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//
// Copyright (C) 2024 Niels Maeder 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 "TorsionAngleContribs.h"
#include <cmath>
#include <utility>
#include <vector>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
#include <ForceField/MMFF/Params.h>
#include <ForceField/MMFF/TorsionAngle.h>
namespace ForceFields {
namespace CrystalFF {
namespace {
double calcTorsionEnergyM6(const std::vector<double> &forceConstants,
const std::vector<int> &signs, const double cosPhi) {
const double cosPhi2 = cosPhi * cosPhi;
const double cosPhi3 = cosPhi * cosPhi2;
const double cosPhi4 = cosPhi * cosPhi3;
const double cosPhi5 = cosPhi * cosPhi4;
const double cosPhi6 = cosPhi * cosPhi5;
const double cos2Phi = 2.0 * cosPhi2 - 1.0;
const double cos3Phi = 4.0 * cosPhi3 - 3.0 * cosPhi;
const double cos4Phi = 8.0 * cosPhi4 - 8.0 * cosPhi2 + 1.0;
const double cos5Phi = 16.0 * cosPhi5 - 20.0 * cosPhi3 + 5.0 * cosPhi;
const double cos6Phi = 32.0 * cosPhi6 - 48.0 * cosPhi4 + 18.0 * cosPhi2 - 1.0;
return (forceConstants[0] * (1.0 + signs[0] * cosPhi) +
forceConstants[1] * (1.0 + signs[1] * cos2Phi) +
forceConstants[2] * (1.0 + signs[2] * cos3Phi) +
forceConstants[3] * (1.0 + signs[3] * cos4Phi) +
forceConstants[4] * (1.0 + signs[4] * cos5Phi) +
forceConstants[5] * (1.0 + signs[5] * cos6Phi));
}
} // namespace
TorsionAngleContribs::TorsionAngleContribs(ForceField *owner) {
PRECONDITION(owner, "bad owner");
dp_forceField = owner;
}
void TorsionAngleContribs::addContrib(unsigned int idx1, unsigned int idx2,
unsigned int idx3, unsigned int idx4,
std::vector<double> forceConstants,
std::vector<int> signs) {
PRECONDITION((idx1 != idx2) && (idx1 != idx3) && (idx1 != idx4) &&
(idx2 != idx3) && (idx2 != idx4) && (idx3 != idx4),
"degenerate points");
URANGE_CHECK(idx1, dp_forceField->positions().size());
URANGE_CHECK(idx2, dp_forceField->positions().size());
URANGE_CHECK(idx3, dp_forceField->positions().size());
URANGE_CHECK(idx4, dp_forceField->positions().size());
d_contribs.emplace_back(idx1, idx2, idx3, idx4, std::move(forceConstants),
std::move(signs));
}
double TorsionAngleContribs::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double accum = 0.0;
for (const auto &contrib : d_contribs) {
const RDGeom::Point3D iPoint(pos[3 * contrib.idx1],
pos[3 * contrib.idx1 + 1],
pos[3 * contrib.idx1 + 2]);
const RDGeom::Point3D jPoint(pos[3 * contrib.idx2],
pos[3 * contrib.idx2 + 1],
pos[3 * contrib.idx2 + 2]);
const RDGeom::Point3D kPoint(pos[3 * contrib.idx3],
pos[3 * contrib.idx3 + 1],
pos[3 * contrib.idx3 + 2]);
const RDGeom::Point3D lPoint(pos[3 * contrib.idx4],
pos[3 * contrib.idx4 + 1],
pos[3 * contrib.idx4 + 2]);
accum += calcTorsionEnergyM6(
contrib.forceConstants, contrib.signs,
MMFF::Utils::calcTorsionCosPhi(iPoint, jPoint, kPoint, lPoint));
}
return accum;
}
void TorsionAngleContribs::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
for (const auto &contrib : d_contribs) {
const RDGeom::Point3D iPoint(pos[3 * contrib.idx1],
pos[3 * contrib.idx1 + 1],
pos[3 * contrib.idx1 + 2]);
const RDGeom::Point3D jPoint(pos[3 * contrib.idx2],
pos[3 * contrib.idx2 + 1],
pos[3 * contrib.idx2 + 2]);
const RDGeom::Point3D kPoint(pos[3 * contrib.idx3],
pos[3 * contrib.idx3 + 1],
pos[3 * contrib.idx3 + 2]);
const RDGeom::Point3D lPoint(pos[3 * contrib.idx4],
pos[3 * contrib.idx4 + 1],
pos[3 * contrib.idx4 + 2]);
double *g[4] = {&(grad[3 * contrib.idx1]), &(grad[3 * contrib.idx2]),
&(grad[3 * contrib.idx3]), &(grad[3 * contrib.idx4])};
RDGeom::Point3D r[4] = {iPoint - jPoint, kPoint - jPoint, jPoint - kPoint,
lPoint - kPoint};
RDGeom::Point3D t[2] = {r[0].crossProduct(r[1]), r[2].crossProduct(r[3])};
double d[2] = {t[0].length(), t[1].length()};
if (MMFF::isDoubleZero(d[0]) || MMFF::isDoubleZero(d[1])) {
return;
}
t[0] /= d[0];
t[1] /= d[1];
double cosPhi = t[0].dotProduct(t[1]);
cosPhi = std::clamp(cosPhi, -1.0, 1.0);
const double sinPhiSq = 1.0 - cosPhi * cosPhi;
const double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
const double cosPhi2 = cosPhi * cosPhi;
const double cosPhi3 = cosPhi * cosPhi2;
const double cosPhi4 = cosPhi * cosPhi3;
const double cosPhi5 = cosPhi * cosPhi4;
// dE/dPhi is independent of cartesians:
const double dE_dPhi =
(-contrib.forceConstants[0] * contrib.signs[0] * sinPhi -
2.0 * contrib.forceConstants[1] * contrib.signs[1] *
(2.0 * cosPhi * sinPhi) -
3.0 * contrib.forceConstants[2] * contrib.signs[2] *
(4.0 * cosPhi2 * sinPhi - sinPhi) -
4.0 * contrib.forceConstants[3] * contrib.signs[3] *
(8.0 * cosPhi3 * sinPhi - 4.0 * cosPhi * sinPhi) -
5.0 * contrib.forceConstants[4] * contrib.signs[4] *
(16.0 * cosPhi4 * sinPhi - 12.0 * cosPhi2 * sinPhi + sinPhi) -
6.0 * contrib.forceConstants[4] * contrib.signs[4] *
(32.0 * cosPhi5 * sinPhi - 32.0 * cosPhi3 * sinPhi +
6.0 * sinPhi));
// FIX: use a tolerance here
// this is hacky, but it's per the
// recommendation from Niketic and Rasmussen:
double sinTerm = -dE_dPhi * (MMFF::isDoubleZero(sinPhi) ? (1.0 / cosPhi)
: (1.0 / sinPhi));
MMFF::Utils::calcTorsionGrad(r, t, d, g, sinTerm, cosPhi);
}
}
} // namespace CrystalFF
} // namespace ForceFields
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