| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
#include "selection/NameFinder.hpp" |
| 43 |
|
#include "utils/wildcards.hpp" |
| 54 |
|
children.clear(); |
| 55 |
|
} |
| 56 |
|
|
| 56 |
– |
|
| 57 |
|
NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){ |
| 58 |
|
nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
| 59 |
|
loadNames(); |
| 60 |
|
} |
| 61 |
|
|
| 62 |
– |
|
| 62 |
|
NameFinder::~NameFinder(){ |
| 63 |
|
delete root_; |
| 64 |
|
} |
| 65 |
|
|
| 66 |
|
void NameFinder::loadNames() { |
| 67 |
|
|
| 69 |
– |
std::map<std::string, TreeNode*>::iterator foundIter; |
| 68 |
|
SimInfo::MoleculeIterator mi; |
| 69 |
|
Molecule* mol; |
| 70 |
|
Molecule::AtomIterator ai; |
| 76 |
|
root_->bs.resize(nStuntDouble_); |
| 77 |
|
root_->bs.setAll(); // |
| 78 |
|
|
| 79 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 79 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 80 |
> |
mol = info_->nextMolecule(mi)) { |
| 81 |
|
|
| 82 |
|
std::string molName = mol->getMoleculeName(); |
| 83 |
|
TreeNode* currentMolNode = createNode(root_, molName); |
| 90 |
|
currentAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
| 91 |
|
} |
| 92 |
|
|
| 93 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 93 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 94 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 95 |
|
std::string rbName = rb->getType(); |
| 96 |
|
TreeNode* currentRbNode = createNode(currentMolNode, rbName); |
| 97 |
|
|
| 105 |
|
|
| 106 |
|
currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
| 107 |
|
} |
| 108 |
– |
|
| 108 |
|
} |
| 109 |
< |
|
| 111 |
< |
} |
| 112 |
< |
|
| 109 |
> |
} |
| 110 |
|
} |
| 111 |
|
|
| 112 |
|
TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) { |
| 222 |
|
} |
| 223 |
|
|
| 224 |
|
bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) { |
| 225 |
< |
return Wildcard::wildcardfit (wildcard.c_str(), str.c_str()); |
| 225 |
> |
return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false; |
| 226 |
|
} |
| 227 |
|
|
| 228 |
|
|
| 229 |
|
void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs){ |
| 230 |
|
|
| 234 |
– |
std::map<std::string, TreeNode*>::iterator foundIter; |
| 231 |
|
SimInfo::MoleculeIterator mi; |
| 232 |
|
Molecule* mol; |
| 233 |
|
|
| 234 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 234 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 235 |
> |
mol = info_->nextMolecule(mi)) { |
| 236 |
|
|
| 237 |
|
if (isMatched(mol->getMoleculeName(), name) ) { |
| 238 |
|
int natoms = mol->getNAtoms(); |
| 246 |
|
bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex()); |
| 247 |
|
} |
| 248 |
|
} |
| 249 |
< |
|
| 253 |
< |
} |
| 254 |
< |
|
| 249 |
> |
} |
| 250 |
|
} |
| 251 |
|
|
| 252 |
< |
bool NameFinder::isInteger(const std::string str) { |
| 253 |
< |
for(int i =0; i < str.size(); ++i){ |
| 252 |
> |
bool NameFinder::isInteger(const std::string &str) { |
| 253 |
> |
for(unsigned int i = 0; i < str.size(); ++i){ |
| 254 |
|
if (!std::isdigit(str[i])) { |
| 255 |
|
return false; |
| 256 |
|
} |
| 257 |
|
} |
| 263 |
– |
|
| 258 |
|
return true; |
| 259 |
|
} |
| 266 |
– |
|
| 260 |
|
} |
