From 561bed4e478f8fcb8e5172e09e22cef63c22d03b Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 5 Oct 2018 18:32:19 -0700
Subject: [PATCH] improved finding of closest element for vertices
---
.../structure/visual/gaussian-surface-mesh.ts | 30 ++++++++++++++-----
1 file changed, 23 insertions(+), 7 deletions(-)
diff --git a/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
index 8517f99c3..d15b9fe3f 100644
--- a/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, Structure } from 'mol-model/structure';
+import { Unit, Structure, StructureElement, ElementIndex } from 'mol-model/structure';
import { UnitsVisual, VisualUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../geometry/mesh/mesh';
@@ -13,9 +13,11 @@ import { StructureElementIterator, getElementLoci, markElement } from './util/el
import { computeMarchingCubesMesh } from '../../../util/marching-cubes/algorithm';
import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
import { paramDefaultValues } from 'mol-view/parameter';
+import { SizeTheme } from 'mol-view/theme/size';
+import { OrderedSet } from 'mol-data/int';
async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianDensityProps, mesh?: Mesh): Promise<Mesh> {
- const { smoothness } = props
+ const { smoothness, radiusOffset } = props
const { transform, field, idField } = await unit.computeGaussianDensity(props, ctx)
const params = {
@@ -28,16 +30,30 @@ async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, struct
Mesh.transformImmediate(surface, transform)
if (props.useGpu) {
- console.time('find closest atom for vertices')
+ console.time('find max element radius')
+ const { elements } = unit
+ const n = OrderedSet.size(elements)
+ const l = StructureElement.create(unit)
+ const sizeTheme = SizeTheme({ name: 'physical' })
+ const radius = (index: number) => {
+ l.element = index as ElementIndex
+ return sizeTheme.size(l)
+ }
+ let maxRadius = 0
+ for (let i = 0; i < n; ++i) {
+ const r = radius(OrderedSet.getAt(elements, i)) + radiusOffset
+ if (maxRadius < r) maxRadius = r
+ }
+ console.timeEnd('find max element radius')
+
+ console.time('find closest element for vertices')
const { lookup3d } = unit
- const maxRadius = 2
- const maxRadiusSq = maxRadius * maxRadius
const { vertexCount, vertexBuffer, groupBuffer } = surface
const vertices = vertexBuffer.ref.value
const groups = groupBuffer.ref.value
for (let i = 0; i < vertexCount; ++i) {
- const r = lookup3d.find(vertices[i * 3], vertices[i * 3 + 1], vertices[i * 3 + 2], maxRadiusSq)
+ const r = lookup3d.find(vertices[i * 3], vertices[i * 3 + 1], vertices[i * 3 + 2], maxRadius * 2)
let minDsq = Infinity
let group = 0
for (let j = 0, jl = r.count; j < jl; ++j) {
@@ -49,7 +65,7 @@ async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, struct
}
groups[i] = group
}
- console.timeEnd('find closest atom for vertices')
+ console.timeEnd('find closest element for vertices')
}
Mesh.computeNormalsImmediate(surface)
--
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