From 5ea81a5d2fb8683ed60b10d1c85defe18aba720f Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 30 Aug 2018 09:35:05 -0700
Subject: [PATCH] fixed boundingSphere calculation
---
.../structure/structure/util/boundary.ts | 81 +++----------------
1 file changed, 10 insertions(+), 71 deletions(-)
diff --git a/src/mol-model/structure/structure/util/boundary.ts b/src/mol-model/structure/structure/util/boundary.ts
index ec3821263..b90370614 100644
--- a/src/mol-model/structure/structure/util/boundary.ts
+++ b/src/mol-model/structure/structure/util/boundary.ts
@@ -37,13 +37,13 @@ function computeElementsPositionBoundary(elements: SortedArray<ElementIndex>, po
for (let j = 0, _j = elements.length; j < _j; j++) {
position(elements[j], p)
const d = Vec3.squaredDistance(p, center)
- if (d > radiusSq) radiusSq = d;
+ if (d > radiusSq) radiusSq = d
}
return {
box: { min, max },
sphere: { center, radius: Math.sqrt(radiusSq) }
- };
+ }
}
function computeInvariantUnitBoundary(u: Unit): Boundary {
@@ -62,7 +62,7 @@ export function computeStructureBoundary(s: Structure): Boundary {
const max = Vec3.create(-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE)
const center = Vec3.zero()
- const { units } = s;
+ const { units } = s
const boundaryMap: Map<number, Boundary> = new Map()
function getInvariantBoundary(u: Unit) {
@@ -76,19 +76,19 @@ export function computeStructureBoundary(s: Structure): Boundary {
return boundary
}
- let radiusSq = 0;
- let size = 0;
+ let radius = 0
+ let size = 0
for (let i = 0, _i = units.length; i < _i; i++) {
- size += 1
const u = units[i]
const invariantBoundary = getInvariantBoundary(u)
const m = u.conformation.operator.matrix
+ size += u.elements.length
Box3D.transform(tmpBox, invariantBoundary.box, m)
Vec3.min(min, min, tmpBox.min)
Vec3.max(max, max, tmpBox.max)
Sphere3D.transform(tmpSphere, invariantBoundary.sphere, m)
- Vec3.add(center, center, tmpSphere.center)
+ Vec3.scaleAndAdd(center, center, tmpSphere.center, u.elements.length)
}
if (size > 0) Vec3.scale(center, center, 1/size)
@@ -98,70 +98,9 @@ export function computeStructureBoundary(s: Structure): Boundary {
const invariantBoundary = getInvariantBoundary(u)
const m = u.conformation.operator.matrix
Sphere3D.transform(tmpSphere, invariantBoundary.sphere, m)
- const d = Vec3.squaredDistance(tmpSphere.center, center) + (tmpSphere.radius * tmpSphere.radius) * 4
- if (d > radiusSq) radiusSq = d
- }
-
- const b = {
- box: { min, max },
- sphere: { center, radius: Math.sqrt(radiusSq) }
- };
- console.log(b, computeStructureBoundary2(s))
- return b
-}
-
-export function computeStructureBoundary2(s: Structure): Boundary {
- const min = [Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE];
- const max = [-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE];
-
- const { units } = s;
-
- let cx = 0, cy = 0, cz = 0;
- let radiusSq = 0;
- let size = 0;
-
- for (let i = 0, _i = units.length; i < _i; i++) {
- const { x, y, z } = units[i].conformation;
-
- const elements = units[i].elements;
- size += elements.length;
- for (let j = 0, _j = elements.length; j < _j; j++) {
- const e = elements[j];
- const xx = x(e), yy = y(e), zz = z(e);
-
- min[0] = Math.min(xx, min[0]);
- min[1] = Math.min(yy, min[1]);
- min[2] = Math.min(zz, min[2]);
- max[0] = Math.max(xx, max[0]);
- max[1] = Math.max(yy, max[1]);
- max[2] = Math.max(zz, max[2]);
-
- cx += xx;
- cy += yy;
- cz += zz;
- }
- }
-
- if (size > 0) {
- cx /= size;
- cy /= size;
- cz /= size;
+ const d = Vec3.distance(tmpSphere.center, center) + tmpSphere.radius
+ if (d > radius) radius = d
}
- for (let i = 0, _i = units.length; i < _i; i++) {
- const { x, y, z } = units[i].conformation;
-
- const elements = units[i].elements;
- for (let j = 0, _j = elements.length; j < _j; j++) {
- const e = elements[j];
- const dx = x(e) - cx, dy = y(e) - cy, dz = z(e) - cz;
- const d = dx * dx + dy * dy + dz * dz;
- if (d > radiusSq) radiusSq = d;
- }
- }
-
- return {
- box: { min: Vec3.ofArray(min), max: Vec3.ofArray(max) },
- sphere: { center: Vec3.create(cx, cy, cz), radius: Math.sqrt(radiusSq) }
- };
+ return { box: { min, max }, sphere: { center, radius } }
}
\ No newline at end of file
--
GitLab