--- trunk/src/selection/NameFinder.cpp	2009/11/25 20:02:06	1390
+++ trunk/src/selection/NameFinder.cpp	2012/10/01 18:21:15	1801
@@ -36,7 +36,8 @@
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
  * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 #include "selection/NameFinder.hpp"
 #include "utils/wildcards.hpp"
@@ -53,13 +54,11 @@ namespace OpenMD {
     children.clear();
   }
 
-
   NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
     nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
     loadNames();
   }
 
-
   NameFinder::~NameFinder(){
     delete root_;
   }
@@ -78,7 +77,8 @@ namespace OpenMD {
     root_->bs.resize(nStuntDouble_);
     root_->bs.setAll(); //
     
-    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
+    for (mol = info_->beginMolecule(mi); mol != NULL; 
+         mol = info_->nextMolecule(mi)) {
            
       std::string molName = mol->getMoleculeName();
       TreeNode* currentMolNode = createNode(root_, molName);
@@ -91,7 +91,8 @@ namespace OpenMD {
 	currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
       }
 
-      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
+      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
+           rb = mol->nextRigidBody(rbIter)) {
 	std::string rbName = rb->getType();
 	TreeNode* currentRbNode = createNode(currentMolNode, rbName);
             
@@ -105,11 +106,8 @@ namespace OpenMD {
 
 	  currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
 	}
-
       }
-        
-    }    
-
+    }
   }
 
   TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
@@ -225,7 +223,7 @@ namespace OpenMD {
   }
 
   bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
-    return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
+    return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false;
   }
 
 
@@ -235,7 +233,8 @@ namespace OpenMD {
     SimInfo::MoleculeIterator mi;
     Molecule* mol;
 
-    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
+    for (mol = info_->beginMolecule(mi); mol != NULL; 
+         mol = info_->nextMolecule(mi)) {
            
       if (isMatched(mol->getMoleculeName(), name) ) {
 	int natoms = mol->getNAtoms();
@@ -249,19 +248,15 @@ namespace OpenMD {
 	  bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
 	}
       }
-        
-    }    
-    
+    }
   }
 
   bool NameFinder::isInteger(const std::string str) {
-    for(int i =0; i < str.size(); ++i){
+    for(unsigned int i = 0; i < str.size(); ++i){
       if (!std::isdigit(str[i])) {
 	return false;
       }
     }
-
     return true;
   }
-
 }