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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.
//
#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 VdWContrib : public ForceFieldContrib {
public:
VdWContrib() : d_at1Idx(-1), d_at2Idx(-1) {};
//! 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,
MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsAtom1,
const MMFFVdW *mmffVdWParamsAtom2);
double getEnergy(double *pos) const;
void getGrad(double *pos, double *grad) const;
private:
int d_at1Idx, d_at2Idx;
double d_R_star_ij; //!< the preferred length of the contact
double d_wellDepth; //!< the vdW well depth (strength of the interaction)
};
//! the electrostatic term for MMFF
class EleContrib : public ForceFieldContrib {
public:
EleContrib() : d_at1Idx(-1), d_at2Idx(-1) {};
//! 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, boost::uint8_t dielModel, bool is1_4);
double getEnergy(double *pos) const;
void getGrad(double *pos, double *grad) const;
private:
int d_at1Idx, d_at2Idx;
double d_chargeTerm; //!< q1 * q2 / D
boost::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
double calcUnscaledVdWMinimum(MMFFVdWCollection *mmffVdW,
const MMFFVdW *mmffVdWParamsAtom1, const MMFFVdW *mmffVdWParamsAtom2);
//! calculates and returns the unscaled well depth (epsilon) for a MMFF VdW contact
double calcUnscaledVdWWellDepth(double R_star_ij,
const MMFFVdW *mmffVdWParamsIAtom, const MMFFVdW *mmffVdWParamsJAtom);
//! scales the VdW parameters
void scaleVdWParams(double &R_star_ij, double &wellDepth,
MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsIAtom,
const MMFFVdW *mmffVdWParamsJAtom);
//! calculates and returns the Van der Waals MMFF energy
double calcVdWEnergy(const double dist,
const double R_star_ij, const double wellDepth);
//! calculates and returns the electrostatic MMFF energy
double calcEleEnergy(unsigned int idx1, unsigned int idx2, double dist,
double chargeTerm, boost::uint8_t dielModel, bool is1_4);
}
}
}
#endif
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