FourthDimContrib.h
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//
// Created by Santosh Putta, Nov 2006
//
#include <RDGeneral/export.h>
#ifndef __RD_FOURTHDIMCONTRIB_H__
#define __RD_FOURTHDIMCONTRIB_H__
#include <RDGeneral/Invariant.h>
#include <ForceField/Contrib.h>
#include <ForceField/ForceField.h>
namespace DistGeom {
//! A term used in penalizing chirality violations
//!
class RDKIT_DISTGEOMETRY_EXPORT FourthDimContrib
: public ForceFields::ForceFieldContrib {
public:
FourthDimContrib() : d_idx(0), d_weight(0.0){};
//! Constructor
/*!
\param owner pointer to the owning ForceField
\param idx the index of the atom to be considered
\param weight (optional) the weight to be used for this contrib
*/
FourthDimContrib(ForceFields::ForceField *owner, unsigned int idx,
double weight)
: d_idx(idx), d_weight(weight) {
PRECONDITION(owner, "bad force field");
PRECONDITION(owner->dimension() == 4, "force field has wrong dimension");
dp_forceField = owner;
};
//! return the contribution of this contrib to the energy of a given state
double getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(dp_forceField->dimension() == 4,
"force field has wrong dimension");
PRECONDITION(pos, "bad vector");
unsigned int pid = d_idx * dp_forceField->dimension() + 3;
return d_weight * pos[pid] * pos[pid];
}
//! calculate the contribution of this contrib to the gradient at a given
// state
void getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(dp_forceField->dimension() == 4,
"force field has wrong dimension");
PRECONDITION(pos, "bad vector");
unsigned int pid = d_idx * dp_forceField->dimension() + 3;
grad[pid] += d_weight * pos[pid];
}
virtual FourthDimContrib *copy() const {
return new FourthDimContrib(*this);
};
private:
unsigned int d_idx;
double d_weight;
};
} // namespace DistGeom
#endif
DistGeom::FourthDimContrib::FourthDimContrib
FourthDimContrib(ForceFields::ForceField *owner, unsigned int idx, double weight)
Constructor.
Definition: FourthDimContrib.h:27
DistGeom::FourthDimContrib::FourthDimContrib
FourthDimContrib()
Definition: FourthDimContrib.h:18
DistGeom::FourthDimContrib::getGrad
void getGrad(double *pos, double *grad) const
calculate the contribution of this contrib to the gradient at a given
Definition: FourthDimContrib.h:47
ForceFields::ForceField::dimension
unsigned int dimension() const
returns the dimension of the forcefield
Definition: ForceField.h:221
RDKIT_DISTGEOMETRY_EXPORT
#define RDKIT_DISTGEOMETRY_EXPORT
Definition: export.h:164
DistGeom::FourthDimContrib
Definition: FourthDimContrib.h:15
ForceFields::ForceField
A class to store forcefields and handle minimization.
Definition: ForceField.h:79
ForceFields::ForceFieldContrib
abstract base class for contributions to ForceFields
Definition: Contrib.h:18
Invariant.h
Contrib.h
DistGeom
Definition: BoundsMatrix.h:20
PRECONDITION
#define PRECONDITION(expr, mess)
Definition: Invariant.h:109
ForceField.h
DistGeom::FourthDimContrib::copy
virtual FourthDimContrib * copy() const
return a copy
Definition: FourthDimContrib.h:55
DistGeom::FourthDimContrib::getEnergy
double getEnergy(double *pos) const
return the contribution of this contrib to the energy of a given state
Definition: FourthDimContrib.h:36
export.h