Kind.Spheres, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres, getSphereRadiusFunc(model)));
+ case Kind.Gaussians: return createCoarse(id, unitIdFactory(), model, Kind.Gaussians, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians, getGaussianRadiusFunc(model)));
}
}
@@ -64,6 +64,16 @@ namespace Unit {
readonly lookup3d: Lookup3D
}
+ function getSphereRadiusFunc(model: Model) {
+ const r = model.coarseConformation.spheres.radius;
+ return (i: number) => r[i];
+ }
+
+ function getGaussianRadiusFunc(model: Model) {
+ // TODO: compute radius for gaussians
+ return (i: number) => 0;
+ }
+
const unitIdFactory = idFactory();
// A bulding block of a structure that corresponds
@@ -95,7 +105,7 @@ namespace Unit {
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), this.props);
+ return new Atomic(id, this.invariantId, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation, this.conformation.r), this.props);
}
get lookup3d() {
@@ -163,7 +173,7 @@ namespace Unit {
applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
- const ret = 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(), this.conformation.r));
(ret as Coarse<K, C>)._lookup3d = this._lookup3d;
return ret;
}