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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() {}
//! 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 override {
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 override {
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];
}
FourthDimContrib *copy() const override {
return new FourthDimContrib(*this);
}
private:
unsigned int d_idx{0};
double d_weight{0.0};
};
} // namespace DistGeom
#endif
Contrib.h
ForceField.h
Invariant.h
PRECONDITION
#define PRECONDITION(expr, mess)
Definition Invariant.h:109
DistGeom::FourthDimContrib
Definition FourthDimContrib.h:16
DistGeom::FourthDimContrib::FourthDimContrib
FourthDimContrib(ForceFields::ForceField *owner, unsigned int idx, double weight)
Constructor.
Definition FourthDimContrib.h:27
DistGeom::FourthDimContrib::copy
FourthDimContrib * copy() const override
return a copy
Definition FourthDimContrib.h:55
DistGeom::FourthDimContrib::FourthDimContrib
FourthDimContrib()
Definition FourthDimContrib.h:18
DistGeom::FourthDimContrib::getGrad
void getGrad(double *pos, double *grad) const override
Definition FourthDimContrib.h:47
DistGeom::FourthDimContrib::getEnergy
double getEnergy(double *pos) const override
return the contribution of this contrib to the energy of a given state
Definition FourthDimContrib.h:36
ForceFields::ForceFieldContrib
abstract base class for contributions to ForceFields
Definition Contrib.h:18
ForceFields::ForceField
A class to store forcefields and handle minimization.
Definition ForceField.h:79
ForceFields::ForceField::dimension
unsigned int dimension() const
returns the dimension of the forcefield
Definition ForceField.h:220
export.h
RDKIT_DISTGEOMETRY_EXPORT
#define RDKIT_DISTGEOMETRY_EXPORT
Definition export.h:129
DistGeom
Definition BoundsMatrix.h:20