From 2ad23d6c2929681497857567c3db4f659b594bc4 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 3 Jun 2018 00:19:12 -0400
Subject: [PATCH] refactored spacefill creation a bit
---
.../representation/structure/spacefill.ts | 62 +++++--------------
src/mol-geo/representation/structure/utils.ts | 43 ++++++++++++-
src/mol-geo/shape/mesh.ts | 22 +++++++
src/mol-geo/util/marching-cubes/algorithm.ts | 1 +
4 files changed, 77 insertions(+), 51 deletions(-)
diff --git a/src/mol-geo/representation/structure/spacefill.ts b/src/mol-geo/representation/structure/spacefill.ts
index f2ace9de1..ebfbe71a1 100644
--- a/src/mol-geo/representation/structure/spacefill.ts
+++ b/src/mol-geo/representation/structure/spacefill.ts
@@ -8,15 +8,11 @@
import { ValueCell } from 'mol-util/value-cell'
import { RenderObject, createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object'
-// import { createColorTexture } from 'mol-gl/util';
-import { Vec3, Mat4 } from 'mol-math/linear-algebra'
import { Unit, Element, Queries } from 'mol-model/structure';
import { UnitsRepresentation, DefaultStructureProps } from './index';
import { Task } from 'mol-task'
-import { MeshBuilder } from '../../shape/mesh-builder';
-import { createTransforms, createColors, createFlags, createEmptyFlags } from './utils';
+import { createTransforms, createColors, createFlags, createEmptyFlags, createSphereMesh } from './utils';
import VertexMap from '../../shape/vertex-map';
-import { icosahedronVertexCount } from '../../primitive/icosahedron';
import { deepEqual, defaults } from 'mol-util';
import { fillSerial } from 'mol-gl/renderable/util';
import { RenderableState, MeshValues } from 'mol-gl/renderable';
@@ -24,6 +20,19 @@ import { getMeshData } from '../../util/mesh-data';
import { Mesh } from '../../shape/mesh';
import { PickingId } from '../../util/picking';
+function createSpacefillMesh(unit: Unit, detail: number, mesh?: Mesh) {
+ let radius: Element.Property<number>
+ if (Unit.isAtomic(unit)) {
+ radius = Queries.props.atom.vdw_radius
+ } else if (Unit.isSpheres(unit)) {
+ radius = Queries.props.coarse.sphere_radius
+ } else {
+ console.warn('Unsupported unit type')
+ return Task.constant('Empty mesh', Mesh.createEmpty(mesh))
+ }
+ return createSphereMesh(unit, radius, detail, mesh)
+}
+
export const DefaultSpacefillProps = {
...DefaultStructureProps,
flipSided: false,
@@ -32,49 +41,6 @@ export const DefaultSpacefillProps = {
}
export type SpacefillProps = Partial<typeof DefaultSpacefillProps>
-function createSpacefillMesh(unit: Unit, detail: number, mesh?: Mesh) {
- return Task.create('Sphere mesh', async ctx => {
- const { elements } = unit;
- const elementCount = elements.length;
- const vertexCount = elementCount * icosahedronVertexCount(detail)
- const meshBuilder = MeshBuilder.create(vertexCount, vertexCount / 2, mesh)
-
- let radius: Element.Property<number>
- if (Unit.isAtomic(unit)) {
- radius = Queries.props.atom.vdw_radius
- } else if (Unit.isSpheres(unit)) {
- radius = Queries.props.coarse.sphere_radius
- } else {
- console.warn('Unsupported unit type')
- return meshBuilder.getMesh()
- }
-
- const v = Vec3.zero()
- const m = Mat4.identity()
-
- const { x, y, z } = unit.conformation
- const l = Element.Location()
- l.unit = unit
-
- for (let i = 0; i < elementCount; i++) {
- l.element = elements[i]
- v[0] = x(l.element)
- v[1] = y(l.element)
- v[2] = z(l.element)
- Mat4.setTranslation(m, v)
-
- meshBuilder.setId(i)
- meshBuilder.addIcosahedron(m, { radius: radius(l), detail })
-
- if (i % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Sphere mesh', current: i, max: elementCount });
- }
- }
-
- return meshBuilder.getMesh()
- })
-}
-
export default function Spacefill(): UnitsRepresentation<SpacefillProps> {
const renderObjects: RenderObject[] = []
let spheres: MeshRenderObject
diff --git a/src/mol-geo/representation/structure/utils.ts b/src/mol-geo/representation/structure/utils.ts
index cee35dd1e..5771c3f12 100644
--- a/src/mol-geo/representation/structure/utils.ts
+++ b/src/mol-geo/representation/structure/utils.ts
@@ -5,8 +5,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Unit } from 'mol-model/structure';
-import { Mat4, Vec2 } from 'mol-math/linear-algebra'
+import { Unit, Element } from 'mol-model/structure';
+import { Mat4, Vec2, Vec3 } from 'mol-math/linear-algebra'
import { createUniformColor, ColorData } from '../../util/color-data';
import { createUniformSize } from '../../util/size-data';
@@ -16,6 +16,10 @@ import { ColorTheme, SizeTheme } from '../../theme';
import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../theme/structure/color';
import { ValueCell } from 'mol-util';
import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
+import { Mesh } from '../../shape/mesh';
+import { Task } from 'mol-task';
+import { icosahedronVertexCount } from '../../primitive/icosahedron';
+import { MeshBuilder } from '../../shape/mesh-builder';
export function createTransforms({ units }: Unit.SymmetryGroup, transforms?: ValueCell<Float32Array>) {
const unitCount = units.length
@@ -93,4 +97,37 @@ export function createEmptyFlags(flagData?: FlagData) {
uFlagTexSize: ValueCell.create(Vec2.create(1, 1)),
}
}
-}
\ No newline at end of file
+}
+
+export function createSphereMesh(unit: Unit, radius: Element.Property<number>, detail: number, mesh?: Mesh) {
+ return Task.create('Sphere mesh', async ctx => {
+ const { elements } = unit;
+ const elementCount = elements.length;
+ const vertexCount = elementCount * icosahedronVertexCount(detail)
+ const meshBuilder = MeshBuilder.create(vertexCount, vertexCount / 2, mesh)
+
+ const v = Vec3.zero()
+ const m = Mat4.identity()
+
+ const { x, y, z } = unit.conformation
+ const l = Element.Location()
+ l.unit = unit
+
+ for (let i = 0; i < elementCount; i++) {
+ l.element = elements[i]
+ v[0] = x(l.element)
+ v[1] = y(l.element)
+ v[2] = z(l.element)
+ Mat4.setTranslation(m, v)
+
+ meshBuilder.setId(i)
+ meshBuilder.addIcosahedron(m, { radius: radius(l), detail })
+
+ if (i % 10000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'Sphere mesh', current: i, max: elementCount });
+ }
+ }
+
+ return meshBuilder.getMesh()
+ })
+}
diff --git a/src/mol-geo/shape/mesh.ts b/src/mol-geo/shape/mesh.ts
index 6d63fd851..9447404a3 100644
--- a/src/mol-geo/shape/mesh.ts
+++ b/src/mol-geo/shape/mesh.ts
@@ -15,6 +15,8 @@ export interface Mesh {
vertexCount: number,
/** Number of triangles in the mesh */
triangleCount: number,
+ /** Number of offsets in the mesh */
+ offsetCount: number,
/** Vertex buffer as array of xyz values wrapped in a value cell */
vertexBuffer: ValueCell<Float32Array>,
@@ -37,6 +39,26 @@ export interface Mesh {
}
export namespace Mesh {
+ export function createEmpty(mesh?: Mesh): Mesh {
+ const vb = mesh ? mesh.vertexBuffer.ref.value : new Float32Array(0)
+ const ib = mesh ? mesh.indexBuffer.ref.value : new Uint32Array(0)
+ const nb = mesh ? mesh.normalBuffer.ref.value : new Float32Array(0)
+ const idb = mesh ? mesh.idBuffer.ref.value : new Float32Array(0)
+ const ob = mesh ? mesh.offsetBuffer.ref.value : new Uint32Array(0)
+ return {
+ vertexCount: 0,
+ triangleCount: 0,
+ offsetCount: 0,
+ vertexBuffer: mesh ? ValueCell.update(mesh.vertexBuffer, vb) : ValueCell.create(vb),
+ indexBuffer: mesh ? ValueCell.update(mesh.indexBuffer, ib) : ValueCell.create(ib),
+ normalBuffer: mesh ? ValueCell.update(mesh.normalBuffer, nb) : ValueCell.create(nb),
+ idBuffer: mesh ? ValueCell.update(mesh.idBuffer, idb) : ValueCell.create(idb),
+ offsetBuffer: mesh ? ValueCell.update(mesh.offsetBuffer, ob) : ValueCell.create(ob),
+ normalsComputed: true,
+ offsetsComputed: true,
+ }
+ }
+
export function computeNormalsImmediate(surface: Mesh) {
if (surface.normalsComputed) return;
diff --git a/src/mol-geo/util/marching-cubes/algorithm.ts b/src/mol-geo/util/marching-cubes/algorithm.ts
index 248f05397..4b2eaf964 100644
--- a/src/mol-geo/util/marching-cubes/algorithm.ts
+++ b/src/mol-geo/util/marching-cubes/algorithm.ts
@@ -76,6 +76,7 @@ class MarchingCubesComputation {
const ret: Mesh = {
vertexCount: this.state.vertexCount,
triangleCount: this.state.triangleCount,
+ offsetCount: 0,
vertexBuffer: os ? ValueCell.update(os.vertexBuffer, vb) : ValueCell.create(vb),
indexBuffer: os ? ValueCell.update(os.indexBuffer, ib) : ValueCell.create(ib),
normalBuffer: os ? os.normalBuffer : ValueCell.create(new Float32Array(0)),
--
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