--- trunk/src/UseTheForce/ForceField.cpp	2008/07/04 20:54:29	1275
+++ trunk/src/UseTheForce/ForceField.cpp	2008/10/13 21:35:22	1303
@@ -133,20 +133,20 @@ namespace oopse {
 	ii++;
       }
 
-      // sort the foundBonds by the score:
 
-      std::sort(foundBonds.begin(), foundBonds.end());
-      
-      int bestScore = foundBonds[0].first;
-      std::vector<std::string> theKeys = foundBonds[0].second;
-
-      std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1]  << "\t(score = "<< bestScore << ")\n";      
-      BondType* bestType = bondTypeCont_.find(theKeys);
-      if (bestType) 
-	return bestType;
-      else {
-	//if no exact match found, try wild card match
-	return bondTypeCont_.find(keys, wildCardAtomTypeName_);      
+      if (foundBonds.size() > 0) {
+        // sort the foundBonds by the score:
+        std::sort(foundBonds.begin(), foundBonds.end());
+     
+        int bestScore = foundBonds[0].first;
+        std::vector<std::string> theKeys = foundBonds[0].second;
+        
+        BondType* bestType = bondTypeCont_.find(theKeys);
+        
+        return bestType;
+      } else {
+        //if no exact match found, try wild card match
+        return bondTypeCont_.find(keys, wildCardAtomTypeName_);      
       }
     }
   }
@@ -220,26 +220,21 @@ namespace oopse {
 	jj++;
       }
       
-      std::sort(foundBends.begin(), foundBends.end());
-
-      int jscore = foundBends[0].first;
-      int ikscore = foundBends[0].second;
-      std::vector<std::string> theKeys = foundBends[0].third;
-
-      std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n";      
-
-      BendType* bestType = bendTypeCont_.find(theKeys);  
-      if (bestType) 
-	return bestType;
-      else {
-      
+      if (foundBends.size() > 0) {
+        std::sort(foundBends.begin(), foundBends.end());
+        int jscore = foundBends[0].first;
+        int ikscore = foundBends[0].second;
+        std::vector<std::string> theKeys = foundBends[0].third;       
+        
+        BendType* bestType = bendTypeCont_.find(theKeys);  
+        return bestType;
+      } else {        
 	//if no exact match found, try wild card match
 	return bendTypeCont_.find(keys, wildCardAtomTypeName_);      
       }
     }
   }
 
-
   TorsionType* ForceField::getTorsionType(const std::string &at1, 
 					  const std::string &at2,
 					  const std::string &at3, 
@@ -327,18 +322,14 @@ namespace oopse {
 	jj++;
       }
       
-      std::sort(foundTorsions.begin(), foundTorsions.end());
-
-      int jkscore = foundTorsions[0].first;
-      int ilscore = foundTorsions[0].second;
-      std::vector<std::string> theKeys = foundTorsions[0].third;
-
-      std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n";
-
-      
-      TorsionType* bestType = torsionTypeCont_.find(theKeys);
-      if (bestType) {
-	return bestType;
+      if (foundTorsions.size() > 0) {
+        std::sort(foundTorsions.begin(), foundTorsions.end());
+        int jkscore = foundTorsions[0].first;
+        int ilscore = foundTorsions[0].second;
+        std::vector<std::string> theKeys = foundTorsions[0].third;
+        
+        TorsionType* bestType = torsionTypeCont_.find(theKeys);
+        return bestType;
       } else {
 	//if no exact match found, try wild card match
 	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
@@ -357,7 +348,7 @@ namespace oopse {
     keys.push_back(at4);    
 
     //try exact match first
-    InversionType* inversionType = inversionTypeCont_.find(keys);
+    InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
     if (inversionType) {
       return inversionType;
     } else {
@@ -419,7 +410,7 @@ namespace oopse {
 	      myKeys.push_back((*k)->getName());
 	      myKeys.push_back((*l)->getName());
 	      
-	      InversionType* inversionType = inversionTypeCont_.find(myKeys);
+	      InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
 	      if (inversionType) { 
 		foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
 	      }
@@ -431,19 +422,15 @@ namespace oopse {
 	}
 	jj++;
       }
-      
-      std::sort(foundInversions.begin(), foundInversions.end());
-      
-      int iscore = foundInversions[0].first;
-      int jklscore = foundInversions[0].second;
-      std::vector<std::string> theKeys = foundInversions[0].third;
-      
-      std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n";
-      
-      
-      InversionType* bestType = inversionTypeCont_.find(theKeys);
-      if (bestType) {
-	return bestType;
+         
+      if (foundInversions.size() > 0) {
+        std::sort(foundInversions.begin(), foundInversions.end());
+        int iscore = foundInversions[0].first;
+        int jklscore = foundInversions[0].second;
+        std::vector<std::string> theKeys = foundInversions[0].third;
+        
+        InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
+        return bestType;
       } else {
 	//if no exact match found, try wild card match
 	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
@@ -522,6 +509,12 @@ namespace oopse {
     return atomTypeCont_.add(keys, atomType);
   }
 
+  bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
+    std::vector<std::string> keys;
+    keys.push_back(at);
+    return atomTypeCont_.replace(keys, atomType);
+  }
+
   bool ForceField::addBondType(const std::string &at1, const std::string &at2,
 			       BondType* bondType) {
     std::vector<std::string> keys;