RDKit: Nonbonded.h Source File

| RDKit Open-source cheminformatics and machine learning.

- Main Page
- Namespaces
- Classes
- Files

- File List
- File Members

MMFF/Nonbonded.h
Go to the documentation of this file.
1 //
2 // Copyright (C) 2013 Paolo Tosco
3 //
4 // Copyright (C) 2004-2006 Rational Discovery LLC
5 //
6 // @@ All Rights Reserved @@
7 // This file is part of the RDKit.
8 // The contents are covered by the terms of the BSD license
9 // which is included in the file license.txt, found at the root
10 // of the RDKit source tree.
11 //
12 #ifndef __RD_MMFFNONBONDED_H__
13 #define __RD_MMFFNONBONDED_H__
14 #include <ForceField/Contrib.h>
15 #include <GraphMol/RDKitBase.h>
16 #include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
17
18 namespace ForceFields {
19 namespace MMFF {
20 class MMFFVdWCollection;
21 class MMFFVdW;
22 //! the van der Waals term for MMFF
23 class VdWContrib : public ForceFieldContrib {
24 public:
25 VdWContrib() : d_at1Idx(-1), d_at2Idx(-1){};
26
27 //! Constructor
28 /*!
29 \param owner pointer to the owning ForceField
30 \param idx1 index of end1 in the ForceField's positions
31 \param idx2 index of end2 in the ForceField's positions
32
33 */
34 VdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2,
35 const MMFFVdWRijstarEps *mmffVdWConstants);
36 double getEnergy(double *pos) const;
37 void getGrad(double *pos, double *grad) const;
38 virtual VdWContrib *copy() const { return new VdWContrib(*this); };
39
40 private:
41 int d_at1Idx, d_at2Idx;
42 double d_R_ij_star; //!< the preferred length of the contact
43 double d_wellDepth; //!< the vdW well depth (strength of the interaction)
44 };
45
46 //! the electrostatic term for MMFF
47 class EleContrib : public ForceFieldContrib {
48 public:
49 EleContrib() : d_at1Idx(-1), d_at2Idx(-1){};
50
51 //! Constructor
52 /*!
53 \param owner pointer to the owning ForceField
54 \param idx1 index of end1 in the ForceField's positions
55 \param idx2 index of end2 in the ForceField's positions
56
57 */
58 EleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2,
59 double chargeTerm, boost::uint8_t dielModel, bool is1_4);
60 double getEnergy(double *pos) const;
61 void getGrad(double *pos, double *grad) const;
62
63 virtual EleContrib *copy() const { return new EleContrib(*this); };
64
65 private:
66 int d_at1Idx, d_at2Idx;
67 double d_chargeTerm; //!< q1 * q2 / D
68 boost::uint8_t
69 d_dielModel; //!< dielectric model (1: constant; 2: distance-dependent)
70 bool d_is1_4; //!< flag set for atoms in a 1,4 relationship
71 };
72
73 namespace Utils {
74 //! calculates and returns the unscaled minimum distance (R*ij) for a MMFF VdW
75 //contact
76 double calcUnscaledVdWMinimum(MMFFVdWCollection *mmffVdW,
77 const MMFFVdW *mmffVdWParamsAtom1,
78 const MMFFVdW *mmffVdWParamsAtom2);
79 //! calculates and returns the unscaled well depth (epsilon) for a MMFF VdW
80 //contact
81 double calcUnscaledVdWWellDepth(double R_star_ij,
82 const MMFFVdW *mmffVdWParamsIAtom,
83 const MMFFVdW *mmffVdWParamsJAtom);
84 //! scales the VdW parameters
85 void scaleVdWParams(double &R_star_ij, double &wellDepth,
86 MMFFVdWCollection *mmffVdW,
87 const MMFFVdW *mmffVdWParamsIAtom,
88 const MMFFVdW *mmffVdWParamsJAtom);
89 //! calculates and returns the Van der Waals MMFF energy
90 double calcVdWEnergy(const double dist, const double R_star_ij,
91 const double wellDepth);
92 //! calculates and returns the electrostatic MMFF energy
93 double calcEleEnergy(unsigned int idx1, unsigned int idx2, double dist,
94 double chargeTerm, boost::uint8_t dielModel, bool is1_4);
95 }
96 }
97 }
98 #endif
ForceFields::MMFF::EleContrib::EleContrib
EleContrib()
Definition: MMFF/Nonbonded.h:49
ForceFields::MMFF::VdWContrib::getEnergy
double getEnergy(double *pos) const
returns our contribution to the energy of a position
ForceFields::MMFF::EleContrib::getEnergy
double getEnergy(double *pos) const
returns our contribution to the energy of a position
ForceFields::MMFF::EleContrib::getGrad
void getGrad(double *pos, double *grad) const
calculates our contribution to the gradients of a position
ForceFields::MMFF::EleContrib
the electrostatic term for MMFF
Definition: MMFF/Nonbonded.h:47
ForceFields::MMFF::Utils::calcVdWEnergy
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::calcUnscaledVdWWellDepth
double calcUnscaledVdWWellDepth(double R_star_ij, const MMFFVdW *mmffVdWParamsIAtom, const MMFFVdW *mmffVdWParamsJAtom)
calculates and returns the unscaled well depth (epsilon) for a MMFF VdW
ForceFields::ForceFieldContrib
abstract base class for contributions to ForceFields
Definition: Contrib.h:17
ForceFields::MMFF::VdWContrib::copy
virtual VdWContrib * copy() const
return a copy
Definition: MMFF/Nonbonded.h:38
RDKitBase.h
pulls in the core RDKit functionality
Contrib.h
ForceFields
Definition: TorsionAngleM6.h:23
ForceFields::MMFF::EleContrib::copy
virtual EleContrib * copy() const
return a copy
Definition: MMFF/Nonbonded.h:63
ForceFields::MMFF::Utils::calcUnscaledVdWMinimum
double calcUnscaledVdWMinimum(MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsAtom1, const MMFFVdW *mmffVdWParamsAtom2)
calculates and returns the unscaled minimum distance (R*ij) for a MMFF VdW
ForceFields::MMFF::Utils::calcEleEnergy
double calcEleEnergy(unsigned int idx1, unsigned int idx2, double dist, double chargeTerm, boost::uint8_t dielModel, bool is1_4)
calculates and returns the electrostatic MMFF energy
AtomTyper.h
ForceFields::MMFF::VdWContrib::getGrad
void getGrad(double *pos, double *grad) const
calculates our contribution to the gradients of a position
ForceFields::MMFF::VdWContrib
the van der Waals term for MMFF
Definition: MMFF/Nonbonded.h:23
ForceFields::MMFF::MMFFVdWRijstarEps
Definition: MMFF/Params.h:148
ForceFields::MMFF::Utils::scaleVdWParams
void scaleVdWParams(double &R_star_ij, double &wellDepth, MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsIAtom, const MMFFVdW *mmffVdWParamsJAtom)
scales the VdW parameters
ForceFields::MMFF::VdWContrib::VdWContrib
VdWContrib()
Definition: MMFF/Nonbonded.h:25
ForceFields::ForceField
A class to store forcefields and handle minimization.
Definition: ForceField.h:56