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Commit ec379968 authored by Alexander Rose's avatar Alexander Rose
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wip, molsurf

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src/mol-math/geometry/molecular-surface.ts
+ 116
− 85
View file @ ec379968
......@@ -45,6 +45,12 @@ function getAngleTables (probePositions: number): AnglesTables {
return { cosTable, sinTable}
}
function fillGridDim(a: Float32Array, start: number, step: number) {
for (let i = 0; i < a.length; i++) {
a[i] = start + (step * i)
}
}
/**
* Is the point at x,y,z obscured by any of the atoms specifeid by indices in neighbours.
* Ignore indices a and b (these are the relevant atoms in projectPoints/Torii)
......@@ -74,7 +80,7 @@ function obscured (state: MolSurfCalcState, x: number, y: number, z: number, a:
function singleAtomObscures (state: MolSurfCalcState, ai: number, x: number, y: number, z: number) {
const j = OrderedSet.getAt(state.position.indices, ai)
const r = state.position.radius[j] + state.probeRadius
const r = state.position.radius[j]
const dx = state.position.x[j] - x
const dy = state.position.y[j] - y
const dz = state.position.z[j] - z
......@@ -93,75 +99,73 @@ function singleAtomObscures (state: MolSurfCalcState, ai: number, x: number, y:
* itself and delta
*/
async function projectPoints (ctx: RuntimeContext, state: MolSurfCalcState) {
const { position, probeRadius, lookup3d, min, delta, space, data, idData } = state
const { position, lookup3d, min, space, data, idData, scaleFactor } = state
const { gridx, gridy, gridz } = state
const { indices, x, y, z, radius } = position
const n = OrderedSet.size(indices)
const v = Vec3()
const p = Vec3()
const c = Vec3()
const sp = Vec3()
const beg = Vec3()
const end = Vec3()
// const gridPad = 1 / Math.max(...delta)
const [ dimX, dimY, dimZ ] = space.dimensions
const iu = dimZ, iv = dimY, iuv = iu * iv
for (let i = 0; i < n; ++i) {
const j = OrderedSet.getAt(indices, i)
const vx = x[j], vy = y[j], vz = z[j]
const rad = radius[j]
const rSq = rad * rad
Vec3.set(v, x[j], y[j], z[j])
state.neighbours = lookup3d.find(v[0], v[1], v[2], radius[j] + probeRadius)
state.neighbours = lookup3d.find(vx, vy, vz, rad)
Vec3.sub(v, v, min)
Vec3.mul(c, v, delta)
// Number of grid points, round this up...
const ng = Math.ceil(rad * scaleFactor)
const rad = radius[j] + probeRadius
const rSq = rad * rad
// Center of the atom, mapped to grid points (take floor)
const iax = Math.floor(scaleFactor * (vx - min[0]))
const iay = Math.floor(scaleFactor * (vy - min[1]))
const iaz = Math.floor(scaleFactor * (vz - min[2]))
const r2 = rad // * 2 + gridPad
const rad2 = Vec3.create(r2, r2, r2)
Vec3.mul(rad2, rad2, delta)
// Extents of grid to consider for this atom
const begX = Math.max(0, iax - ng)
const begY = Math.max(0, iay - ng)
const begZ = Math.max(0, iaz - ng)
const [ begX, begY, begZ ] = Vec3.floor(beg, Vec3.sub(beg, c, rad2))
const [ endX, endY, endZ ] = Vec3.ceil(end, Vec3.add(end, c, rad2))
// Add two to these points:
// - iax are floor'd values so this ensures coverage
// - these are loop limits (exclusive)
const endX = Math.min(dimX, iax + ng + 2)
const endY = Math.min(dimY, iay + ng + 2)
const endZ = Math.min(dimZ, iaz + ng + 2)
for (let xi = begX; xi < endX; ++xi) {
const dx = gridx[xi] - vx
const xIdx = xi * iuv
for (let yi = begY; yi < endY; ++yi) {
const dy = gridy[yi] - vy
const dxySq = dx * dx + dy * dy
const xyIdx = yi * iu + xIdx
for (let zi = begZ; zi < endZ; ++zi) {
Vec3.set(p, xi, yi, zi)
Vec3.div(p, p, delta)
const dv = Vec3()
Vec3.sub(dv, p, v)
// const distSq = Vec3.squaredDistance(p, v)
const dSq = Vec3.squaredMagnitude(dv)
const dz = gridz[zi] - vz
const dSq = dxySq + dz * dz
if (dSq < rSq) {
const val = space.get(data, xi, yi, zi)
if (val < 0.0) {
// Unvisited, make positive
space.set(data, xi, yi, zi, -val)
}
const idx = zi + xyIdx
// if unvisited, make positive
if (data[idx] < 0.0) data[idx] *= -1
// Project on to the surface of the sphere
// sp is the projected point ( dx, dy, dz ) * ( ra / d )
// const dist = Math.sqrt(distSq)
const d = Math.sqrt(dSq)
const ap = rad / d
Vec3.scale(sp, dv, ap)
Vec3.add(sp, sp, v)
Vec3.add(sp, sp, min)
// Vec3.add(sp, v, Vec3.setMagnitude(sp, Vec3.sub(sp, p, v), rad - probeRadius))
const spx = dx * ap + vx
const spy = dy * ap + vy
const spz = dz * ap + vz
if (obscured(state, sp[0], sp[1], sp[2], i, -1) === -1) {
if (obscured(state, spx, spy, spz, i, -1) === -1) {
const dd = rad - d
if (dd < space.get(data, xi, yi, zi)) {
space.set(data, xi, yi, zi, dd)
space.set(idData, xi, yi, zi, i)
if (dd < data[idx]) {
data[idx] = dd
idData[idx] = i
}
}
}
......@@ -180,34 +184,34 @@ const atob = Vec3()
const mid = Vec3()
const n1 = Vec3()
const n2 = Vec3()
const v = Vec3()
const p = Vec3()
const c = Vec3()
const beg = Vec3()
const end = Vec3()
const radVec = Vec3()
function projectTorus (state: MolSurfCalcState, a: number, b: number) {
const { position, min, delta, space, data, idData } = state
const { cosTable, sinTable, probePositions, probeRadius, resolution } = state
const { position, min, space, data, idData } = state
const { cosTable, sinTable, probePositions, probeRadius, scaleFactor } = state
const { gridx, gridy, gridz } = state
const r1 = position.radius[a] + probeRadius
const r2 = position.radius[b] + probeRadius
const [ dimX, dimY, dimZ ] = space.dimensions
const iu = dimZ, iv = dimY, iuv = iu * iv
const ng = Math.max(5, 2 + Math.floor(probeRadius * scaleFactor))
const rA = position.radius[a]
const rB = position.radius[b]
const dx = atob[0] = position.x[b] - position.x[a]
const dy = atob[1] = position.y[b] - position.y[a]
const dz = atob[2] = position.z[b] - position.z[a]
const dSq = dx * dx + dy * dy + dz * dz
// This check now redundant as already done in AVHash.withinRadii
if (dSq > ((r1 + r2) * (r1 + r2))) { return }
if (dSq > ((rA + rB) * (rA + rB))) { return }
const d = Math.sqrt(dSq)
// Find angle between a->b vector and the circle
// of their intersection by cosine rule
const cosA = (r1 * r1 + d * d - r2 * r2) / (2.0 * r1 * d)
const cosA = (rA * rA + d * d - rB * rB) / (2.0 * rA * d)
// distance along a->b at intersection
const dmp = r1 * cosA
const dmp = rA * cosA
Vec3.normalize(atob, atob)
......@@ -220,7 +224,7 @@ function projectTorus (state: MolSurfCalcState, a: number, b: number) {
Vec3.normalize(n2, n2)
// r is radius of circle of intersection
const rInt = Math.sqrt(r1 * r1 - dmp * dmp)
const rInt = Math.sqrt(rA * rA - dmp * dmp)
Vec3.scale(n1, n1, rInt)
Vec3.scale(n2, n2, rInt)
......@@ -241,38 +245,40 @@ function projectTorus (state: MolSurfCalcState, a: number, b: number) {
const pz = mid[2] + cost * n1[2] + sint * n2[2]
if (obscured(state, px, py, pz, a, b) === -1) {
const iax = Math.floor(scaleFactor * (px - min[0]))
const iay = Math.floor(scaleFactor * (py - min[1]))
const iaz = Math.floor(scaleFactor * (pz - min[2]))
Vec3.set(v, px, py, pz)
Vec3.sub(v, v, min)
Vec3.mul(c, v, delta)
const begX = Math.max(0, iax - ng)
const begY = Math.max(0, iay - ng)
const begZ = Math.max(0, iaz - ng)
const rad = probeRadius / resolution
Vec3.set(radVec, rad, rad, rad)
Vec3.mul(radVec, radVec, delta)
const [ begX, begY, begZ ] = Vec3.floor(beg, Vec3.sub(beg, c, radVec))
const [ endX, endY, endZ ] = Vec3.ceil(end, Vec3.add(end, c, radVec))
const endX = Math.min(dimX, iax + ng + 2)
const endY = Math.min(dimY, iay + ng + 2)
const endZ = Math.min(dimZ, iaz + ng + 2)
for (let xi = begX; xi < endX; ++xi) {
const dx = px - gridx[xi]
const xIdx = xi * iuv
for (let yi = begY; yi < endY; ++yi) {
for (let zi = begZ; zi < endZ; ++zi) {
Vec3.set(p, xi, yi, zi)
Vec3.div(p, p, delta)
const dy = py - gridy[yi]
const dxySq = dx * dx + dy * dy
const xyIdx = yi * iu + xIdx
const dv = Vec3()
Vec3.sub(dv, v, p)
const dSq = Vec3.squaredMagnitude(dv)
for (let zi = begZ; zi < endZ; ++zi) {
const dz = pz - gridz[zi]
const dSq = dxySq + dz * dz
// const distSq = Vec3.squaredDistance(p, v)
const current = space.get(data, xi, yi, zi)
const idx = zi + xyIdx
const current = data[idx]
if (current > 0.0 && dSq < (current * current)) {
space.set(data, xi, yi, zi, Math.sqrt(dSq))
data[idx] = Math.sqrt(dSq)
// Is this grid point closer to a or b?
// Take dot product of atob and gridpoint->p (dx, dy, dz)
const dp = dx * atob[0] + dy * atob [1] + dz * atob[2]
space.set(idData, xi, yi, zi, dp < 0.0 ? b : a)
const dp = dx * atob[0] + dy * atob[1] + dz * atob[2]
idData[idx] = dp < 0.0 ? b : a
}
}
}
......@@ -282,13 +288,14 @@ function projectTorus (state: MolSurfCalcState, a: number, b: number) {
}
async function projectTorii (ctx: RuntimeContext, state: MolSurfCalcState) {
const { n, lookup3d, position, probeRadius, resolution } = state
const { x, y, z, radius } = position
const { n, lookup3d, position } = state
const { x, y, z, indices, radius } = position
for (let i = 0; i < n; ++i) {
state.neighbours = lookup3d.find(x[i], y[i], z[i], radius[i] + probeRadius / resolution)
const k = OrderedSet.getAt(indices, i)
state.neighbours = lookup3d.find(x[k], y[k], z[k], radius[k])
for (let j = 0, jl = state.neighbours.count; j < jl; ++j) {
const ib = state.neighbours.indices[j]
if (i < ib) projectTorus(state, i, ib)
const l = state.neighbours.indices[j]
if (k < l) projectTorus(state, k, l)
}
if (i % 10000 === 0 && ctx.shouldUpdate) {
......@@ -308,12 +315,14 @@ interface MolSurfCalcState {
lookup3d: Lookup3D
position: Required<PositionData>
delta: Vec3
invDelta: Vec3
min: Vec3
maxRadius: number
n: number
resolution: number
scaleFactor: number
probeRadius: number
/** Angle lookup tables */
......@@ -321,6 +330,11 @@ interface MolSurfCalcState {
sinTable: Float32Array
probePositions: number
/** grid lookup tables */
gridx: Float32Array
gridy: Float32Array
gridz: Float32Array
expandedBox: Box3D
space: Tensor.Space
data: Tensor.Data
......@@ -330,6 +344,8 @@ 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)
const box = lookup3d.boundary.box
const { indices } = position
......@@ -344,6 +360,7 @@ async function createState(ctx: RuntimeContext, position: Required<PositionData>
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 { cosTable, sinTable } = getAngleTables(probePositions)
......@@ -354,6 +371,14 @@ async function createState(ctx: RuntimeContext, position: Required<PositionData>
fillUniform(data, -1001.0)
fillUniform(idData, -1)
const gridx = new Float32Array(dim[0])
const gridy = new Float32Array(dim[1])
const gridz = new Float32Array(dim[2])
fillGridDim(gridx, min[0], resolution)
fillGridDim(gridy, min[1], resolution)
fillGridDim(gridz, min[2], resolution)
return {
lastClip: -1,
neighbours: lookup3d.find(0, 0, 0, 0),
......@@ -361,18 +386,24 @@ async function createState(ctx: RuntimeContext, position: Required<PositionData>
lookup3d,
position,
delta,
invDelta,
min,
maxRadius,
n,
resolution,
scaleFactor,
probeRadius,
cosTable,
sinTable,
probePositions,
gridx,
gridy,
gridz,
expandedBox,
space,
data,
......
src/mol-repr/structure/visual/util/molecular-surface.ts
+ 1
− 1
View file @ ec379968
......@@ -23,7 +23,7 @@ export function computeUnitMolecularSurface(unit: Unit, props: MolecularSurfaceC
for (let i = 0; i < n; ++i) {
const r = radius(OrderedSet.getAt(indices, i))
if (maxRadius < r) maxRadius = r
radii[i] = r
radii[i] = r + props.probeRadius
if (i % 10000 === 0 && ctx.shouldUpdate) {
await ctx.update({ message: 'calculating max radius', current: i, max: n })
......
src/tests/browser/render-structure.ts
+ 28
− 11
View file @ ec379968
......@@ -15,6 +15,7 @@ import { trajectoryFromMmCIF } from 'mol-model-formats/structure/mmcif';
import { computeModelDSSP } from 'mol-model/structure/model/properties/utils/secondary-structure';
import { MolecularSurfaceRepresentationProvider } from 'mol-repr/structure/representation/molecular-surface';
import { BallAndStickRepresentationProvider } from 'mol-repr/structure/representation/ball-and-stick';
import { GaussianSurfaceRepresentationProvider } from 'mol-repr/structure/representation/gaussian-surface';
const parent = document.getElementById('app')!
parent.style.width = '100%'
......@@ -71,6 +72,10 @@ function getMolecularSurfaceRepr() {
return MolecularSurfaceRepresentationProvider.factory(reprCtx, MolecularSurfaceRepresentationProvider.getParams)
}
function getGaussianSurfaceRepr() {
return GaussianSurfaceRepresentationProvider.factory(reprCtx, GaussianSurfaceRepresentationProvider.getParams)
}
async function init() {
const cif = await downloadFromPdb('1crn')
const models = await getModels(cif)
......@@ -82,28 +87,40 @@ async function init() {
const cartoonRepr = getCartoonRepr()
const ballAndStick = getBallAndStickRepr()
const molecularSurfaceRepr = getMolecularSurfaceRepr()
const gaussianSurfaceRepr = getGaussianSurfaceRepr()
cartoonRepr.setTheme({
color: reprCtx.colorThemeRegistry.create('secondary-structure', { structure }),
size: reprCtx.sizeThemeRegistry.create('uniform', { structure })
})
await cartoonRepr.createOrUpdate({ ...CartoonRepresentationProvider.defaultValues, quality: 'auto' }, structure).run()
// cartoonRepr.setTheme({
// color: reprCtx.colorThemeRegistry.create('secondary-structure', { structure }),
// size: reprCtx.sizeThemeRegistry.create('uniform', { structure })
// })
// await cartoonRepr.createOrUpdate({ ...CartoonRepresentationProvider.defaultValues, quality: 'auto' }, structure).run()
ballAndStick.setTheme({
color: reprCtx.colorThemeRegistry.create('secondary-structure', { structure }),
size: reprCtx.sizeThemeRegistry.create('uniform', { structure })
})
await ballAndStick.createOrUpdate({ ...BallAndStickRepresentationProvider.defaultValues, quality: 'auto' }, structure).run()
// ballAndStick.setTheme({
// color: reprCtx.colorThemeRegistry.create('secondary-structure', { structure }),
// size: reprCtx.sizeThemeRegistry.create('uniform', { structure })
// })
// await ballAndStick.createOrUpdate({ ...BallAndStickRepresentationProvider.defaultValues, quality: 'auto' }, structure).run()
molecularSurfaceRepr.setTheme({
color: reprCtx.colorThemeRegistry.create('secondary-structure', { structure }),
size: reprCtx.sizeThemeRegistry.create('physical', { structure })
})
await molecularSurfaceRepr.createOrUpdate({ ...MolecularSurfaceRepresentationProvider.defaultValues, quality: 'custom', alpha: 1.0, flatShaded: true, doubleSided: true, resolution: 0.5 }, structure).run()
console.time('molecular surface')
await molecularSurfaceRepr.createOrUpdate({ ...MolecularSurfaceRepresentationProvider.defaultValues, quality: 'custom', alpha: 1.0, flatShaded: true, doubleSided: true, resolution: 0.3 }, structure).run()
console.timeEnd('molecular surface')
// gaussianSurfaceRepr.setTheme({
// color: reprCtx.colorThemeRegistry.create('secondary-structure', { structure }),
// size: reprCtx.sizeThemeRegistry.create('physical', { structure })
// })
// console.time('gaussian surface')
// await gaussianSurfaceRepr.createOrUpdate({ ...GaussianSurfaceRepresentationProvider.defaultValues, quality: 'custom', alpha: 1.0, flatShaded: true, doubleSided: true, resolution: 0.3 }, structure).run()
// console.timeEnd('gaussian surface')
// canvas3d.add(cartoonRepr)
// canvas3d.add(ballAndStick)
canvas3d.add(molecularSurfaceRepr)
// canvas3d.add(gaussianSurfaceRepr)
canvas3d.resetCamera()
}
......
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