| 197 |
|
std::vector<AtomType*> ayb = at->allYourBase(); |
| 198 |
|
// use the last type in the chain of base types for the name: |
| 199 |
|
std::string bn = ayb[ayb.size()-1]->getName(); |
| 200 |
+ |
|
| 201 |
+ |
if (bn.compare("O")==0 || bn.compare("N")==0 || bn.compare("F")==0) |
| 202 |
+ |
hBondAcceptors_.push_back( atom ); |
| 203 |
|
|
| 201 |
– |
int obanum = etab.GetAtomicNum(bn.c_str()); |
| 202 |
– |
if (obanum != 0) { |
| 203 |
– |
RealType eneg = etab.GetElectroNeg(obanum); |
| 204 |
– |
if (eneg > 3.01) { |
| 205 |
– |
hBondAcceptors_.push_back( atom ); |
| 206 |
– |
} |
| 207 |
– |
} |
| 204 |
|
} |
| 209 |
– |
|
| 210 |
– |
// find electronegative atoms that are either bonded to hydrogens or are |
| 211 |
– |
// present in the same rigid bodies: |
| 205 |
|
|
| 206 |
+ |
// find electronegative atoms that are either bonded to |
| 207 |
+ |
// hydrogens or are present in the same rigid bodies: |
| 208 |
+ |
|
| 209 |
|
for (bond = beginBond(bi); bond != NULL; bond = nextBond(bi)) { |
| 210 |
|
Atom* atom1 = bond->getAtomA(); |
| 211 |
|
Atom* atom2 = bond->getAtomB(); |
| 217 |
|
// use the last type in the chain of base types for the name: |
| 218 |
|
std::string bn1 = ayb1[ayb1.size()-1]->getName(); |
| 219 |
|
std::string bn2 = ayb2[ayb2.size()-1]->getName(); |
| 220 |
< |
int obanum1 = etab.GetAtomicNum(bn1.c_str()); |
| 221 |
< |
int obanum2 = etab.GetAtomicNum(bn2.c_str()); |
| 222 |
< |
|
| 223 |
< |
if (obanum1 == 1) { |
| 224 |
< |
if (obanum2 != 0) { |
| 225 |
< |
RealType eneg = etab.GetElectroNeg(obanum2); |
| 226 |
< |
if (eneg > 3.01) { |
| 227 |
< |
HBondDonor* donor = new HBondDonor(); |
| 232 |
< |
donor->donorAtom = atom2; |
| 233 |
< |
donor->donatedHydrogen = atom1; |
| 234 |
< |
hBondDonors_.push_back( donor ); |
| 235 |
< |
} |
| 220 |
> |
|
| 221 |
> |
if (bn1.compare("H")==0) { |
| 222 |
> |
if (bn2.compare("O")==0 || bn2.compare("N")==0 |
| 223 |
> |
|| bn2.compare("F")==0) { |
| 224 |
> |
HBondDonor* donor = new HBondDonor(); |
| 225 |
> |
donor->donorAtom = atom2; |
| 226 |
> |
donor->donatedHydrogen = atom1; |
| 227 |
> |
hBondDonors_.push_back( donor ); |
| 228 |
|
} |
| 229 |
|
} |
| 230 |
< |
if (obanum2 == 1) { |
| 231 |
< |
if (obanum1 != 0) { |
| 232 |
< |
RealType eneg = etab.GetElectroNeg(obanum1); |
| 233 |
< |
if (eneg > 3.01) { |
| 234 |
< |
HBondDonor* donor = new HBondDonor(); |
| 235 |
< |
donor->donorAtom = atom1; |
| 244 |
< |
donor->donatedHydrogen = atom2; |
| 230 |
> |
if (bn2.compare("H")==0) { |
| 231 |
> |
if (bn1.compare("O")==0 || bn1.compare("N")==0 |
| 232 |
> |
|| bn1.compare("F")==0) { |
| 233 |
> |
HBondDonor* donor = new HBondDonor(); |
| 234 |
> |
donor->donorAtom = atom1; |
| 235 |
> |
donor->donatedHydrogen = atom2; |
| 236 |
|
hBondDonors_.push_back( donor ); |
| 246 |
– |
} |
| 237 |
|
} |
| 238 |
< |
} |
| 238 |
> |
} |
| 239 |
|
} |
| 240 |
< |
|
| 241 |
< |
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 242 |
< |
for(atom1 = rb->beginAtom(ai); atom1 != NULL; atom1 = rb->nextAtom(ai)) { |
| 240 |
> |
|
| 241 |
> |
for (rb = beginRigidBody(rbIter); rb != NULL; |
| 242 |
> |
rb = nextRigidBody(rbIter)) { |
| 243 |
> |
for(atom1 = rb->beginAtom(ai); atom1 != NULL; |
| 244 |
> |
atom1 = rb->nextAtom(ai)) { |
| 245 |
|
AtomType* at1 = atom1->getAtomType(); |
| 246 |
|
// get the chain of base types for this atom type: |
| 247 |
|
std::vector<AtomType*> ayb1 = at1->allYourBase(); |
| 248 |
|
// use the last type in the chain of base types for the name: |
| 249 |
|
std::string bn1 = ayb1[ayb1.size()-1]->getName(); |
| 250 |
< |
int obanum1 = etab.GetAtomicNum(bn1.c_str()); |
| 251 |
< |
if (obanum1 != 0) { |
| 252 |
< |
RealType eneg = etab.GetElectroNeg(obanum1); |
| 253 |
< |
if (eneg > 3.01) { |
| 254 |
< |
for(atom2 = rb->beginAtom(aj); atom2 != NULL; |
| 255 |
< |
atom2 = rb->nextAtom(aj)) { |
| 256 |
< |
AtomType* at2 = atom2->getAtomType(); |
| 257 |
< |
// get the chain of base types for this atom type: |
| 258 |
< |
std::vector<AtomType*> ayb2 = at2->allYourBase(); |
| 259 |
< |
// use the last type in the chain of base types for the name: |
| 260 |
< |
std::string bn2 = ayb2[ayb2.size()-1]->getName(); |
| 261 |
< |
int obanum2 = etab.GetAtomicNum(bn2.c_str()); |
| 262 |
< |
if (obanum2 == 1) { |
| 263 |
< |
HBondDonor* donor = new HBondDonor(); |
| 264 |
< |
donor->donorAtom = atom1; |
| 273 |
< |
donor->donatedHydrogen = atom2; |
| 274 |
< |
hBondDonors_.push_back( donor ); |
| 275 |
< |
} |
| 250 |
> |
|
| 251 |
> |
if (bn1.compare("O")==0 || bn1.compare("N")==0 |
| 252 |
> |
|| bn1.compare("F")==0) { |
| 253 |
> |
for(atom2 = rb->beginAtom(aj); atom2 != NULL; |
| 254 |
> |
atom2 = rb->nextAtom(aj)) { |
| 255 |
> |
AtomType* at2 = atom2->getAtomType(); |
| 256 |
> |
// get the chain of base types for this atom type: |
| 257 |
> |
std::vector<AtomType*> ayb2 = at2->allYourBase(); |
| 258 |
> |
// use the last type in the chain of base types for the name: |
| 259 |
> |
std::string bn2 = ayb2[ayb2.size()-1]->getName(); |
| 260 |
> |
if (bn2.compare("H")==0) { |
| 261 |
> |
HBondDonor* donor = new HBondDonor(); |
| 262 |
> |
donor->donorAtom = atom1; |
| 263 |
> |
donor->donatedHydrogen = atom2; |
| 264 |
> |
hBondDonors_.push_back( donor ); |
| 265 |
|
} |
| 266 |
|
} |
| 267 |
|
} |
| 268 |
|
} |
| 269 |
< |
} |
| 269 |
> |
} |
| 270 |
|
} |
| 271 |
< |
|
| 271 |
> |
|
| 272 |
|
RealType Molecule::getMass() { |
| 273 |
|
StuntDouble* sd; |
| 274 |
|
std::vector<StuntDouble*>::iterator i; |
