mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-06 22:39:55 +08:00
6c373ef11f
(i.e., equilibrium distances/angles and force constants) from UFF and MMFF in response to two requests recently appeared on the RDKit-discuss mailing list: http://sourceforge.net/p/rdkit/mailman/message/32953737/ http://sourceforge.net/p/rdkit/mailman/message/32880156/ - did some clean up on the MMFF code - NB there are two ABI changes: 1) StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2); previously was: StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const std::pair<bool, const MMFFStbn *> mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2); 2) std::pair<double, double> calcStbnForceConstants(const MMFFStbn *mmffStbnParams); previously was: std::pair<double, double> calcStbnForceConstants (const std::pair<bool, const MMFFStbn *> mmffStbnParams); The two changes are NOT mandatory - however, both the StretchBendContrib constructor and calcStbnForceConstants(), though public, are basically "internal" method that most likely no-one has ever invoked. Given that the current API is MUCH better and cleaner, I would really advise for the new version.
105 lines
3.0 KiB
C++
105 lines
3.0 KiB
C++
// $Id$
|
|
//
|
|
// 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");
|
|
RANGE_CHECK(0, idx1, owner->positions().size() - 1);
|
|
RANGE_CHECK(0, idx2, owner->positions().size() - 1);
|
|
|
|
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;
|
|
}
|
|
}
|
|
}
|
|
}
|