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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 "TorsionAngle.h"
#include "TorsionConstraint.h"
#include "Params.h"
#include <cmath>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/math/special_functions/round.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
namespace ForceFields {
namespace MMFF {
inline void checkPrecondition(const ForceField *owner, unsigned int idx1,
unsigned int idx2, unsigned int idx3, unsigned int idx4) {
PRECONDITION(owner, "bad owner");
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
URANGE_CHECK(idx3, owner->positions().size());
URANGE_CHECK(idx4, owner->positions().size());
}
double TorsionConstraintContrib::computeDihedralTerm(double dihedral) const {
double dihedralTarget = dihedral;
if (!(dihedral > d_minDihedralDeg && dihedral < d_maxDihedralDeg)
&& !(dihedral > d_minDihedralDeg && d_minDihedralDeg > d_maxDihedralDeg)
&& !(dihedral < d_maxDihedralDeg && d_minDihedralDeg > d_maxDihedralDeg)) {
double minDihedralTarget = dihedral - d_minDihedralDeg;
double maxDihedralTarget = dihedral - d_maxDihedralDeg;
RDKit::ForceFieldsHelper::normalizeAngleDeg(minDihedralTarget);
RDKit::ForceFieldsHelper::normalizeAngleDeg(maxDihedralTarget);
dihedralTarget = (fabs(minDihedralTarget) < fabs(maxDihedralTarget)
? d_minDihedralDeg : d_maxDihedralDeg);
}
double dihedralTerm = dihedral - dihedralTarget;
RDKit::ForceFieldsHelper::normalizeAngleDeg(dihedralTerm);
return dihedralTerm;
}
void TorsionConstraintContrib::setParameters(ForceField *owner, unsigned int idx1,
unsigned int idx2, unsigned int idx3, unsigned int idx4, double minDihedralDeg,
double maxDihedralDeg, double forceConst) {
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
d_at4Idx = idx4;
d_minDihedralDeg = minDihedralDeg;
d_maxDihedralDeg = maxDihedralDeg;
d_forceConstant = forceConst;
}
TorsionConstraintContrib::TorsionConstraintContrib(
ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3,
unsigned int idx4, double minDihedralDeg, double maxDihedralDeg,
double forceConst) {
checkPrecondition(owner, idx1, idx2, idx3, idx4);
RDKit::ForceFieldsHelper::normalizeAngleDeg(minDihedralDeg);
RDKit::ForceFieldsHelper::normalizeAngleDeg(maxDihedralDeg);
setParameters(owner, idx1, idx2, idx3, idx4,
minDihedralDeg, maxDihedralDeg, forceConst);
}
TorsionConstraintContrib::TorsionConstraintContrib(
ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3,
unsigned int idx4, bool relative, double minDihedralDeg,
double maxDihedralDeg, double forceConst) {
checkPrecondition(owner, idx1, idx2, idx3, idx4);
RDKit::ForceFieldsHelper::normalizeAngleDeg(minDihedralDeg);
RDKit::ForceFieldsHelper::normalizeAngleDeg(maxDihedralDeg);
if (relative) {
double dihedral;
RDKit::ForceFieldsHelper::computeDihedral(
owner->positions(), idx1, idx2, idx3, idx4, &dihedral);
dihedral *= RAD2DEG;
minDihedralDeg += dihedral;
maxDihedralDeg += dihedral;
RDKit::ForceFieldsHelper::normalizeAngleDeg(minDihedralDeg);
RDKit::ForceFieldsHelper::normalizeAngleDeg(maxDihedralDeg);
}
setParameters(owner, idx1, idx2, idx3, idx4,
minDihedralDeg, maxDihedralDeg, forceConst);
}
double TorsionConstraintContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double dihedral;
RDKit::ForceFieldsHelper::computeDihedral(
pos, d_at1Idx, d_at2Idx, d_at3Idx, d_at4Idx, &dihedral);
dihedral *= RAD2DEG;
double dihedralTerm = computeDihedralTerm(dihedral);
static double const c = 0.5 * DEG2RAD * DEG2RAD;
double res = c * d_forceConstant * dihedralTerm * dihedralTerm;
return res;
}
void TorsionConstraintContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
double *g[4] = {&(grad[3 * d_at1Idx]), &(grad[3 * d_at2Idx]),
&(grad[3 * d_at3Idx]), &(grad[3 * d_at4Idx])};
RDGeom::Point3D r[4];
RDGeom::Point3D t[2];
double d[2];
double cosPhi;
double dihedral;
RDKit::ForceFieldsHelper::computeDihedral(
pos, d_at1Idx, d_at2Idx, d_at3Idx, d_at4Idx, &dihedral, &cosPhi, r, t, d);
dihedral *= RAD2DEG;
double sinPhiSq = 1.0 - cosPhi * cosPhi;
double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
// dE/dPhi is independent of cartesians:
double dihedralTerm = computeDihedralTerm(dihedral);
double dE_dPhi = DEG2RAD * d_forceConstant * dihedralTerm;
// FIX: use a tolerance here
// this is hacky, but it's per the
// recommendation from Niketic and Rasmussen:
double sinTerm =
-dE_dPhi * (isDoubleZero(sinPhi) ? (1.0 / cosPhi) : (1.0 / sinPhi));
Utils::calcTorsionGrad(r, t, d, g, sinTerm, cosPhi);
}
}
}
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