MMFF/Nonbonded.h

Go to the documentation of this file.

//
//  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