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// Copyright (C) 2013-2025 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 "StretchBend.h"
#include "AngleBend.h"
#include "BondStretch.h"
#include "Params.h"
#include <cmath>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/utils.h>
namespace ForceFields {
namespace MMFF {
namespace Utils {
std::pair<double, double> calcStbnForceConstants(
const MMFFStbn *mmffStbnParams) {
PRECONDITION(mmffStbnParams, "stretch-bend parameters not found");
return std::make_pair(mmffStbnParams->kbaIJK, mmffStbnParams->kbaKJI);
}
std::pair<double, double> calcStretchBendEnergy(
const double deltaDist1, const double deltaDist2, const double deltaTheta,
const std::pair<double, double> forceConstants) {
double factor = MDYNE_A_TO_KCAL_MOL * DEG2RAD * deltaTheta;
return std::make_pair(factor * forceConstants.first * deltaDist1,
factor * forceConstants.second * deltaDist2);
}
} // end of namespace Utils
StretchBendContrib::StretchBendContrib(ForceField *owner) {
PRECONDITION(owner, "bad owner");
dp_forceField = owner;
}
void StretchBendContrib::addTerm(
const unsigned int idx1, const unsigned int idx2, const unsigned int idx3,
const ForceFields::MMFF::MMFFStbn *mmffStbnParams,
const ForceFields::MMFF::MMFFAngle *mmffAngleParams,
const ForceFields::MMFF::MMFFBond *mmffBondParams1,
const ForceFields::MMFF::MMFFBond *mmffBondParams2) {
PRECONDITION(((idx1 != idx2) && (idx2 != idx3) && (idx1 != idx3)),
"degenerate points");
URANGE_CHECK(idx1, dp_forceField->positions().size());
URANGE_CHECK(idx2, dp_forceField->positions().size());
URANGE_CHECK(idx3, dp_forceField->positions().size());
d_at1Idxs.push_back(idx1);
d_at2Idxs.push_back(idx2);
d_at3Idxs.push_back(idx3);
d_restLen1s.push_back(Utils::calcBondRestLength(mmffBondParams1));
d_restLen2s.push_back(Utils::calcBondRestLength(mmffBondParams2));
d_theta0s.push_back(Utils::calcAngleRestValue(mmffAngleParams));
std::pair<double, double> forceConstants =
Utils::calcStbnForceConstants(mmffStbnParams);
d_forceConstants1.push_back(forceConstants.first);
d_forceConstants2.push_back(forceConstants.second);
}
double StretchBendContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double totalEnergy = 0.0;
const int numTerms = d_at1Idxs.size();
for (int i = 0; i < numTerms; i++) {
const int16_t at1Idx = d_at1Idxs[i];
const int16_t at2Idx = d_at2Idxs[i];
const int16_t at3Idx = d_at3Idxs[i];
double dist1 = dp_forceField->distance(at1Idx, at2Idx, pos);
double dist2 = dp_forceField->distance(at2Idx, at3Idx, pos);
RDGeom::Point3D p1(pos[3 * at1Idx], pos[3 * at1Idx + 1],
pos[3 * at1Idx + 2]);
RDGeom::Point3D p2(pos[3 * at2Idx], pos[3 * at2Idx + 1],
pos[3 * at2Idx + 2]);
RDGeom::Point3D p3(pos[3 * at3Idx], pos[3 * at3Idx + 1],
pos[3 * at3Idx + 2]);
std::pair<double, double> forceConstantsPair =
std::make_pair(d_forceConstants1[i], d_forceConstants2[i]);
std::pair<double, double> stretchBendEnergies =
Utils::calcStretchBendEnergy(
dist1 - d_restLen1s[i], dist2 - d_restLen2s[i],
RAD2DEG * acos(Utils::calcCosTheta(p1, p2, p3, dist1, dist2)) -
d_theta0s[i],
forceConstantsPair);
totalEnergy += (stretchBendEnergies.first + stretchBendEnergies.second);
}
return totalEnergy;
}
void StretchBendContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
const int numTerms = d_at1Idxs.size();
for (int i = 0; i < numTerms; ++i) {
const int16_t at1Idx = d_at1Idxs[i];
const int16_t at2Idx = d_at2Idxs[i];
const int16_t at3Idx = d_at3Idxs[i];
const double theta0 = d_theta0s[i];
const double forceConstant1 = d_forceConstants1[i];
const double forceConstant2 = d_forceConstants2[i];
const double restLen1 = d_restLen1s[i];
const double restLen2 = d_restLen2s[i];
double dist1 = dp_forceField->distance(at1Idx, at2Idx, pos);
double dist2 = dp_forceField->distance(at2Idx, at3Idx, pos);
RDGeom::Point3D p1(pos[3 * at1Idx], pos[3 * at1Idx + 1],
pos[3 * at1Idx + 2]);
RDGeom::Point3D p2(pos[3 * at2Idx], pos[3 * at2Idx + 1],
pos[3 * at2Idx + 2]);
RDGeom::Point3D p3(pos[3 * at3Idx], pos[3 * at3Idx + 1],
pos[3 * at3Idx + 2]);
double *g1 = &(grad[3 * at1Idx]);
double *g2 = &(grad[3 * at2Idx]);
double *g3 = &(grad[3 * at3Idx]);
RDGeom::Point3D p12 = (p1 - p2) / dist1;
RDGeom::Point3D p32 = (p3 - p2) / dist2;
double const c5 = MDYNE_A_TO_KCAL_MOL * DEG2RAD;
double cosTheta = p12.dotProduct(p32);
clipToOne(cosTheta);
double sinThetaSq = 1.0 - cosTheta * cosTheta;
double sinTheta = std::max(sqrt(sinThetaSq), 1.0e-8);
double angleTerm = RAD2DEG * acos(cosTheta) - theta0;
double distTerm = RAD2DEG * (forceConstant1 * (dist1 - restLen1) +
forceConstant2 * (dist2 - restLen2));
double dCos_dS1 = 1.0 / dist1 * (p32.x - cosTheta * p12.x);
double dCos_dS2 = 1.0 / dist1 * (p32.y - cosTheta * p12.y);
double dCos_dS3 = 1.0 / dist1 * (p32.z - cosTheta * p12.z);
double dCos_dS4 = 1.0 / dist2 * (p12.x - cosTheta * p32.x);
double dCos_dS5 = 1.0 / dist2 * (p12.y - cosTheta * p32.y);
double dCos_dS6 = 1.0 / dist2 * (p12.z - cosTheta * p32.z);
g1[0] += c5 * (p12.x * forceConstant1 * angleTerm +
dCos_dS1 / (-sinTheta) * distTerm);
g1[1] += c5 * (p12.y * forceConstant1 * angleTerm +
dCos_dS2 / (-sinTheta) * distTerm);
g1[2] += c5 * (p12.z * forceConstant1 * angleTerm +
dCos_dS3 / (-sinTheta) * distTerm);
g2[0] +=
c5 * ((-p12.x * forceConstant1 - p32.x * forceConstant2) * angleTerm +
(-dCos_dS1 - dCos_dS4) / (-sinTheta) * distTerm);
g2[1] +=
c5 * ((-p12.y * forceConstant1 - p32.y * forceConstant2) * angleTerm +
(-dCos_dS2 - dCos_dS5) / (-sinTheta) * distTerm);
g2[2] +=
c5 * ((-p12.z * forceConstant1 - p32.z * forceConstant2) * angleTerm +
(-dCos_dS3 - dCos_dS6) / (-sinTheta) * distTerm);
g3[0] += c5 * (p32.x * forceConstant2 * angleTerm +
dCos_dS4 / (-sinTheta) * distTerm);
g3[1] += c5 * (p32.y * forceConstant2 * angleTerm +
dCos_dS5 / (-sinTheta) * distTerm);
g3[2] += c5 * (p32.z * forceConstant2 * angleTerm +
dCos_dS6 / (-sinTheta) * distTerm);
}
}
} // namespace MMFF
} // namespace ForceFields
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