| 60 |
|
nObjects_.push_back(info_->getNGlobalBends()); |
| 61 |
|
nObjects_.push_back(info_->getNGlobalTorsions()); |
| 62 |
|
nObjects_.push_back(info_->getNGlobalInversions()); |
| 63 |
+ |
nObjects_.push_back(info_->getNGlobalMolecules()); |
| 64 |
+ |
|
| 65 |
|
loadNames(); |
| 66 |
|
} |
| 67 |
|
|
| 95 |
|
|
| 96 |
|
std::string molName = mol->getMoleculeName(); |
| 97 |
|
TreeNode* molNode = createNode(root_, molName); |
| 98 |
+ |
molNode->bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex()); |
| 99 |
|
|
| 100 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 101 |
|
std::string atomName = atom->getType(); |
| 113 |
|
molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex()); |
| 114 |
|
rbNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex()); |
| 115 |
|
|
| 116 |
< |
//create nodes for atoms belong to this rigidbody |
| 117 |
< |
for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
| 118 |
< |
std::string rbAtomName = atom->getType(); |
| 119 |
< |
TreeNode* rbAtomNode = createNode(rbNode, rbAtomName); |
| 116 |
> |
// COMMENTED OUT because rigid bodies are IntegrableObjects |
| 117 |
> |
// (e.g. they are independently mobile, so selecting their |
| 118 |
> |
// member atoms will give some odd results if we are computing |
| 119 |
> |
// degrees of freedom elsewhere. |
| 120 |
|
|
| 121 |
< |
rbAtomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex()); |
| 122 |
< |
} |
| 121 |
> |
// //create nodes for atoms belong to this rigidbody |
| 122 |
> |
// for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
| 123 |
> |
// std::string rbAtomName = atom->getType(); |
| 124 |
> |
// TreeNode* rbAtomNode = createNode(rbNode, rbAtomName); |
| 125 |
> |
|
| 126 |
> |
// rbAtomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex()); |
| 127 |
> |
// } |
| 128 |
|
} |
| 129 |
|
|
| 130 |
|
for (bond = mol->beginBond(bondIter); bond != NULL; |
