molstar
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A comprehensive macromolecular library.
111 lines (110 loc) • 5.25 kB
JavaScript
;
/**
* Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.Grid = void 0;
const geometry_1 = require("../../mol-math/geometry");
const linear_algebra_1 = require("../../mol-math/linear-algebra");
const histogram_1 = require("../../mol-math/histogram");
const interpolate_1 = require("../../mol-math/interpolate");
var Grid;
(function (Grid) {
Grid.One = {
transform: { kind: 'matrix', matrix: linear_algebra_1.Mat4.identity() },
cells: linear_algebra_1.Tensor.create(linear_algebra_1.Tensor.Space([1, 1, 1], [0, 1, 2]), linear_algebra_1.Tensor.Data1([0])),
stats: { min: 0, max: 0, mean: 0, sigma: 0 },
};
const _scale = linear_algebra_1.Mat4.zero(), _translate = linear_algebra_1.Mat4.zero();
function getGridToCartesianTransform(grid) {
if (grid.transform.kind === 'matrix') {
return linear_algebra_1.Mat4.copy((0, linear_algebra_1.Mat4)(), grid.transform.matrix);
}
if (grid.transform.kind === 'spacegroup') {
const { cells: { space } } = grid;
const scale = linear_algebra_1.Mat4.fromScaling(_scale, linear_algebra_1.Vec3.div(linear_algebra_1.Vec3.zero(), geometry_1.Box3D.size(linear_algebra_1.Vec3.zero(), grid.transform.fractionalBox), linear_algebra_1.Vec3.ofArray(space.dimensions)));
const translate = linear_algebra_1.Mat4.fromTranslation(_translate, grid.transform.fractionalBox.min);
return linear_algebra_1.Mat4.mul3(linear_algebra_1.Mat4.zero(), grid.transform.cell.fromFractional, translate, scale);
}
return linear_algebra_1.Mat4.identity();
}
Grid.getGridToCartesianTransform = getGridToCartesianTransform;
function areEquivalent(gridA, gridB) {
return gridA === gridB;
}
Grid.areEquivalent = areEquivalent;
function isEmpty(grid) {
return grid.cells.data.length === 0;
}
Grid.isEmpty = isEmpty;
function getBoundingSphere(grid, boundingSphere) {
if (!boundingSphere)
boundingSphere = (0, geometry_1.Sphere3D)();
const dimensions = grid.cells.space.dimensions;
const transform = Grid.getGridToCartesianTransform(grid);
return geometry_1.Sphere3D.fromDimensionsAndTransform(boundingSphere, dimensions, transform);
}
Grid.getBoundingSphere = getBoundingSphere;
/**
* Compute histogram with given bin count.
* Cached on the Grid object.
*/
function getHistogram(grid, binCount) {
let histograms = grid._historams;
if (!histograms) {
histograms = grid._historams = {};
}
if (!histograms[binCount]) {
histograms[binCount] = (0, histogram_1.calculateHistogram)(grid.cells.data, binCount, { min: grid.stats.min, max: grid.stats.max });
}
return histograms[binCount];
}
Grid.getHistogram = getHistogram;
function makeGetTrilinearlyInterpolated(grid, transform) {
const cartnToGrid = Grid.getGridToCartesianTransform(grid);
linear_algebra_1.Mat4.invert(cartnToGrid, cartnToGrid);
const gridCoords = (0, linear_algebra_1.Vec3)();
const { stats } = grid;
const { dimensions, get } = grid.cells.space;
const data = grid.cells.data;
const [mi, mj, mk] = dimensions;
return function getTrilinearlyInterpolated(position) {
linear_algebra_1.Vec3.copy(gridCoords, position);
linear_algebra_1.Vec3.transformMat4(gridCoords, gridCoords, cartnToGrid);
const i = Math.trunc(gridCoords[0]);
const j = Math.trunc(gridCoords[1]);
const k = Math.trunc(gridCoords[2]);
if (i < 0 || i >= mi || j < 0 || j >= mj || k < 0 || k >= mk) {
return Number.NaN;
}
const u = gridCoords[0] - i;
const v = gridCoords[1] - j;
const w = gridCoords[2] - k;
// Tri-linear interpolation for the value
const ii = Math.min(i + 1, mi - 1);
const jj = Math.min(j + 1, mj - 1);
const kk = Math.min(k + 1, mk - 1);
let a = get(data, i, j, k);
let b = get(data, ii, j, k);
let c = get(data, i, jj, k);
let d = get(data, ii, jj, k);
const x = (0, interpolate_1.lerp)((0, interpolate_1.lerp)(a, b, u), (0, interpolate_1.lerp)(c, d, u), v);
a = get(data, i, j, kk);
b = get(data, ii, j, kk);
c = get(data, i, jj, kk);
d = get(data, ii, jj, kk);
const y = (0, interpolate_1.lerp)((0, interpolate_1.lerp)(a, b, u), (0, interpolate_1.lerp)(c, d, u), v);
const value = (0, interpolate_1.lerp)(x, y, w);
if (transform === 'relative') {
return (value - stats.mean) / stats.sigma;
}
else {
return value;
}
};
}
Grid.makeGetTrilinearlyInterpolated = makeGetTrilinearlyInterpolated;
})(Grid || (exports.Grid = Grid = {}));