BALL  1.5.0
polarSolvation.h
Go to the documentation of this file.
1 // $Id: polarSolvation.h,v 1.2 2006/05/21 17:49:46 anker Exp $
2 
3 #ifndef BALL_SCORING_COMPONENTS_POLARSOLVATION_H
4 #define BALL_SCORING_COMPONENTS_POLARSOLVATION_H
5 
7 
10 
11 namespace BALL
12 {
17  {
18  public:
19 
23  {
24 
28 
32 
36 
40 
44 
47  CALCULATION__EEF1
48 
49  };
50 
54  {
58 
63 
68 
73  AVERAGING__RANDOM
74 
75  };
76 
77 
79  {
80 
83  static const char* POLAR_METHOD;
84 
87  static const char* POLAR_GB;
88 
91  static const char* POLAR_AVG;
92 
95  static const char* POLAR_FOCUS_GRID_AROUND_LIGAND;
96 
99  static const char* GB_SCALING_FILE;
100 
103  static const char* UNITE_ATOMS;
104 
107  static const char* VERBOSITY;
108 
111  static const char* POLAR_OVERWRITE_RADII;
112 
115  static const char* POLAR_OVERWRITE_CHARGES;
116 
119  static const char* POLAR_RADIUS_RULES;
120 
123  static const char* POLAR_CHARGE_RULES;
124 
125  };
126 
127 
128  struct Default
129  {
130 
133  static const Size POLAR_METHOD;
134 
137  static const bool POLAR_GB;
138 
141  static const Size POLAR_AVG;
142 
146 
149  static const String GB_SCALING_FILE;
150 
153  static const bool UNITE_ATOMS;
154 
157  static const Size VERBOSITY;
158 
161  static const bool POLAR_OVERWRITE_RADII;
162 
165  static const bool POLAR_OVERWRITE_CHARGES;
166 
170 
174 
175  };
176 
177 
181 
185  ;
186 
190  ;
191 
194  PolarSolvation(const PolarSolvation& fhb)
195  ;
196 
199  virtual ~PolarSolvation()
200  ;
201 
203 
206 
209  const PolarSolvation& operator = (const PolarSolvation& fr)
210  ;
211 
214  virtual void clear()
215  ;
216 
218 
221 
222  bool operator == (const PolarSolvation& fr) const
223  ;
224 
226 
229 
233  virtual bool setup();
234 
235  void update(const vector<std::pair<Atom*, Atom*> >& /* pair_vector */);
236 
240  virtual double updateScore();
241 
243 
246 
248 
249  private:
250 
251  /*_
252  */
253  Molecule desolv_protein_;
254 
255  /*_
256  */
257  Molecule desolv_ligand_;
258 
259  /*_
260  */
261  Size calculation_method_;
262 
263  /*_
264  */
265  Size averaging_;
266 
267  /*_
268  */
269  bool unite_atoms_;
270 
271  /*_
272  */
273  Size verbosity_;
274 
275  /*_
276  */
277  FDPB fdpb_;
278 
279  /*_
280  */
282 
283  /*_
284  */
285  bool use_gb_;
286 
287  /*_
288  */
289  float spacing_;
290 
291  /*_
292  */
293  float bulk_water_dc_;
294 
295  /*_
296  */
297  float vacuum_dc_;
298 
299  /*_
300  */
301  bool computeEnergyDifference_(System& system, float& energy)
302  ;
303 
304  /*_
305  */
306  bool computeESEnergy_(System& system, float& energy)
307  ;
308 
309  /*_
310  */
311  float computeESInteractionEnergy_(const Molecule& molecule, const
313  ;
314 
315  /*_
316  */
317  bool computeFullCycle_(System& system, Molecule& protein,
318  Molecule& ligand, float& energy)
319  ;
320 
321  /*_
322  */
323  Vector3 permuteComponentSigns_(Vector3 vector, Size permutation)
324  ;
325 
326  /*_ Condense hydrogens without radius but bearing charges on the heavy
327  atom they are attached to
328  */
329  Size uniteAtoms_(Molecule& molecule)
330  ;
331 
332  };
333 
334 } // namespace BALL
335 
336 #endif // BALL_SCORING_COMPONENTS_POLARSOLVATION_H
BALL::PolarSolvation::Default
Definition: polarSolvation.h:128
BALL::PolarSolvation::AVERAGING__RANDOM_FACTOR
@ AVERAGING__RANDOM_FACTOR
Definition: polarSolvation.h:67
BALL::PolarSolvation::CALCULATION__COULOMB
@ CALCULATION__COULOMB
Definition: polarSolvation.h:43
BALL::PolarSolvation::Option::VERBOSITY
static const char * VERBOSITY
Definition: polarSolvation.h:107
BALL::PolarSolvation::Option::POLAR_OVERWRITE_RADII
static const char * POLAR_OVERWRITE_RADII
Definition: polarSolvation.h:111
BALL::HashMap< const Atom *, float >
BALL::Molecule
Definition: molecule.h:29
BALL::System
Definition: KERNEL/system.h:38
BALL::PolarSolvation::Option::POLAR_CHARGE_RULES
static const char * POLAR_CHARGE_RULES
Definition: polarSolvation.h:123
BALL::PolarSolvation::CALCULATION__FULL_SLICK
@ CALCULATION__FULL_SLICK
Definition: polarSolvation.h:31
BALL::PolarSolvation::Default::POLAR_RADIUS_RULES
static const String POLAR_RADIUS_RULES
Definition: polarSolvation.h:169
BALL::PolarSolvation
Definition: polarSolvation.h:16
BALL::String
Definition: string.h:56
poissonBoltzmann.h
BALL::PolarSolvation::Default::POLAR_GB
static const bool POLAR_GB
Definition: polarSolvation.h:137
BALL
Definition: constants.h:12
BALL::PolarSolvation::Default::POLAR_AVG
static const Size POLAR_AVG
Definition: polarSolvation.h:141
BALL::PolarSolvation::Option::POLAR_METHOD
static const char * POLAR_METHOD
Definition: polarSolvation.h:83
BALL::PolarSolvation::AVERAGING__NONE
@ AVERAGING__NONE
Definition: polarSolvation.h:57
BALL::PolarSolvation::Default::POLAR_CHARGE_RULES
static const String POLAR_CHARGE_RULES
Definition: polarSolvation.h:173
scoringComponent.h
BALL::PolarSolvation::Default::POLAR_FOCUS_GRID_AROUND_LIGAND
static const bool POLAR_FOCUS_GRID_AROUND_LIGAND
Definition: polarSolvation.h:145
BALL::PolarSolvation::CALCULATION__FULL_CYCLE
@ CALCULATION__FULL_CYCLE
Definition: polarSolvation.h:35
BALL::PolarSolvation::Default::POLAR_OVERWRITE_CHARGES
static const bool POLAR_OVERWRITE_CHARGES
Definition: polarSolvation.h:165
BALL::PolarSolvation::CALCULATION__FRESNO
@ CALCULATION__FRESNO
Definition: polarSolvation.h:27
BALL_SIZE_TYPE
BALL::PolarSolvation::AveragingMethod
AveragingMethod
Definition: polarSolvation.h:53
BALL::TVector3< float >
BALL::ScoringComponent
Definition: scoringComponent.h:20
BALL::PolarSolvation::Option
Definition: polarSolvation.h:78
BALL::PolarSolvation::Default::POLAR_OVERWRITE_RADII
static const bool POLAR_OVERWRITE_RADII
Definition: polarSolvation.h:161
generalizedBornCase.h
BALL::PolarSolvation::Option::GB_SCALING_FILE
static const char * GB_SCALING_FILE
Definition: polarSolvation.h:99
BALL::PolarSolvation::Option::POLAR_FOCUS_GRID_AROUND_LIGAND
static const char * POLAR_FOCUS_GRID_AROUND_LIGAND
Definition: polarSolvation.h:95
BALL::operator==
BALL_EXPORT bool operator==(const String &s1, const String &s2)
BALL::PolarSolvation::Option::UNITE_ATOMS
static const char * UNITE_ATOMS
Definition: polarSolvation.h:103
BALL::PolarSolvation::Option::POLAR_GB
static const char * POLAR_GB
Definition: polarSolvation.h:87
BALL::PolarSolvation::Option::POLAR_AVG
static const char * POLAR_AVG
Definition: polarSolvation.h:91
BALL::GeneralizedBornModel
Definition: generalizedBornCase.h:61
BALL::PolarSolvation::CALCULATION__FULL_CYCLE_FOCUSED
@ CALCULATION__FULL_CYCLE_FOCUSED
Definition: polarSolvation.h:39
BALL::PolarSolvation::Default::UNITE_ATOMS
static const bool UNITE_ATOMS
Definition: polarSolvation.h:153
BALL::PolarSolvation::Option::POLAR_RADIUS_RULES
static const char * POLAR_RADIUS_RULES
Definition: polarSolvation.h:119
BALL::PolarSolvation::Default::POLAR_METHOD
static const Size POLAR_METHOD
Definition: polarSolvation.h:133
BALL::PolarSolvation::Default::VERBOSITY
static const Size VERBOSITY
Definition: polarSolvation.h:157
BALL::PolarSolvation::Default::GB_SCALING_FILE
static const String GB_SCALING_FILE
Definition: polarSolvation.h:149
BALL_EXPORT
#define BALL_EXPORT
Definition: COMMON/global.h:50
BALL::PolarSolvation::CalculationMethod
CalculationMethod
Definition: polarSolvation.h:22
BALL::PolarSolvation::Option::POLAR_OVERWRITE_CHARGES
static const char * POLAR_OVERWRITE_CHARGES
Definition: polarSolvation.h:115
BALL::ScoringFunction
Definition: scoringFunction.h:28
BALL::PolarSolvation::AVERAGING__STATIC
@ AVERAGING__STATIC
Definition: polarSolvation.h:62
BALL::FDPB
Definition: poissonBoltzmann.h:36