mirror of
https://github.com/rdkit/rdkit.git
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a45d4d9857
* add angles and distances * add Inversions * add torsiona angle contribs * use new contribs in test * use new inversion and torsion contribs in dg * use new distance contribs in dg * use new angle constraints in dg * use new constraints in FF tests * update docstrings * remove unused import * include new contribs * cleanup includes * make changes requested by @greglandrum * use std::move instead of release
84 lines
2.1 KiB
C++
84 lines
2.1 KiB
C++
//
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// Copyright (C) 2013-2024 Paolo Tosco and other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "Utils.h"
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#include <cmath>
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namespace ForceFields {
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namespace UFF {
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namespace Utils {
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double calculateCosY(const RDGeom::Point3D &iPoint,
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const RDGeom::Point3D &jPoint,
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const RDGeom::Point3D &kPoint,
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const RDGeom::Point3D &lPoint) {
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RDGeom::Point3D rJI = iPoint - jPoint;
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RDGeom::Point3D rJK = kPoint - jPoint;
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RDGeom::Point3D rJL = lPoint - jPoint;
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rJI.normalize();
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rJK.normalize();
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rJL.normalize();
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RDGeom::Point3D n = rJI.crossProduct(rJK);
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n.normalize();
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return n.dotProduct(rJL);
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}
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std::tuple<double, double, double, double>
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calcInversionCoefficientsAndForceConstant(int at2AtomicNum, bool isCBoundToO) {
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double res = 0.0;
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double C0 = 0.0;
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double C1 = 0.0;
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double C2 = 0.0;
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// if the central atom is sp2 carbon, nitrogen or oxygen
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if ((at2AtomicNum == 6) || (at2AtomicNum == 7) || (at2AtomicNum == 8)) {
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C0 = 1.0;
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C1 = -1.0;
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C2 = 0.0;
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res = (isCBoundToO ? 50.0 : 6.0);
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} else {
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// group 5 elements are not clearly explained in the UFF paper
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// the following code was inspired by MCCCS Towhee's ffuff.F
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double w0 = M_PI / 180.0;
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switch (at2AtomicNum) {
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// if the central atom is phosphorous
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case 15:
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w0 *= 84.4339;
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break;
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// if the central atom is arsenic
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case 33:
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w0 *= 86.9735;
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break;
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// if the central atom is antimonium
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case 51:
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w0 *= 87.7047;
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break;
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// if the central atom is bismuth
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case 83:
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w0 *= 90.0;
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break;
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}
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C2 = 1.0;
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C1 = -4.0 * cos(w0);
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C0 = -(C1 * cos(w0) + C2 * cos(2.0 * w0));
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res = 22.0 / (C0 + C1 + C2);
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}
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res /= 3.0;
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return std::make_tuple(res, C0, C1, C2);
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}
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} // end of namespace Utils
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} // namespace UFF
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} // namespace ForceFields
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