BALL 1.5.0
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polarSolvation.h
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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
11namespace BALL
12{
17 {
18 public:
19
50
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
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
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
195 ;
196
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
HashMap class based on the STL map (containing serveral convenience functions)
PolarSolvation(ScoringFunction &sf)
void update(const vector< std::pair< Atom *, Atom * > > &)
virtual bool setup()
virtual ~PolarSolvation()
PolarSolvation(const PolarSolvation &fhb)
virtual double updateScore()
virtual void clear()
static const char * POLAR_FOCUS_GRID_AROUND_LIGAND
static const char * UNITE_ATOMS
static const char * POLAR_CHARGE_RULES
static const char * POLAR_GB
static const char * GB_SCALING_FILE
static const char * VERBOSITY
static const char * POLAR_OVERWRITE_CHARGES
static const char * POLAR_OVERWRITE_RADII
static const char * POLAR_AVG
static const char * POLAR_RADIUS_RULES
static const char * POLAR_METHOD
static const String POLAR_CHARGE_RULES
static const bool POLAR_FOCUS_GRID_AROUND_LIGAND
static const String GB_SCALING_FILE
static const bool POLAR_OVERWRITE_CHARGES
static const String POLAR_RADIUS_RULES
static const bool POLAR_OVERWRITE_RADII
#define BALL_EXPORT