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FourthDimContribs.h
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//
// Copyright (C) 2024 Greg Landrum and other RDKit contributors
//
// @@ 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 <RDGeneral/export.h>
#ifndef RD_FOURTHDIMCONTRIBS_H
#define RD_FOURTHDIMCONTRIBS_H
#include <vector>
#include <RDGeneral/Invariant.h>
#include <ForceField/Contrib.h>
#include <ForceField/ForceField.h>
namespace DistGeom {
struct FourthDimContribsParams {
unsigned int idx{0};
double weight{0.0};
FourthDimContribsParams(unsigned int idx, double w) : idx(idx), weight(w) {};
};
//! A term used in penalizing the 4th dimension in order to move from 4D->3D
//!
class RDKIT_DISTGEOMETRY_EXPORT FourthDimContribs
: public ForceFields::ForceFieldContrib {
public:
FourthDimContribs() = default;
//! 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
*/
FourthDimContribs(ForceFields::ForceField *owner) {
PRECONDITION(owner, "bad force field");
PRECONDITION(owner->dimension() == 4, "force field has wrong dimension");
dp_forceField = owner;
}
void addContrib(unsigned int idx, double weight) {
d_contribs.emplace_back(idx, weight);
}
//! return the contribution of this contrib to the energy of a given state
double getEnergy(double *pos) const override {
PRECONDITION(pos, "bad vector");
constexpr unsigned int ffdim = 4;
double res = 0.0;
for (const auto &contrib : d_contribs) {
unsigned int pid = contrib.idx * ffdim + 3;
res += contrib.weight * pos[pid] * pos[pid];
}
return res;
}
//! calculate the contribution of this contrib to the gradient at a given
/// state
void getGrad(double *pos, double *grad) const override {
PRECONDITION(pos, "bad vector");
constexpr unsigned int ffdim = 4;
for (const auto &contrib : d_contribs) {
unsigned int pid = contrib.idx * ffdim + 3;
grad[pid] += contrib.weight * pos[pid];
}
}
FourthDimContribs *copy() const override {
return new FourthDimContribs(*this);
}
bool empty() const { return d_contribs.empty(); }
unsigned int size() const { return d_contribs.size(); }
private:
std::vector<FourthDimContribsParams> d_contribs;
};
} // namespace DistGeom
#endif
Contrib.h
ForceField.h
Invariant.h
PRECONDITION
#define PRECONDITION(expr, mess)
Definition Invariant.h:109
DistGeom::FourthDimContribs
Definition FourthDimContribs.h:30
DistGeom::FourthDimContribs::FourthDimContribs
FourthDimContribs()=default
DistGeom::FourthDimContribs::copy
FourthDimContribs * copy() const override
return a copy
Definition FourthDimContribs.h:73
DistGeom::FourthDimContribs::FourthDimContribs
FourthDimContribs(ForceFields::ForceField *owner)
Constructor.
Definition FourthDimContribs.h:41
DistGeom::FourthDimContribs::size
unsigned int size() const
Definition FourthDimContribs.h:77
DistGeom::FourthDimContribs::empty
bool empty() const
Definition FourthDimContribs.h:76
DistGeom::FourthDimContribs::addContrib
void addContrib(unsigned int idx, double weight)
Definition FourthDimContribs.h:47
DistGeom::FourthDimContribs::getEnergy
double getEnergy(double *pos) const override
return the contribution of this contrib to the energy of a given state
Definition FourthDimContribs.h:52
DistGeom::FourthDimContribs::getGrad
void getGrad(double *pos, double *grad) const override
Definition FourthDimContribs.h:65
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:235
export.h
RDKIT_DISTGEOMETRY_EXPORT
#define RDKIT_DISTGEOMETRY_EXPORT
Definition export.h:129
DistGeom
Definition BoundsMatrix.h:20
DistGeom::FourthDimContribsParams
Definition FourthDimContribs.h:21
DistGeom::FourthDimContribsParams::idx
unsigned int idx
Definition FourthDimContribs.h:22
DistGeom::FourthDimContribsParams::FourthDimContribsParams
FourthDimContribsParams(unsigned int idx, double w)
Definition FourthDimContribs.h:24
DistGeom::FourthDimContribsParams::weight
double weight
Definition FourthDimContribs.h:23