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// $Id$
//
// Copyright (C) 2013 Paolo Tosco
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ 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 "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 {
double calcBondRestLength(const MMFFBond *mmffBondParams) {
PRECONDITION(mmffBondParams, "bond parameters not found");
return mmffBondParams->r0;
}
double calcBondForceConstant(const MMFFBond *mmffBondParams) {
PRECONDITION(mmffBondParams, "bond parameters not found");
return mmffBondParams->kb;
}
double calcBondStretchEnergy(const double r0, const double kb,
const double distance) {
double distTerm = distance - r0;
double distTerm2 = distTerm * distTerm;
double const c1 = MDYNE_A_TO_KCAL_MOL;
double const cs = -2.0;
double const c3 = 7.0 / 12.0;
return (0.5 * c1 * kb * distTerm2 *
(1.0 + cs * distTerm + c3 * cs * cs * distTerm2));
}
} // end of namespace Utils
BondStretchContrib::BondStretchContrib(ForceField *owner,
const unsigned int idx1,
const unsigned int idx2,
const MMFFBond *mmffBondParams) {
PRECONDITION(owner, "bad owner");
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_r0 = mmffBondParams->r0;
d_kb = mmffBondParams->kb;
}
double BondStretchContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
return Utils::calcBondStretchEnergy(
d_r0, d_kb, dp_forceField->distance(d_at1Idx, d_at2Idx, pos));
}
void BondStretchContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
double dist = dp_forceField->distance(d_at1Idx, d_at2Idx, pos);
double *at1Coords = &(pos[3 * d_at1Idx]);
double *at2Coords = &(pos[3 * d_at2Idx]);
double *g1 = &(grad[3 * d_at1Idx]);
double *g2 = &(grad[3 * d_at2Idx]);
double const cs = -2.0;
double const c1 = MDYNE_A_TO_KCAL_MOL;
double const c3 = 7.0 / 12.0;
double distTerm = dist - d_r0;
double dE_dr =
c1 * d_kb * distTerm *
(1.0 + 1.5 * cs * distTerm + 2.0 * c3 * cs * cs * distTerm * distTerm);
double dGrad;
for (unsigned int i = 0; i < 3; ++i) {
dGrad = ((dist > 0.0) ? (dE_dr * (at1Coords[i] - at2Coords[i]) / dist)
: d_kb * 0.01);
g1[i] += dGrad;
g2[i] -= dGrad;
}
}
}
}
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