| 64 |
|
MemoryUtils::deletePointers(bonds_); |
| 65 |
|
MemoryUtils::deletePointers(bends_); |
| 66 |
|
MemoryUtils::deletePointers(torsions_); |
| 67 |
+ |
MemoryUtils::deletePointers(inversions_); |
| 68 |
|
MemoryUtils::deletePointers(rigidBodies_); |
| 69 |
|
MemoryUtils::deletePointers(cutoffGroups_); |
| 70 |
|
MemoryUtils::deletePointers(constraintPairs_); |
| 96 |
|
if (std::find(torsions_.begin(), torsions_.end(), torsion) == |
| 97 |
|
torsions_.end()) { |
| 98 |
|
torsions_.push_back(torsion); |
| 99 |
+ |
} |
| 100 |
+ |
} |
| 101 |
+ |
|
| 102 |
+ |
void Molecule::addInversion(Inversion* inversion) { |
| 103 |
+ |
if (std::find(inversions_.begin(), inversions_.end(), inversion) == |
| 104 |
+ |
inversions_.end()) { |
| 105 |
+ |
inversions_.push_back(inversion); |
| 106 |
|
} |
| 107 |
|
} |
| 108 |
|
|
| 245 |
|
Bond* bond; |
| 246 |
|
Bend* bend; |
| 247 |
|
Torsion* torsion; |
| 248 |
+ |
Inversion* inversion; |
| 249 |
|
Molecule::BondIterator bondIter;; |
| 250 |
|
Molecule::BendIterator bendIter; |
| 251 |
|
Molecule::TorsionIterator torsionIter; |
| 252 |
+ |
Molecule::InversionIterator inversionIter; |
| 253 |
|
|
| 254 |
|
RealType potential = 0.0; |
| 255 |
|
|
| 266 |
|
potential += torsion->getPotential(); |
| 267 |
|
} |
| 268 |
|
|
| 269 |
+ |
for (inversion = beginInversion(inversionIter); torsion != NULL; |
| 270 |
+ |
inversion = nextInversion(inversionIter)) { |
| 271 |
+ |
potential += inversion->getPotential(); |
| 272 |
+ |
} |
| 273 |
+ |
|
| 274 |
|
return potential; |
| 275 |
|
|
| 276 |
|
} |
| 277 |
|
|
| 278 |
+ |
void Molecule::addProperty(GenericData* genData) { |
| 279 |
+ |
properties_.addProperty(genData); |
| 280 |
+ |
} |
| 281 |
+ |
|
| 282 |
+ |
void Molecule::removeProperty(const std::string& propName) { |
| 283 |
+ |
properties_.removeProperty(propName); |
| 284 |
+ |
} |
| 285 |
+ |
|
| 286 |
+ |
void Molecule::clearProperties() { |
| 287 |
+ |
properties_.clearProperties(); |
| 288 |
+ |
} |
| 289 |
+ |
|
| 290 |
+ |
std::vector<std::string> Molecule::getPropertyNames() { |
| 291 |
+ |
return properties_.getPropertyNames(); |
| 292 |
+ |
} |
| 293 |
+ |
|
| 294 |
+ |
std::vector<GenericData*> Molecule::getProperties() { |
| 295 |
+ |
return properties_.getProperties(); |
| 296 |
+ |
} |
| 297 |
+ |
|
| 298 |
+ |
GenericData* Molecule::getPropertyByName(const std::string& propName) { |
| 299 |
+ |
return properties_.getPropertyByName(propName); |
| 300 |
+ |
} |
| 301 |
+ |
|
| 302 |
+ |
|
| 303 |
+ |
|
| 304 |
+ |
|
| 305 |
|
std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
| 306 |
|
o << std::endl; |
| 307 |
|
o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
| 309 |
|
o << mol.getNBonds() << " bonds" << std::endl; |
| 310 |
|
o << mol.getNBends() << " bends" << std::endl; |
| 311 |
|
o << mol.getNTorsions() << " torsions" << std::endl; |
| 312 |
+ |
o << mol.getNInversions() << " inversions" << std::endl; |
| 313 |
|
o << mol.getNRigidBodies() << " rigid bodies" << std::endl; |
| 314 |
|
o << mol.getNIntegrableObjects() << "integrable objects" << std::endl; |
| 315 |
|
o << mol.getNCutoffGroups() << "cutoff groups" << std::endl; |
