MMFF/Nonbonded.h
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//
// Copyright (C) 2013 Paolo Tosco
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ 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_MMFFNONBONDED_H__
#define __RD_MMFFNONBONDED_H__
#include <ForceField/Contrib.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
namespace ForceFields {
namespace MMFF {
class MMFFVdWCollection;
class MMFFVdW;
//! the van der Waals term for MMFF
class RDKIT_FORCEFIELD_EXPORT VdWContrib : public ForceFieldContrib {
public:
VdWContrib() {}
//! Constructor
/*!
\param owner pointer to the owning ForceField
\param idx1 index of end1 in the ForceField's positions
\param idx2 index of end2 in the ForceField's positions
*/
VdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2,
const MMFFVdWRijstarEps *mmffVdWConstants);
double getEnergy(double *pos) const override;
void getGrad(double *pos, double *grad) const override;
VdWContrib *copy() const override { return new VdWContrib(*this); }
private:
int d_at1Idx{-1}, d_at2Idx{-1};
double d_R_ij_star; //!< the preferred length of the contact
double d_wellDepth; //!< the vdW well depth (strength of the interaction)
};
//! the electrostatic term for MMFF
class RDKIT_FORCEFIELD_EXPORT EleContrib : public ForceFieldContrib {
public:
EleContrib() {}
//! Constructor
/*!
\param owner pointer to the owning ForceField
\param idx1 index of end1 in the ForceField's positions
\param idx2 index of end2 in the ForceField's positions
*/
EleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2,
double chargeTerm, std::uint8_t dielModel, bool is1_4);
double getEnergy(double *pos) const override;
void getGrad(double *pos, double *grad) const override;
EleContrib *copy() const override { return new EleContrib(*this); }
private:
int d_at1Idx{-1}, d_at2Idx{-1};
double d_chargeTerm; //!< q1 * q2 / D
std::uint8_t
d_dielModel; //!< dielectric model (1: constant; 2: distance-dependent)
bool d_is1_4; //!< flag set for atoms in a 1,4 relationship
};
namespace Utils {
//! calculates and returns the unscaled minimum distance (R*ij) for a MMFF VdW
/// contact
RDKIT_FORCEFIELD_EXPORT double calcUnscaledVdWMinimum(
const MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsAtom1,
const MMFFVdW *mmffVdWParamsAtom2);
//! calculates and returns the unscaled well depth (epsilon) for a MMFF VdW
/// contact
RDKIT_FORCEFIELD_EXPORT double calcUnscaledVdWWellDepth(
double R_star_ij, const MMFFVdW *mmffVdWParamsIAtom,
const MMFFVdW *mmffVdWParamsJAtom);
//! scales the VdW parameters
RDKIT_FORCEFIELD_EXPORT void scaleVdWParams(double &R_star_ij,
double &wellDepth,
const MMFFVdWCollection *mmffVdW,
const MMFFVdW *mmffVdWParamsIAtom,
const MMFFVdW *mmffVdWParamsJAtom);
//! calculates and returns the Van der Waals MMFF energy
RDKIT_FORCEFIELD_EXPORT double calcVdWEnergy(const double dist,
const double R_star_ij,
const double wellDepth);
//! calculates and returns the electrostatic MMFF energy
// FIX: idx1 and idx2 are not used
RDKIT_FORCEFIELD_EXPORT double calcEleEnergy(unsigned int idx1,
unsigned int idx2, double dist,
double chargeTerm,
std::uint8_t dielModel,
bool is1_4);
} // namespace Utils
} // namespace MMFF
} // namespace ForceFields
#endif
Contrib.h
AtomTyper.h
RDKitBase.h
pulls in the core RDKit functionality
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::MMFF::EleContrib
the electrostatic term for MMFF
Definition: MMFF/Nonbonded.h:48
ForceFields::MMFF::EleContrib::EleContrib
EleContrib()
Definition: MMFF/Nonbonded.h:50
ForceFields::MMFF::EleContrib::copy
EleContrib * copy() const override
return a copy
Definition: MMFF/Nonbonded.h:64
ForceFields::MMFF::EleContrib::getEnergy
double getEnergy(double *pos) const override
returns our contribution to the energy of a position
ForceFields::MMFF::EleContrib::getGrad
void getGrad(double *pos, double *grad) const override
calculates our contribution to the gradients of a position
ForceFields::MMFF::EleContrib::EleContrib
EleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, double chargeTerm, std::uint8_t dielModel, bool is1_4)
Constructor.
ForceFields::MMFF::MMFFVdWCollection
Definition: MMFF/Params.h:1095
ForceFields::MMFF::MMFFVdWRijstarEps
Definition: MMFF/Params.h:150
ForceFields::MMFF::MMFFVdW
class to store MMFF parameters for non-bonded Van der Waals
Definition: MMFF/Params.h:140
ForceFields::MMFF::VdWContrib
the van der Waals term for MMFF
Definition: MMFF/Nonbonded.h:24
ForceFields::MMFF::VdWContrib::VdWContrib
VdWContrib()
Definition: MMFF/Nonbonded.h:26
ForceFields::MMFF::VdWContrib::copy
VdWContrib * copy() const override
return a copy
Definition: MMFF/Nonbonded.h:39
ForceFields::MMFF::VdWContrib::getEnergy
double getEnergy(double *pos) const override
returns our contribution to the energy of a position
ForceFields::MMFF::VdWContrib::VdWContrib
VdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, const MMFFVdWRijstarEps *mmffVdWConstants)
Constructor.
ForceFields::MMFF::VdWContrib::getGrad
void getGrad(double *pos, double *grad) const override
calculates our contribution to the gradients of a position
export.h
RDKIT_FORCEFIELD_EXPORT
#define RDKIT_FORCEFIELD_EXPORT
Definition: export.h:177
ForceFields::MMFF::Utils::calcUnscaledVdWMinimum
RDKIT_FORCEFIELD_EXPORT double calcUnscaledVdWMinimum(const MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsAtom1, const MMFFVdW *mmffVdWParamsAtom2)
ForceFields::MMFF::Utils::calcVdWEnergy
RDKIT_FORCEFIELD_EXPORT double calcVdWEnergy(const double dist, const double R_star_ij, const double wellDepth)
calculates and returns the Van der Waals MMFF energy
ForceFields::MMFF::Utils::scaleVdWParams
RDKIT_FORCEFIELD_EXPORT void scaleVdWParams(double &R_star_ij, double &wellDepth, const MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsIAtom, const MMFFVdW *mmffVdWParamsJAtom)
scales the VdW parameters
ForceFields::MMFF::Utils::calcUnscaledVdWWellDepth
RDKIT_FORCEFIELD_EXPORT double calcUnscaledVdWWellDepth(double R_star_ij, const MMFFVdW *mmffVdWParamsIAtom, const MMFFVdW *mmffVdWParamsJAtom)
ForceFields::MMFF::Utils::calcEleEnergy
RDKIT_FORCEFIELD_EXPORT double calcEleEnergy(unsigned int idx1, unsigned int idx2, double dist, double chargeTerm, std::uint8_t dielModel, bool is1_4)
calculates and returns the electrostatic MMFF energy
ForceFields
Definition: TorsionAngleM6.h:24