From ce0ff2fed8bcd312eae126a1ec4d125e45f03396 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 29 Aug 2019 15:46:20 +0200
Subject: [PATCH] mol-model: optionally compute centroid based bounding sphere
(disabled for now)
---
src/mol-math/geometry/centroid-helper.ts | 5 ++
.../structure/structure/structure.ts | 7 +++
.../structure/structure/util/boundary.ts | 49 ++++++++++++++++++-
3 files changed, 59 insertions(+), 2 deletions(-)
diff --git a/src/mol-math/geometry/centroid-helper.ts b/src/mol-math/geometry/centroid-helper.ts
index 7387757fc..637e92483 100644
--- a/src/mol-math/geometry/centroid-helper.ts
+++ b/src/mol-math/geometry/centroid-helper.ts
@@ -5,6 +5,7 @@
*/
import { Vec3 } from '../../mol-math/linear-algebra/3d';
+import { Sphere3D } from './primitives/sphere3d';
export { CentroidHelper }
@@ -35,6 +36,10 @@ class CentroidHelper {
if (d > this.radiusSq) this.radiusSq = d;
}
+ getSphere(): Sphere3D {
+ return { center: Vec3.clone(this.center), radius: Math.sqrt(this.radiusSq) };
+ }
+
constructor() {
}
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index a88ab91f8..0cf0f2fe7 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -221,6 +221,13 @@ class Structure {
|| (this._props.uniqueAtomicResidueIndices = getUniqueAtomicResidueIndices(this));
}
+ get isAtomic() {
+ for (const u of this.units) {
+ if (u.kind !== Unit.Kind.Atomic) return false;
+ }
+ return true;
+ }
+
/**
* Provides mapping for serial element indices accross all units.
*
diff --git a/src/mol-model/structure/structure/util/boundary.ts b/src/mol-model/structure/structure/util/boundary.ts
index 1b9026a6a..98e7e0968 100644
--- a/src/mol-model/structure/structure/util/boundary.ts
+++ b/src/mol-model/structure/structure/util/boundary.ts
@@ -9,15 +9,60 @@ import { Box3D, Sphere3D } from '../../../../mol-math/geometry';
import { BoundaryHelper } from '../../../../mol-math/geometry/boundary-helper';
import { Vec3 } from '../../../../mol-math/linear-algebra';
import Structure from '../structure';
+import { CentroidHelper } from '../../../../mol-math/geometry/centroid-helper';
export type Boundary = { box: Box3D, sphere: Sphere3D }
-const tmpBox = Box3D.empty()
-const tmpSphere = Sphere3D.zero()
+const tmpBox = Box3D.empty();
+const tmpSphere = Sphere3D.zero();
+const tmpVec = Vec3.zero();
const boundaryHelper = new BoundaryHelper();
+const centroidHelper = new CentroidHelper();
+
+// TODO: show this be enabled? does not solve problem with "renderable bounding spheres"
+const CENTROID_COMPUTATION_THRESHOLD = -1;
export function computeStructureBoundary(s: Structure): Boundary {
+ if (s.elementCount <= CENTROID_COMPUTATION_THRESHOLD && s.isAtomic) return computeStructureBoundaryFromElements(s);
+ return computeStructureBoundaryFromUnits(s);
+}
+
+function computeStructureBoundaryFromElements(s: Structure): Boundary {
+ centroidHelper.reset();
+
+ const min = Vec3.create(Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE)
+ const max = Vec3.create(-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE)
+
+ const v = tmpVec;
+ for (const unit of s.units) {
+ const { x, y, z } = unit.conformation;
+ const elements = unit.elements;
+ for (let j = 0, _j = elements.length; j < _j; j++) {
+ const e = elements[j];
+ Vec3.set(v, x(e), y(e), z(e));
+ centroidHelper.includeStep(v);
+ Vec3.min(min, min, v);
+ Vec3.max(max, max, v);
+ };
+ }
+
+ centroidHelper.finishedIncludeStep();
+
+ for (const unit of s.units) {
+ const { x, y, z } = unit.conformation;
+ const elements = unit.elements;
+ for (let j = 0, _j = elements.length; j < _j; j++) {
+ const e = elements[j];
+ Vec3.set(v, x(e), y(e), z(e));
+ centroidHelper.radiusStep(v);
+ };
+ }
+
+ return { box: { min, max }, sphere: centroidHelper.getSphere() };
+}
+
+function computeStructureBoundaryFromUnits(s: Structure): Boundary {
const min = Vec3.create(Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE)
const max = Vec3.create(-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE)
--
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