molstar
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A comprehensive macromolecular library.
136 lines • 5.94 kB
JavaScript
;
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.MinimizeRmsd = void 0;
var mat4_1 = require("./mat4");
var evd_1 = require("../matrix/evd");
var centroid_helper_1 = require("../../../mol-math/geometry/centroid-helper");
var matrix_1 = require("../matrix/matrix");
var sphere3d_1 = require("../../geometry/primitives/sphere3d");
var MinimizeRmsd;
(function (MinimizeRmsd) {
var Positions;
(function (Positions) {
function empty(n) {
return { x: new Float64Array(n), y: new Float64Array(n), z: new Float64Array(n) };
}
Positions.empty = empty;
})(Positions = MinimizeRmsd.Positions || (MinimizeRmsd.Positions = {}));
function compute(data, result) {
if (typeof result === 'undefined')
result = { bTransform: mat4_1.Mat4.zero(), rmsd: 0.0 };
findMinimalRmsdTransformImpl(new RmsdTransformState(data, result));
return result;
}
MinimizeRmsd.compute = compute;
})(MinimizeRmsd || (MinimizeRmsd = {}));
exports.MinimizeRmsd = MinimizeRmsd;
var RmsdTransformState = /** @class */ (function () {
function RmsdTransformState(data, into) {
this.evdCache = evd_1.EVD.createCache(4);
this.translateB = mat4_1.Mat4.identity();
this.rotateB = mat4_1.Mat4.identity();
this.tempMatrix = mat4_1.Mat4.identity();
this.a = data.a;
this.b = data.b;
if (data.centerA)
this.centerA = data.centerA;
else
this.centerA = data.centerA = centroid_helper_1.CentroidHelper.fromArrays(data.a, (0, sphere3d_1.Sphere3D)()).center;
if (data.centerB)
this.centerB = data.centerB;
else
this.centerB = data.centerB = centroid_helper_1.CentroidHelper.fromArrays(data.b, (0, sphere3d_1.Sphere3D)()).center;
this.result = into;
}
return RmsdTransformState;
}());
function computeN(state) {
var N = state.evdCache.matrix;
matrix_1.Matrix.makeZero(N);
var xsA = state.a.x, ysA = state.a.y, zsA = state.a.z;
var xsB = state.b.x, ysB = state.b.y, zsB = state.b.z;
var cA = state.centerA;
var cB = state.centerB;
var sizeSq = 0.0;
for (var i = 0, _l = state.a.x.length; i < _l; i++) {
var aX = xsA[i] - cA[0], aY = ysA[i] - cA[1], aZ = zsA[i] - cA[2];
var bX = xsB[i] - cB[0], bY = ysB[i] - cB[1], bZ = zsB[i] - cB[2];
sizeSq += aX * aX + aY * aY + aZ * aZ + bX * bX + bY * bY + bZ * bZ;
matrix_1.Matrix.add(N, 0, 0, aX * bX + aY * bY + aZ * bZ);
matrix_1.Matrix.add(N, 0, 1, -(aZ * bY) + aY * bZ);
matrix_1.Matrix.add(N, 0, 2, aZ * bX - aX * bZ);
matrix_1.Matrix.add(N, 0, 3, -(aY * bX) + aX * bY);
matrix_1.Matrix.add(N, 1, 0, -(aZ * bY) + aY * bZ);
matrix_1.Matrix.add(N, 1, 1, aX * bX - aY * bY - aZ * bZ);
matrix_1.Matrix.add(N, 1, 2, aY * bX + aX * bY);
matrix_1.Matrix.add(N, 1, 3, aZ * bX + aX * bZ);
matrix_1.Matrix.add(N, 2, 0, aZ * bX - aX * bZ);
matrix_1.Matrix.add(N, 2, 1, aY * bX + aX * bY);
matrix_1.Matrix.add(N, 2, 2, -(aX * bX) + aY * bY - aZ * bZ);
matrix_1.Matrix.add(N, 2, 3, aZ * bY + aY * bZ);
matrix_1.Matrix.add(N, 3, 0, -(aY * bX) + aX * bY);
matrix_1.Matrix.add(N, 3, 1, aZ * bX + aX * bZ);
matrix_1.Matrix.add(N, 3, 2, aZ * bY + aY * bZ);
matrix_1.Matrix.add(N, 3, 3, -(aX * bX) - aY * bY + aZ * bZ);
// conjugate instead of transpose.
// var l = new Quaternion(-a.X, -a.Y, -a.Z, 0).RightMultiplicationToMatrix();
// l.Transpose();
// var r = new Quaternion(b.X, b.Y, b.Z, 0).LeftMultiplicationToMatrix();
// N += l * r;
}
return sizeSq;
}
function makeTransformMatrix(state) {
var ev = state.evdCache.matrix;
var qX = matrix_1.Matrix.get(ev, 1, 3);
var qY = matrix_1.Matrix.get(ev, 2, 3);
var qZ = matrix_1.Matrix.get(ev, 3, 3);
var qW = matrix_1.Matrix.get(ev, 0, 3);
var n1 = 2 * qY * qY;
var n2 = 2 * qZ * qZ;
var n3 = 2 * qX * qX;
var n4 = 2 * qX * qY;
var n5 = 2 * qW * qZ;
var n6 = 2 * qX * qZ;
var n7 = 2 * qW * qY;
var n8 = 2 * qY * qZ;
var n9 = 2 * qW * qX;
var m = state.translateB;
// translation to center
mat4_1.Mat4.setValue(m, 0, 3, -state.centerB[0]);
mat4_1.Mat4.setValue(m, 1, 3, -state.centerB[1]);
mat4_1.Mat4.setValue(m, 2, 3, -state.centerB[2]);
m = state.rotateB;
// rotation
mat4_1.Mat4.setValue(m, 0, 0, 1 - n1 - n2);
mat4_1.Mat4.setValue(m, 0, 1, n4 + n5);
mat4_1.Mat4.setValue(m, 0, 2, n6 - n7);
mat4_1.Mat4.setValue(m, 1, 0, n4 - n5);
mat4_1.Mat4.setValue(m, 1, 1, 1 - n3 - n2);
mat4_1.Mat4.setValue(m, 1, 2, n8 + n9);
mat4_1.Mat4.setValue(m, 2, 0, n6 + n7);
mat4_1.Mat4.setValue(m, 2, 1, n8 - n9);
mat4_1.Mat4.setValue(m, 2, 2, 1 - n3 - n1);
mat4_1.Mat4.setValue(m, 3, 3, 1);
mat4_1.Mat4.mul(state.tempMatrix, state.rotateB, state.translateB);
m = state.translateB;
// translation to center
mat4_1.Mat4.setValue(m, 0, 3, state.centerA[0]);
mat4_1.Mat4.setValue(m, 1, 3, state.centerA[1]);
mat4_1.Mat4.setValue(m, 2, 3, state.centerA[2]);
mat4_1.Mat4.mul(state.result.bTransform, state.translateB, state.tempMatrix);
}
function findMinimalRmsdTransformImpl(state) {
var sizeSq = computeN(state);
evd_1.EVD.compute(state.evdCache);
var rmsd = sizeSq - 2.0 * state.evdCache.eigenValues[3];
rmsd = rmsd < 0.0 ? 0.0 : Math.sqrt(rmsd / state.a.x.length);
makeTransformMatrix(state);
state.result.rmsd = rmsd;
}
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