mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
a45d4d9857
* add angles and distances * add Inversions * add torsiona angle contribs * use new contribs in test * use new inversion and torsion contribs in dg * use new distance contribs in dg * use new angle constraints in dg * use new constraints in FF tests * update docstrings * remove unused import * include new contribs * cleanup includes * make changes requested by @greglandrum * use std::move instead of release
103 lines
3.4 KiB
C++
103 lines
3.4 KiB
C++
//
|
|
// Copyright (C) 2024 Niels Maeder 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_DISTANCECONSTRAINTS_H
|
|
#define RD_DISTANCECONSTRAINTS_H
|
|
#include <vector>
|
|
#include <iostream>
|
|
#include "Contrib.h"
|
|
|
|
namespace ForceFields {
|
|
|
|
struct DistanceConstraintContribsParams {
|
|
unsigned int idx1{0}; //!< index of atom1 of the distance constraint
|
|
unsigned int idx2{0}; //!< index of atom2 of the distance constraint
|
|
double minLen{0.0}; //!< lower bound of the flat bottom potential
|
|
double maxLen{0.0}; //!< upper bound of the flat bottom potential
|
|
double forceConstant{1.0}; //!< force constant for distance constraint
|
|
DistanceConstraintContribsParams(unsigned int idx1, unsigned int idx2,
|
|
double minLen, double maxLen,
|
|
double forceConstant = 1.0)
|
|
: idx1(idx1),
|
|
idx2(idx2),
|
|
minLen(minLen),
|
|
maxLen(maxLen),
|
|
forceConstant(forceConstant){};
|
|
};
|
|
|
|
//! A term to capture all flat bottom distance constraint potentials.
|
|
class RDKIT_FORCEFIELD_EXPORT DistanceConstraintContribs
|
|
: public ForceFieldContrib {
|
|
public:
|
|
DistanceConstraintContribs() = default;
|
|
|
|
//! Constructor
|
|
/*!
|
|
\param owner pointer to the owning ForceField
|
|
*/
|
|
DistanceConstraintContribs(ForceField *owner);
|
|
~DistanceConstraintContribs() override = default;
|
|
//! Add contribution to this contrib.
|
|
/*!
|
|
\param idx1 index of atom1 in the ForceField's positions
|
|
\param idx2 index of atom2 in the ForceField's positions
|
|
\param minLen minimum distance
|
|
\param maxLen maximum distance
|
|
\param forceConst force Constant
|
|
|
|
*/
|
|
void addContrib(unsigned int idx1, unsigned int idx2, double minLen,
|
|
double maxLen, double forceConstant);
|
|
//! Add contribution to this contrib.
|
|
/*!
|
|
\param idx1 index of atom1 in the ForceField's positions
|
|
\param idx2 index of atom2 in the ForceField's positions
|
|
\param relative whether to add the provided distance to the
|
|
current distance
|
|
\param minLen minimum distance
|
|
\param maxLen maximum distance
|
|
\param forceConst force Constant
|
|
|
|
*/
|
|
void addContrib(unsigned int idx1, unsigned int idx2, bool relative,
|
|
double minLen, double maxLen, double forceConstant);
|
|
|
|
//! return the contribution of this contrib to the energy of a given state
|
|
/*!
|
|
\param pos positions of the atoms in the current state
|
|
*/
|
|
double getEnergy(double *pos) const override;
|
|
//! calculate the contribution of this contrib to the gradient at a given
|
|
/// state
|
|
/*!
|
|
\param pos positions of the atoms in the current state
|
|
\param grad gradients to be adapted
|
|
*/
|
|
void getGrad(double *pos, double *grad) const override;
|
|
|
|
//! Copy constructor
|
|
DistanceConstraintContribs *copy() const override {
|
|
return new DistanceConstraintContribs(*this);
|
|
}
|
|
|
|
//! Return true if there are no contributions in this contrib
|
|
bool empty() const { return d_contribs.empty(); }
|
|
|
|
//! Get number of contributions in this contrib
|
|
unsigned int size() const { return d_contribs.size(); }
|
|
|
|
private:
|
|
std::vector<DistanceConstraintContribsParams> d_contribs;
|
|
};
|
|
|
|
} // namespace ForceFields
|
|
|
|
#endif |