molstar
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A comprehensive macromolecular library.
311 lines (310 loc) • 13.8 kB
JavaScript
/**
* Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Fred Ludlow <fred.ludlow@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*
* ported from NGL (https://github.com/arose/ngl), licensed under MIT
*/
import { Vec3, Tensor } from '../../mol-math/linear-algebra';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { OrderedSet } from '../../mol-data/int';
import { Mat4 } from '../../mol-math/linear-algebra/3d/mat4';
import { Box3D, GridLookup3D, fillGridDim } from '../../mol-math/geometry';
import { BaseGeometry } from '../../mol-geo/geometry/base';
function normalToLine(out, p) {
out[0] = out[1] = out[2] = 1.0;
if (p[0] !== 0) {
out[0] = (p[1] + p[2]) / -p[0];
}
else if (p[1] !== 0) {
out[1] = (p[0] + p[2]) / -p[1];
}
else if (p[2] !== 0) {
out[2] = (p[0] + p[1]) / -p[2];
}
return out;
}
function getAngleTables(probePositions) {
let theta = 0.0;
const step = 2 * Math.PI / probePositions;
const cosTable = new Float32Array(probePositions);
const sinTable = new Float32Array(probePositions);
for (let i = 0; i < probePositions; i++) {
cosTable[i] = Math.cos(theta);
sinTable[i] = Math.sin(theta);
theta += step;
}
return { cosTable, sinTable };
}
//
export const MolecularSurfaceCalculationParams = {
probeRadius: PD.Numeric(1.4, { min: 0, max: 10, step: 0.1 }, { description: 'Radius of the probe tracing the molecular surface.' }),
resolution: PD.Numeric(0.5, { min: 0.01, max: 20, step: 0.01 }, { description: 'Grid resolution/cell spacing.', ...BaseGeometry.CustomQualityParamInfo }),
probePositions: PD.Numeric(36, { min: 12, max: 90, step: 1 }, { description: 'Number of positions tested for probe target intersection.', ...BaseGeometry.CustomQualityParamInfo }),
};
export const DefaultMolecularSurfaceCalculationProps = PD.getDefaultValues(MolecularSurfaceCalculationParams);
export async function calcMolecularSurface(ctx, position, boundary, maxRadius, box, props) {
// Field generation method adapted from AstexViewer (Mike Hartshorn) by Fred Ludlow.
// Other parts based heavily on NGL (Alexander Rose) EDT Surface class
let lastClip = -1;
/**
* 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)
*
* Cache the last clipped atom (as very often the same one in subsequent calls)
*
* `a` and `b` must be resolved indices
*/
function obscured(x, y, z, a, b) {
if (lastClip !== -1) {
const ai = lastClip;
if (ai !== a && ai !== b && singleAtomObscures(ai, x, y, z)) {
return ai;
}
else {
lastClip = -1;
}
}
for (let j = 0, jl = neighbours.count; j < jl; ++j) {
const ai = OrderedSet.getAt(indices, neighbours.indices[j]);
if (ai !== a && ai !== b && singleAtomObscures(ai, x, y, z)) {
lastClip = ai;
return ai;
}
}
return -1;
}
/**
* `ai` must be a resolved index
*/
function singleAtomObscures(ai, x, y, z) {
const r = radius[ai];
const dx = px[ai] - x;
const dy = py[ai] - y;
const dz = pz[ai] - z;
const dSq = dx * dx + dy * dy + dz * dz;
return dSq < (r * r);
}
/**
* For each atom:
* Iterate over a subsection of the grid, for each point:
* If current value < 0.0, unvisited, set positive
*
* In any case: Project this point onto surface of the atomic sphere
* If this projected point is not obscured by any other atom
* Calculate delta distance and set grid value to minimum of
* itself and delta
*/
function projectPointsRange(begI, endI) {
for (let i = begI; i < endI; ++i) {
const j = OrderedSet.getAt(indices, i);
const vx = px[j], vy = py[j], vz = pz[j];
const rad = radius[j];
const rSq = rad * rad;
lookup3d.find(vx, vy, vz, rad);
// Number of grid points, round this up...
const ng = Math.ceil(rad * scaleFactor);
// Center of the atom, mapped to grid points (take floor)
const iax = Math.floor(scaleFactor * (vx - minX));
const iay = Math.floor(scaleFactor * (vy - minY));
const iaz = Math.floor(scaleFactor * (vz - minZ));
// 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);
// 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) {
const dz = gridz[zi] - vz;
const dSq = dxySq + dz * dz;
if (dSq < rSq) {
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 d = Math.sqrt(dSq);
const ap = rad / d;
const spx = dx * ap + vx;
const spy = dy * ap + vy;
const spz = dz * ap + vz;
if (obscured(spx, spy, spz, j, -1) === -1) {
const dd = rad - d;
if (dd < data[idx]) {
data[idx] = dd;
idData[idx] = id[i];
}
}
}
}
}
}
}
}
async function projectPoints() {
for (let i = 0; i < n; i += updateChunk) {
projectPointsRange(i, Math.min(i + updateChunk, n));
if (ctx.shouldUpdate) {
await ctx.update({ message: 'projecting points', current: i, max: n });
}
}
}
// Vectors for Torus Projection
const atob = Vec3();
const mid = Vec3();
const n1 = Vec3();
const n2 = Vec3();
/**
* `a` and `b` must be resolved indices
*/
function projectTorus(a, b) {
const rA = radius[a];
const rB = radius[b];
const dx = atob[0] = px[b] - px[a];
const dy = atob[1] = py[b] - py[a];
const dz = atob[2] = pz[b] - pz[a];
const dSq = dx * dx + dy * dy + dz * dz;
// This check now redundant as already done in AVHash.withinRadii
// 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 = (rA * rA + d * d - rB * rB) / (2.0 * rA * d);
// distance along a->b at intersection
const dmp = rA * cosA;
Vec3.normalize(atob, atob);
// Create normal to line
normalToLine(n1, atob);
Vec3.normalize(n1, n1);
// Cross together for second normal vector
Vec3.cross(n2, atob, n1);
Vec3.normalize(n2, n2);
// r is radius of circle of intersection
const rInt = Math.sqrt(rA * rA - dmp * dmp);
Vec3.scale(n1, n1, rInt);
Vec3.scale(n2, n2, rInt);
Vec3.scale(atob, atob, dmp);
mid[0] = atob[0] + px[a];
mid[1] = atob[1] + py[a];
mid[2] = atob[2] + pz[a];
lastClip = -1;
for (let i = 0; i < probePositions; ++i) {
const cost = cosTable[i];
const sint = sinTable[i];
const px = mid[0] + cost * n1[0] + sint * n2[0];
const py = mid[1] + cost * n1[1] + sint * n2[1];
const pz = mid[2] + cost * n1[2] + sint * n2[2];
if (obscured(px, py, pz, a, b) === -1) {
const iax = Math.floor(scaleFactor * (px - minX));
const iay = Math.floor(scaleFactor * (py - minY));
const iaz = Math.floor(scaleFactor * (pz - minZ));
const begX = Math.max(0, iax - ngTorus);
const begY = Math.max(0, iay - ngTorus);
const begZ = Math.max(0, iaz - ngTorus);
const endX = Math.min(dimX, iax + ngTorus + 2);
const endY = Math.min(dimY, iay + ngTorus + 2);
const endZ = Math.min(dimZ, iaz + ngTorus + 2);
for (let xi = begX; xi < endX; ++xi) {
const dx = px - gridx[xi];
const xIdx = xi * iuv;
for (let yi = begY; yi < endY; ++yi) {
const dy = py - gridy[yi];
const dxySq = dx * dx + dy * dy;
const xyIdx = yi * iu + xIdx;
for (let zi = begZ; zi < endZ; ++zi) {
const dz = pz - gridz[zi];
const dSq = dxySq + dz * dz;
const idx = zi + xyIdx;
const current = data[idx];
if (current > 0.0 && dSq < (current * current)) {
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];
idData[idx] = id[OrderedSet.indexOf(indices, dp < 0.0 ? b : a)];
}
}
}
}
}
}
}
function projectToriiRange(begI, endI) {
for (let i = begI; i < endI; ++i) {
const k = OrderedSet.getAt(indices, i);
lookup3d.find(px[k], py[k], pz[k], radius[k]);
for (let j = 0, jl = neighbours.count; j < jl; ++j) {
const l = OrderedSet.getAt(indices, neighbours.indices[j]);
if (k < l)
projectTorus(k, l);
}
}
}
async function projectTorii() {
for (let i = 0; i < n; i += updateChunk) {
projectToriiRange(i, Math.min(i + updateChunk, n));
if (ctx.shouldUpdate) {
await ctx.update({ message: 'projecting torii', current: i, max: n });
}
}
}
// console.time('MolecularSurface')
// console.time('MolecularSurface createState')
const { resolution, probeRadius, probePositions } = props;
const scaleFactor = 1 / resolution;
const ngTorus = Math.max(5, 2 + Math.floor(probeRadius * scaleFactor));
const cellSize = Vec3.create(maxRadius, maxRadius, maxRadius);
Vec3.scale(cellSize, cellSize, 2);
const lookup3d = GridLookup3D(position, boundary, cellSize);
const neighbours = lookup3d.result;
if (box === null)
box = lookup3d.boundary.box;
const { indices, x: px, y: py, z: pz, id, radius } = position;
const n = OrderedSet.size(indices);
const pad = maxRadius + resolution;
const expandedBox = Box3D.expand(Box3D(), box, Vec3.create(pad, pad, pad));
const [minX, minY, minZ] = expandedBox.min;
const scaledBox = Box3D.scale(Box3D(), expandedBox, scaleFactor);
const dim = Box3D.size(Vec3(), scaledBox);
Vec3.ceil(dim, dim);
const [dimX, dimY, dimZ] = dim;
const iu = dimZ, iv = dimY, iuv = iu * iv;
const { cosTable, sinTable } = getAngleTables(probePositions);
const space = Tensor.Space(dim, [0, 1, 2], Float32Array);
const data = space.create();
const idData = space.create();
data.fill(-1001.0);
idData.fill(-1);
const gridx = fillGridDim(dimX, minX, resolution);
const gridy = fillGridDim(dimY, minY, resolution);
const gridz = fillGridDim(dimZ, minZ, resolution);
const updateChunk = Math.ceil(100000 / ((Math.pow(Math.pow(maxRadius, 3), 3) * scaleFactor)));
// console.timeEnd('MolecularSurface createState')
// console.time('MolecularSurface projectPoints')
await projectPoints();
// console.timeEnd('MolecularSurface projectPoints')
// console.time('MolecularSurface projectTorii')
await projectTorii();
// console.timeEnd('MolecularSurface projectTorii')
// console.timeEnd('MolecularSurface')
const field = Tensor.create(space, data);
const idField = Tensor.create(space, idData);
const transform = Mat4.identity();
Mat4.fromScaling(transform, Vec3.create(resolution, resolution, resolution));
Mat4.setTranslation(transform, expandedBox.min);
// console.log({ field, idField, transform, updateChunk })
return { field, idField, transform, resolution, maxRadius };
}