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//
// Copyright (C) 2013-2024 Paolo Tosco and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "Utils.h"
#include <cmath>
namespace ForceFields {
namespace UFF {
namespace Utils {
double calculateCosY(const RDGeom::Point3D &iPoint,
const RDGeom::Point3D &jPoint,
const RDGeom::Point3D &kPoint,
const RDGeom::Point3D &lPoint) {
constexpr double zeroTol = 1.0e-16;
RDGeom::Point3D rJI = iPoint - jPoint;
RDGeom::Point3D rJK = kPoint - jPoint;
RDGeom::Point3D rJL = lPoint - jPoint;
auto l2JI = rJI.lengthSq();
auto l2JK = rJK.lengthSq();
auto l2JL = rJL.lengthSq();
if (l2JI < zeroTol || l2JK < zeroTol || l2JL < zeroTol) {
return 0.0;
}
RDGeom::Point3D n = rJI.crossProduct(rJK);
n /= (sqrt(l2JI) * sqrt(l2JK));
auto l2n = n.lengthSq();
if (l2n < zeroTol) {
return 0.0;
}
return n.dotProduct(rJL) / (sqrt(l2JL) * sqrt(l2n));
}
std::tuple<double, double, double, double>
calcInversionCoefficientsAndForceConstant(int at2AtomicNum, bool isCBoundToO) {
double res = 0.0;
double C0 = 0.0;
double C1 = 0.0;
double C2 = 0.0;
// if the central atom is sp2 carbon, nitrogen or oxygen
if ((at2AtomicNum == 6) || (at2AtomicNum == 7) || (at2AtomicNum == 8)) {
C0 = 1.0;
C1 = -1.0;
C2 = 0.0;
res = (isCBoundToO ? 50.0 : 6.0);
} else {
// group 5 elements are not clearly explained in the UFF paper
// the following code was inspired by MCCCS Towhee's ffuff.F
double w0 = M_PI / 180.0;
switch (at2AtomicNum) {
// if the central atom is phosphorous
case 15:
w0 *= 84.4339;
break;
// if the central atom is arsenic
case 33:
w0 *= 86.9735;
break;
// if the central atom is antimonium
case 51:
w0 *= 87.7047;
break;
// if the central atom is bismuth
case 83:
w0 *= 90.0;
break;
}
C2 = 1.0;
C1 = -4.0 * cos(w0);
C0 = -(C1 * cos(w0) + C2 * cos(2.0 * w0));
res = 22.0 / (C0 + C1 + C2);
}
res /= 3.0;
return std::make_tuple(res, C0, C1, C2);
}
} // end of namespace Utils
} // namespace UFF
} // namespace ForceFields
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