diff --git a/src/apps/canvas/structure-view.ts b/src/apps/canvas/structure-view.ts
index e4acd4e8e3deea2217ac17b790f826bd74becdcb..ea70b750cea30a16ecb9542610fe87a8f0679951 100644
--- a/src/apps/canvas/structure-view.ts
+++ b/src/apps/canvas/structure-view.ts
@@ -68,7 +68,7 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
const active: { [k: string]: boolean } = {
cartoon: true,
point: false,
- surface: false,
+ surface: true,
ballAndStick: false,
carbohydrate: false,
spacefill: false,
@@ -209,7 +209,7 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
console.log('createStructureRepr')
for (const k in structureRepresentations) {
if (active[k]) {
- await structureRepresentations[k].createOrUpdate({}, structure).run(
+ await structureRepresentations[k].createOrUpdate({ colorTheme: { name: 'element-index' } }, structure).run(
// progress => console.log(Progress.format(progress))
)
viewer.add(structureRepresentations[k])
diff --git a/src/mol-geo/geometry/mesh/mesh.ts b/src/mol-geo/geometry/mesh/mesh.ts
index 255cff2ccf44657d55ebec116ba4e714aef29805..c71247c59338ef274f86a26d5db31e0376bd688d 100644
--- a/src/mol-geo/geometry/mesh/mesh.ts
+++ b/src/mol-geo/geometry/mesh/mesh.ts
@@ -15,6 +15,7 @@ import { createMarkers } from '../marker-data';
import { TransformData } from '../transform-data';
import { LocationIterator } from '../../util/location-iterator';
import { createColors } from '../color-data';
+import { ChunkedArray } from 'mol-data/util';
export interface Mesh {
readonly kind: 'mesh',
@@ -160,6 +161,71 @@ export namespace Mesh {
});
}
+ /**
+ * Ensure that each vertices of each triangle have the same group id.
+ * Note that normals are copied over and can't be re-created from the new mesh.
+ */
+ export function uniformTriangleGroup(mesh: Mesh) {
+ const { indexBuffer, vertexBuffer, groupBuffer, normalBuffer, triangleCount, vertexCount } = mesh
+ const ib = indexBuffer.ref.value
+ const vb = vertexBuffer.ref.value
+ const gb = groupBuffer.ref.value
+ const nb = normalBuffer.ref.value
+
+ // new
+ const index = ChunkedArray.create(Uint32Array, 3, 1024, triangleCount)
+
+ // re-use
+ const vertex = ChunkedArray.create(Float32Array, 3, 1024, vb)
+ vertex.currentIndex = vertexCount * 3
+ vertex.elementCount = vertexCount
+ const normal = ChunkedArray.create(Float32Array, 3, 1024, nb)
+ normal.currentIndex = vertexCount * 3
+ normal.elementCount = vertexCount
+ const group = ChunkedArray.create(Float32Array, 1, 1024, gb)
+ group.currentIndex = vertexCount
+ group.elementCount = vertexCount
+
+ const v = Vec3.zero()
+ const n = Vec3.zero()
+
+ function add(i: number) {
+ Vec3.fromArray(v, vb, i * 3)
+ Vec3.fromArray(n, nb, i * 3)
+ ChunkedArray.add3(vertex, v[0], v[1], v[2])
+ ChunkedArray.add3(normal, n[0], n[1], n[2])
+ }
+
+ let newVertexCount = vertexCount
+ for (let i = 0, il = triangleCount; i < il; ++i) {
+ const i0 = ib[i * 3], i1 = ib[i * 3 + 1], i2 = ib[i * 3 + 2]
+ const g0 = gb[i0], g1 = gb[i1], g2 = gb[i2]
+ if (g0 !== g1 || g0 !== g2) {
+ add(i0); add(i1); add(i2)
+ ChunkedArray.add3(index, newVertexCount, newVertexCount + 1, newVertexCount + 2)
+ const g = g1 === g2 ? g1 : g0
+ for (let j = 0; j < 3; ++j) ChunkedArray.add(group, g)
+ newVertexCount += 3
+ } else {
+ ChunkedArray.add3(index, i0, i1, i2)
+ }
+ }
+
+ const newIb = ChunkedArray.compact(index)
+ const newVb = ChunkedArray.compact(vertex)
+ const newNb = ChunkedArray.compact(normal)
+ const newGb = ChunkedArray.compact(group)
+
+ mesh.vertexCount = newVertexCount
+
+ ValueCell.update(vertexBuffer, newVb) as ValueCell<Float32Array>
+ ValueCell.update(groupBuffer, newGb) as ValueCell<Float32Array>
+ ValueCell.update(indexBuffer, newIb) as ValueCell<Uint32Array>
+ ValueCell.update(normalBuffer, newNb) as ValueCell<Float32Array>
+
+ return mesh
+ }
+
//
export const DefaultProps = {
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 6c9cb6e048cd2d63026a5b067988d556303fd102..f4fabf6403bca4f58835e056d5b87b415bdce192 100644
--- a/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
@@ -15,17 +15,24 @@ import { computeGaussianDensity, DefaultGaussianDensityProps } from './util/gaus
async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianSurfaceProps, mesh?: Mesh): Promise<Mesh> {
const { smoothness } = props
- const { transform, field } = await computeGaussianDensity(unit, structure, props).runAsChild(ctx)
+ const { transform, field, idField } = await computeGaussianDensity(unit, structure, props).runAsChild(ctx)
+ console.time('mc')
const surface = await computeMarchingCubes({
isoLevel: Math.exp(-smoothness),
scalarField: field,
+ idField,
oldSurface: mesh
}).runAsChild(ctx)
+ console.timeEnd('mc')
Mesh.transformImmediate(surface, transform)
Mesh.computeNormalsImmediate(surface)
+ console.time('uniformTriangleGroup')
+ Mesh.uniformTriangleGroup(surface)
+ console.timeEnd('uniformTriangleGroup')
+
return surface;
}
diff --git a/src/mol-geo/representation/structure/visual/util/gaussian.ts b/src/mol-geo/representation/structure/visual/util/gaussian.ts
index 20505c1f1573567723ed0b1ef8b5813e82a3ee4f..348bab5c29a94f10ae45f6d4a165e3aa572c276a 100644
--- a/src/mol-geo/representation/structure/visual/util/gaussian.ts
+++ b/src/mol-geo/representation/structure/visual/util/gaussian.ts
@@ -11,7 +11,7 @@ import { Box3D } from 'mol-math/geometry';
import { SizeTheme } from 'mol-view/theme/size';
export const DefaultGaussianDensityProps = {
- resolutionFactor: 7,
+ resolutionFactor: 6,
radiusOffset: 0,
smoothness: 1.5,
}
@@ -28,7 +28,7 @@ function getDelta(box: Box3D, resolutionFactor: number) {
return delta
}
-type Density = { transform: Mat4, field: Tensor }
+type Density = { transform: Mat4, field: Tensor, idField: Tensor }
export function computeGaussianDensity(unit: Unit, structure: Structure, props: GaussianDensityProps) {
return Task.create('Gaussian Density', async ctx => {
@@ -74,6 +74,7 @@ export async function GaussianDensity(ctx: RuntimeContext, unit: Unit, structure
const beg = Vec3.zero()
const end = Vec3.zero()
+ console.time('density grid')
for (let i = 0; i < elementCount; i++) {
l.element = elements[i]
pos(elements[i], v)
@@ -109,13 +110,59 @@ export async function GaussianDensity(ctx: RuntimeContext, unit: Unit, structure
await ctx.update({ message: 'filling density grid', current: i, max: elementCount });
}
}
+ console.timeEnd('density grid')
const t = Mat4.identity()
Mat4.fromScaling(t, Vec3.inverse(Vec3.zero(), delta))
Mat4.setTranslation(t, expandedBox.min)
+ const { dimensions, get } = space
+ const [ xn, yn, zn ] = dimensions
+
+ const n = xn * yn * zn
+ const idData = space.create()
+ const idField = Tensor.create(space, idData)
+
+ const lookup3d = unit.lookup3d
+
+ let i = 0
+
+ // TODO use max radius of radiusTheme instead of 4
+ const _rSq = 4 + 1 / Math.max(...delta)
+ const _minDsq = _rSq * 4
+
+ console.time('id grid')
+ for (let x = 0; x < xn; ++x) {
+ for (let y = 0; y < yn; ++y) {
+ for (let z = 0; z < zn; ++z) {
+ const dens = get(data, x, y, z)
+ let group = -1
+ if (dens > 0 && dens < 2) {
+ Vec3.set(p, x, y, z)
+ Vec3.transformMat4(p, p, t)
+ const r = lookup3d.find(p[0], p[1], p[2], _rSq)
+ let minDsq = _minDsq
+ for (let j = 0, jl = r.count; j < jl; ++j) {
+ const dSq = r.squaredDistances[j]
+ if (dSq < minDsq) {
+ minDsq = dSq
+ group = r.indices[j]
+ }
+ }
+ }
+ space.set(idData, x, y, z, group)
+ if (i % 1000000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'filling id grid', current: i, max: n });
+ }
+ ++i
+ }
+ }
+ }
+ console.timeEnd('id grid')
+
return {
field,
+ idField,
transform: t
}
}
\ No newline at end of file
diff --git a/src/mol-math/geometry/lookup3d/grid.ts b/src/mol-math/geometry/lookup3d/grid.ts
index e91b0aff68af67792644b4ce9f4348b9186d0fb5..6fa09806898f2d7122b88a673613ca356d17a4a6 100644
--- a/src/mol-math/geometry/lookup3d/grid.ts
+++ b/src/mol-math/geometry/lookup3d/grid.ts
@@ -212,7 +212,7 @@ function build(data: PositionData, cellSize?: Vec3) {
}
interface QueryContext {
- structure: Grid3D,
+ grid: Grid3D,
x: number,
y: number,
z: number,
@@ -221,12 +221,12 @@ interface QueryContext {
isCheck: boolean
}
-function createContext(structure: Grid3D): QueryContext {
- return { structure, x: 0.1, y: 0.1, z: 0.1, radius: 0.1, result: Result.create(), isCheck: false }
+function createContext(grid: Grid3D): QueryContext {
+ return { grid, x: 0.1, y: 0.1, z: 0.1, radius: 0.1, result: Result.create(), isCheck: false }
}
function query(ctx: QueryContext): boolean {
- const { min, size: [sX, sY, sZ], bucketOffset, bucketCounts, bucketArray, grid, data: { x: px, y: py, z: pz, indices, radius }, delta, maxRadius } = ctx.structure;
+ const { min, size: [sX, sY, sZ], bucketOffset, bucketCounts, bucketArray, grid, data: { x: px, y: py, z: pz, indices, radius }, delta, maxRadius } = ctx.grid;
const { radius: inputRadius, isCheck, x, y, z, result } = ctx;
const r = inputRadius + maxRadius;