diff --git a/src/mol-math/geometry/gaussian-density.ts b/src/mol-math/geometry/gaussian-density.ts
index 0493f1d2118d62718bbd37f5e47eb4760a83e602..9e4cc3ddede86891e0ce29b0947cb9930cb777f8 100644
--- a/src/mol-math/geometry/gaussian-density.ts
+++ b/src/mol-math/geometry/gaussian-density.ts
@@ -5,7 +5,6 @@
*/
import { Box3D } from '../geometry';
-import { Vec3 } from '../linear-algebra';
import { RuntimeContext, Task } from 'mol-task';
import { PositionData, DensityData } from './common';
import { GaussianDensityCPU } from './gaussian-density/cpu';
@@ -34,14 +33,6 @@ export const DefaultGaussianDensityProps = {
}
export type GaussianDensityProps = typeof DefaultGaussianDensityProps
-export function getDelta(box: Box3D, resolution: number) {
- const extent = Vec3.sub(Vec3.zero(), box.max, box.min)
- const size = Vec3.zero()
- Vec3.ceil(size, Vec3.scale(size, extent, resolution))
- const delta = Vec3.div(Vec3.zero(), extent, size)
- return delta
-}
-
export function computeGaussianDensity(position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps, webgl?: WebGLContext) {
return Task.create('Gaussian Density', async ctx => {
return await GaussianDensity(ctx, position, box, radius, props, webgl)
diff --git a/src/mol-math/geometry/gaussian-density/cpu.ts b/src/mol-math/geometry/gaussian-density/cpu.ts
index a0676f7d722784d302765ab53b68c48f95813ad0..b2d82b4910d3b161e31bdf418902417bf19697e8 100644
--- a/src/mol-math/geometry/gaussian-density/cpu.ts
+++ b/src/mol-math/geometry/gaussian-density/cpu.ts
@@ -9,7 +9,7 @@ import { Vec3, Mat4, Tensor } from '../../linear-algebra';
import { RuntimeContext } from 'mol-task';
import { PositionData, DensityData } from '../common';
import { OrderedSet } from 'mol-data/int';
-import { GaussianDensityProps, getDelta } from '../gaussian-density';
+import { GaussianDensityProps } from '../gaussian-density';
export async function GaussianDensityCPU(ctx: RuntimeContext, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps): Promise<DensityData> {
const { resolution, radiusOffset, smoothness } = props
@@ -31,14 +31,11 @@ export async function GaussianDensityCPU(ctx: RuntimeContext, position: Position
}
const pad = maxRadius * 2 + resolution
- const expandedBox = Box3D.expand(Box3D.empty(), box, Vec3.create(pad, pad, pad))
- const extent = Vec3.sub(Vec3(), expandedBox.max, expandedBox.min)
+ const expandedBox = Box3D.expand(Box3D(), box, Vec3.create(pad, pad, pad));
const min = expandedBox.min
-
- const delta = getDelta(Box3D.expand(Box3D.empty(), box, Vec3.create(pad, pad, pad)), resolution)
- const dim = Vec3()
- Vec3.ceil(dim, Vec3.mul(dim, extent, delta))
- // console.log('grid dim cpu', dim)
+ const scaledBox = Box3D.scale(Box3D(), expandedBox, scaleFactor)
+ const dim = Box3D.size(Vec3(), scaledBox)
+ Vec3.ceil(dim, dim)
const space = Tensor.Space(dim, [0, 1, 2], Float32Array)
const data = space.create()
@@ -59,7 +56,7 @@ export async function GaussianDensityCPU(ctx: RuntimeContext, position: Position
const alpha = smoothness
const updateChunk = Math.ceil(1000000 / (Math.pow(maxRadius * 2, 3) * resolution))
- // console.time('gaussian density cpu')
+ console.time('gaussian density cpu')
for (let i = 0; i < n; ++i) {
const j = OrderedSet.getAt(indices, i)
const vx = x[j], vy = y[j], vz = z[j]
@@ -118,10 +115,10 @@ export async function GaussianDensityCPU(ctx: RuntimeContext, position: Position
await ctx.update({ message: 'filling density grid', current: i, max: n })
}
}
- // console.timeEnd('gaussian density cpu')
+ console.timeEnd('gaussian density cpu')
const transform = Mat4.identity()
- Mat4.fromScaling(transform, Vec3.inverse(Vec3.zero(), delta))
+ Mat4.fromScaling(transform, Vec3.create(resolution, resolution, resolution))
Mat4.setTranslation(transform, expandedBox.min)
return { field, idField, transform }
diff --git a/src/mol-math/geometry/molecular-surface.ts b/src/mol-math/geometry/molecular-surface.ts
index 678af0245ae89f3b24c898074548907972d2f102..254c348155141f0af78576034a760e42ab170b21 100644
--- a/src/mol-math/geometry/molecular-surface.ts
+++ b/src/mol-math/geometry/molecular-surface.ts
@@ -16,7 +16,6 @@ import { OrderedSet } from 'mol-data/int';
import { PositionData } from './common';
import { Mat4 } from 'mol-math/linear-algebra/3d';
import { Box3D, GridLookup3D, fillGridDim } from 'mol-math/geometry';
-import { getDelta } from './gaussian-density';
function normalToLine (out: Vec3, p: Vec3) {
out[0] = out[1] = out[2] = 1.0
@@ -308,8 +307,6 @@ interface MolSurfCalcState {
lookup3d: Lookup3D
position: Required<PositionData>
- delta: Vec3
- invDelta: Vec3
min: Vec3
maxRadius: number
@@ -337,7 +334,6 @@ interface MolSurfCalcState {
async function createState(ctx: RuntimeContext, position: Required<PositionData>, maxRadius: number, props: MolecularSurfaceCalculationProps): Promise<MolSurfCalcState> {
const { resolution, probeRadius, probePositions } = props
-
const scaleFactor = 1 / resolution
const lookup3d = GridLookup3D(position)
@@ -346,15 +342,11 @@ async function createState(ctx: RuntimeContext, position: Required<PositionData>
const n = OrderedSet.size(indices)
const pad = maxRadius * 2 + resolution
- const expandedBox = Box3D.expand(Box3D.empty(), box, Vec3.create(pad, pad, pad))
- const extent = Vec3.sub(Vec3.zero(), expandedBox.max, expandedBox.min)
+ const expandedBox = Box3D.expand(Box3D(), box, Vec3.create(pad, pad, pad));
const min = expandedBox.min
-
- const delta = getDelta(Box3D.expand(Box3D.empty(), box, Vec3.create(pad, pad, pad)), resolution)
- const dim = Vec3.zero()
- Vec3.ceil(dim, Vec3.mul(dim, extent, delta))
- console.log('grid dim surf', dim)
- const invDelta = Vec3.inverse(Vec3(), delta)
+ const scaledBox = Box3D.scale(Box3D(), expandedBox, scaleFactor)
+ const dim = Box3D.size(Vec3(), scaledBox)
+ Vec3.ceil(dim, dim)
const { cosTable, sinTable } = getAngleTables(probePositions)
@@ -377,8 +369,6 @@ async function createState(ctx: RuntimeContext, position: Required<PositionData>
lookup3d,
position,
- delta,
- invDelta,
min,
maxRadius,
@@ -437,9 +427,10 @@ export async function calcMolecularSurface(ctx: RuntimeContext, position: Requir
const field = Tensor.create(state.space, state.data)
const idField = Tensor.create(state.space, state.idData)
+ const { resolution, expandedBox } = state
const transform = Mat4.identity()
- Mat4.fromScaling(transform, Vec3.inverse(Vec3.zero(), state.delta))
- Mat4.setTranslation(transform, state.expandedBox.min)
+ Mat4.fromScaling(transform, Vec3.create(resolution, resolution, resolution))
+ Mat4.setTranslation(transform, expandedBox.min)
console.log({ field, idField, transform, state })
return { field, idField, transform }
}
\ No newline at end of file