/usr/include/rdkit/DistGeom/FourthDimContrib.h is in librdkit-dev 201503-3.
This file is owned by root:root, with mode 0o644.
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// Created by Santosh Putta, Nov 2006
//
#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 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;
};
}
#endif
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