1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
|
//
// 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() : 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,
const MMFFVdWRijstarEps *mmffVdWConstants);
double getEnergy(double *pos) const;
void getGrad(double *pos, double *grad) const;
virtual VdWContrib *copy() const { return new VdWContrib(*this); };
private:
int d_at1Idx, d_at2Idx;
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() : 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;
virtual EleContrib *copy() const { return new EleContrib(*this); };
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
RDKIT_FORCEFIELD_EXPORT double calcUnscaledVdWMinimum(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,
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
RDKIT_FORCEFIELD_EXPORT double calcEleEnergy(unsigned int idx1, unsigned int idx2, double dist,
double chargeTerm, boost::uint8_t dielModel, bool is1_4);
}
}
}
#endif
|
