molstar
Version:
A comprehensive macromolecular library.
107 lines • 4.31 kB
JavaScript
/**
* Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Segmentation } from '../../../mol-data/int/segmentation';
import { SortedRanges } from '../../../mol-data/int/sorted-ranges';
import { OrderedSet } from '../../../mol-data/int';
import { Vec3 } from '../../../mol-math/linear-algebra';
/** Usees same definition as GROMACS' helixorient */
export function calcHelixOrientation(model) {
var _a = model.atomicConformation, x = _a.x, y = _a.y, z = _a.z;
var _b = model.atomicHierarchy.derived.residue, polymerType = _b.polymerType, traceElementIndex = _b.traceElementIndex;
var n = polymerType.length;
var elements = OrderedSet.ofBounds(0, model.atomicConformation.atomId.rowCount);
var polymerIt = SortedRanges.transientSegments(model.atomicRanges.polymerRanges, elements);
var residueIt = Segmentation.transientSegments(model.atomicHierarchy.residueAtomSegments, elements);
var centers = new Float32Array(n * 3);
var axes = new Float32Array(n * 3);
var i = 0;
var j = -1;
var s = -1;
var a1 = Vec3();
var a2 = Vec3();
var a3 = Vec3();
var a4 = Vec3();
var r12 = Vec3();
var r23 = Vec3();
var r34 = Vec3();
var v1 = Vec3();
var v2 = Vec3();
var vt = Vec3();
var diff13 = Vec3();
var diff24 = Vec3();
var axis = Vec3();
var prevAxis = Vec3();
while (polymerIt.hasNext) {
var ps = polymerIt.move();
residueIt.setSegment(ps);
i = -1;
s = -1;
while (residueIt.hasNext) {
i += 1;
var index = residueIt.move().index;
if (i === 0)
s = index;
j = (index - 2);
var j3 = j * 3;
Vec3.copy(a1, a2);
Vec3.copy(a2, a3);
Vec3.copy(a3, a4);
var eI_1 = traceElementIndex[index];
Vec3.set(a4, x[eI_1], y[eI_1], z[eI_1]);
if (i < 3)
continue;
Vec3.sub(r12, a2, a1);
Vec3.sub(r23, a3, a2);
Vec3.sub(r34, a4, a3);
Vec3.sub(diff13, r12, r23);
Vec3.sub(diff24, r23, r34);
Vec3.cross(axis, diff13, diff24);
Vec3.normalize(axis, axis);
Vec3.toArray(axis, axes, j3);
var tmp = Math.cos(Vec3.angle(diff13, diff24));
var diff13Length = Vec3.magnitude(diff13);
var diff24Length = Vec3.magnitude(diff24);
var r = (Math.sqrt(diff24Length * diff13Length) /
// clamp, to avoid numerical instabilities for when
// angle between diff13 and diff24 is close to 0
Math.max(2.0, 2.0 * (1.0 - tmp)));
Vec3.scale(v1, diff13, r / diff13Length);
Vec3.sub(v1, a2, v1);
Vec3.toArray(v1, centers, j3);
Vec3.scale(v2, diff24, r / diff24Length);
Vec3.sub(v2, a3, v2);
Vec3.toArray(v2, centers, j3 + 3);
Vec3.copy(prevAxis, axis);
}
// calc axis as dir of second and third center pos
// project first trace atom onto axis to get first center pos
var s3 = s * 3;
Vec3.fromArray(v1, centers, s3 + 3);
Vec3.fromArray(v2, centers, s3 + 6);
Vec3.normalize(axis, Vec3.sub(axis, v1, v2));
var sI = traceElementIndex[s];
Vec3.set(a1, x[sI], y[sI], z[sI]);
Vec3.copy(vt, a1);
Vec3.projectPointOnVector(vt, vt, axis, v1);
Vec3.toArray(vt, centers, s3);
// calc axis as dir of n-1 and n-2 center pos
// project last traceAtom onto axis to get last center pos
var e = j + 2;
var e3 = e * 3;
Vec3.fromArray(v1, centers, e3 - 3);
Vec3.fromArray(v2, centers, e3 - 6);
Vec3.normalize(axis, Vec3.sub(axis, v1, v2));
var eI = traceElementIndex[e];
Vec3.set(a1, x[eI], y[eI], z[eI]);
Vec3.copy(vt, a1);
Vec3.projectPointOnVector(vt, vt, axis, v1);
Vec3.toArray(vt, centers, e3);
}
return {
centers: centers
};
}
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