BALL  1.5.0
vanDerWaalsSlick.h
Go to the documentation of this file.
1 // $Id: vanDerWaals.h,v 1.3 2006/05/21 17:35:26 anker Exp $
2 // Molecular Mechanics: SLICK force field, modified van-der-Waals term
3 
4 #ifndef BALL_SCORING_COMPONENTS_VANDERWAALSSLICK_H
5 #define BALL_SCORING_COMPONENTS_VANDERWAALSSLICK_H
6 
12 
13 namespace BALL
14 {
19  {
20  public:
21 
24  {
27 
30 
32  CALCULATION__SOFTENED_LJ_POTENTIAL_LOG
33 
34  };
35 
36 
39  {
40 
42  static const String VERBOSITY;
43 
45  static const String VDW_METHOD;
46 
48  static const String VDW_CUT_ON;
49 
51  static const String VDW_CUT_OFF;
52 
55 
57  static const String LENNARD_JONES_FILE;
58 
59  };
60 
61 
62  struct Default
63  {
64 
66  static const Size VERBOSITY;
67 
69  static const Size VDW_METHOD;
70 
72  static const float VDW_CUT_ON;
73 
75  static const float VDW_CUT_OFF;
76 
78  static const float VDW_SOFTENING_LIMIT;
79 
81  static const String LENNARD_JONES_FILE;
82 
83  };
84 
85 
86 
89  ;
90 
93  ;
94 
97  ;
98 
101  ;
102 
104  virtual void clear()
105  ;
106 
110  virtual bool setup();
111 
112  void update(const vector<std::pair<Atom*, Atom*> >& /* pair_vector */);
113 
117  virtual double updateScore();
118 
119 
120  protected:
121 
122  //_
123  std::vector<LennardJones::Data> non_bonded_;
124 
125  //_
126  std::vector<bool> is_hydrogen_bond_;
127 
130 
133 
134 
135  private:
136 
137  //_
138  System vdw_system_;
139 
140  //_
141  Molecule* vdw_receptor_;
142 
143  //_
144  Molecule* vdw_ligand_;
145 
146  //_
147  Size calculation_method_;
148 
149  //_
150  float cut_on_vdw_;
151 
152  //_
153  float cut_off_vdw_;
154 
155  //_
156  float scaling_vdw_1_4_;
157 
158  //_
159  float softening_limit_;
160 
161  //_
162  double calculateVDWEnergy_(const AtomVector& atom_vector)
163  ;
164 
165  //_
166  Size createNonBondedList_(const ForceField::PairVector& atom_pair_vector)
167  ;
168 
169  //_ Verbosity of the code
170  Size verbosity_;
171 
172  };
173 
174 }
175 
176 #endif // BALL_SCORING_COMPONENTS_VANDERWAALSSLICK_H
BALL_EXPORT
#define BALL_EXPORT
Definition: COMMON/global.h:50
atomVector.h
BALL::VanDerWaalsSlick::VanDerWaalsSlick
VanDerWaalsSlick(ScoringFunction &sf)
BALL::VanDerWaalsSlick::number_of_1_4_
Size number_of_1_4_
Definition: vanDerWaalsSlick.h:128
BALL::VanDerWaalsSlick::lennard_jones_
LennardJones lennard_jones_
Definition: vanDerWaalsSlick.h:131
BALL::VanDerWaalsSlick::number_of_h_bonds_
Size number_of_h_bonds_
Definition: vanDerWaalsSlick.h:129
BALL::Molecule
Definition: molecule.h:31
BALL::System
Definition: KERNEL/system.h:40
forceField.h
BALL::VanDerWaalsSlick::VanDerWaalsSlick
VanDerWaalsSlick()
BALL::VanDerWaalsSlick::Option::VDW_SOFTENING_LIMIT
static const String VDW_SOFTENING_LIMIT
Definition: vanDerWaalsSlick.h:54
BALL::VanDerWaalsSlick::CALCULATION__FULL_LJ_POTENTIAL
@ CALCULATION__FULL_LJ_POTENTIAL
Full Lennard-Jones 6-12 potential.
Definition: vanDerWaalsSlick.h:26
BALL::VanDerWaalsSlick::Option::VDW_METHOD
static const String VDW_METHOD
Definition: vanDerWaalsSlick.h:45
BALL::VanDerWaalsSlick::is_hydrogen_bond_
std::vector< bool > is_hydrogen_bond_
Definition: vanDerWaalsSlick.h:126
BALL::VanDerWaalsSlick::clear
virtual void clear()
BALL::String
Definition: string.h:57
BALL
Definition: constants.h:13
BALL::VanDerWaalsSlick::Default::VERBOSITY
static const Size VERBOSITY
Definition: vanDerWaalsSlick.h:66
BALL::VanDerWaalsSlick::~VanDerWaalsSlick
virtual ~VanDerWaalsSlick()
BALL::VanDerWaalsSlick::VanDerWaalsSlick
VanDerWaalsSlick(ScoringComponent &sc)
BALL::VanDerWaalsSlick::hydrogen_bond_
Potential1210 hydrogen_bond_
Definition: vanDerWaalsSlick.h:132
scoringComponent.h
BALL::LennardJones
Definition: lennardJones.h:44
BALL::VanDerWaalsSlick::Option::VDW_CUT_ON
static const String VDW_CUT_ON
Definition: vanDerWaalsSlick.h:48
BALL::VanDerWaalsSlick::Default::LENNARD_JONES_FILE
static const String LENNARD_JONES_FILE
Definition: vanDerWaalsSlick.h:81
BALL::VanDerWaalsSlick::Option::LENNARD_JONES_FILE
static const String LENNARD_JONES_FILE
Definition: vanDerWaalsSlick.h:57
BALL::VanDerWaalsSlick
Definition: vanDerWaalsSlick.h:19
BALL::ForceField::PairVector
std::vector< std::pair< Atom *, Atom * > > PairVector
Definition: forceField.h:99
BALL::AtomVector
Definition: atomVector.h:31
BALL::VanDerWaalsSlick::Option::VERBOSITY
static const String VERBOSITY
Definition: vanDerWaalsSlick.h:42
BALL_SIZE_TYPE
BALL::ScoringComponent
Definition: scoringComponent.h:21
BALL::VanDerWaalsSlick::Default::VDW_SOFTENING_LIMIT
static const float VDW_SOFTENING_LIMIT
Definition: vanDerWaalsSlick.h:78
lennardJones.h
BALL::VanDerWaalsSlick::updateScore
virtual double updateScore()
BALL::VanDerWaalsSlick::Default::VDW_CUT_OFF
static const float VDW_CUT_OFF
Definition: vanDerWaalsSlick.h:75
amberNonBonded.h
BALL::VanDerWaalsSlick::Option::VDW_CUT_OFF
static const String VDW_CUT_OFF
Definition: vanDerWaalsSlick.h:51
BALL::VanDerWaalsSlick::setup
virtual bool setup()
BALL::VanDerWaalsSlick::Default
Definition: vanDerWaalsSlick.h:63
BALL::Potential1210
Definition: potential1210.h:27
BALL::VanDerWaalsSlick::Default::VDW_METHOD
static const Size VDW_METHOD
Definition: vanDerWaalsSlick.h:69
BALL::VanDerWaalsSlick::CalculationMethod
CalculationMethod
Definition: vanDerWaalsSlick.h:24
BALL::VanDerWaalsSlick::CALCULATION__SOFTENED_LJ_POTENTIAL_SIMPLE
@ CALCULATION__SOFTENED_LJ_POTENTIAL_SIMPLE
Softened Lennard-Jones 6-12 potential (simple cut)
Definition: vanDerWaalsSlick.h:29
BALL::VanDerWaalsSlick::update
void update(const vector< std::pair< Atom *, Atom * > > &)
BALL::VanDerWaalsSlick::Option
Definition: vanDerWaalsSlick.h:39
BALL::VanDerWaalsSlick::Default::VDW_CUT_ON
static const float VDW_CUT_ON
Definition: vanDerWaalsSlick.h:72
BALL::VanDerWaalsSlick::non_bonded_
std::vector< LennardJones::Data > non_bonded_
Definition: vanDerWaalsSlick.h:123
BALL::ScoringFunction
Definition: scoringFunction.h:29