--- trunk/src/UseTheForce/ForceField.cpp	2008/07/01 13:28:23	1269
+++ trunk/src/UseTheForce/ForceField.cpp	2008/07/14 12:35:58	1277
@@ -124,6 +124,7 @@ namespace oopse {
 	  myKeys.push_back((*i)->getName());
 	  myKeys.push_back((*j)->getName());
 
+          std::cerr << "looking for " << myKeys[0] << " " << myKeys[1] << "\n";
 	  BondType* bondType = bondTypeCont_.find(myKeys);
 	  if (bondType) {
 	    foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
@@ -133,20 +134,21 @@ 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;
+        
+        std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1]  << "\t(score = "<< bestScore << ")\n";      
+        BondType* bestType = bondTypeCont_.find(theKeys);
+        
+        return bestType;
+      } else {
+        //if no exact match found, try wild card match
+        return bondTypeCont_.find(keys, wildCardAtomTypeName_);      
       }
     }
   }
@@ -220,26 +222,23 @@ 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;
+        
+        std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n";      
+        
+        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, 
@@ -327,25 +326,126 @@ namespace oopse {
 	jj++;
       }
       
-      std::sort(foundTorsions.begin(), foundTorsions.end());
+      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;
+        
+        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);
+        return bestType;
+      } else {
+	//if no exact match found, try wild card match
+	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
+      }
+    }
+  }
 
-      int jkscore = foundTorsions[0].first;
-      int ilscore = foundTorsions[0].second;
-      std::vector<std::string> theKeys = foundTorsions[0].third;
+  InversionType* ForceField::getInversionType(const std::string &at1, 
+					      const std::string &at2,
+					      const std::string &at3, 
+					      const std::string &at4) {
+    std::vector<std::string> keys;
+    keys.push_back(at1);
+    keys.push_back(at2);    
+    keys.push_back(at3);    
+    keys.push_back(at4);    
 
-      std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n";
+    //try exact match first
+    InversionType* inversionType = inversionTypeCont_.find(keys);
+    if (inversionType) {
+      return inversionType;
+    } else {
+      
+      AtomType* atype1;
+      AtomType* atype2;
+      AtomType* atype3;
+      AtomType* atype4;
+      std::vector<std::string> at1key;
+      at1key.push_back(at1);
+      atype1 = atomTypeCont_.find(at1key);
+      
+      std::vector<std::string> at2key;
+      at2key.push_back(at2);
+      atype2 = atomTypeCont_.find(at2key);
+      
+      std::vector<std::string> at3key;
+      at3key.push_back(at3);
+      atype3 = atomTypeCont_.find(at3key);
+      
+      std::vector<std::string> at4key;
+      at4key.push_back(at4);
+      atype4 = atomTypeCont_.find(at4key);
 
+      // query atom types for their chains of responsibility
+      std::vector<AtomType*> at1Chain = atype1->allYourBase();
+      std::vector<AtomType*> at2Chain = atype2->allYourBase();
+      std::vector<AtomType*> at3Chain = atype3->allYourBase();
+      std::vector<AtomType*> at4Chain = atype4->allYourBase();
+
+      std::vector<AtomType*>::iterator i;
+      std::vector<AtomType*>::iterator j;
+      std::vector<AtomType*>::iterator k;
+      std::vector<AtomType*>::iterator l;
+
+      int ii = 0;
+      int jj = 0;
+      int kk = 0;
+      int ll = 0;
+      int Iscore;
+      int JKLscore;
       
-      TorsionType* bestType = torsionTypeCont_.find(theKeys);
-      if (bestType) {
-	return bestType;
+      std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
+      
+      for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
+	kk = 0;
+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
+	  ii = 0;	
+	  for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
+	    ll = 0;
+	    for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
+	      
+	      Iscore = ii;
+	      JKLscore = jj + kk + ll;
+	      
+	      std::vector<std::string> myKeys;
+	      myKeys.push_back((*i)->getName());
+	      myKeys.push_back((*j)->getName());
+	      myKeys.push_back((*k)->getName());
+	      myKeys.push_back((*l)->getName());
+	      
+	      InversionType* inversionType = inversionTypeCont_.find(myKeys);
+	      if (inversionType) { 
+		foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
+	      }
+	      ll++;
+	    }
+	    ii++;
+	  }
+	  kk++;
+	}
+	jj++;
+      }
+         
+      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;
+        
+        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);
+        return bestType;
       } else {
 	//if no exact match found, try wild card match
-	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
+	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
       }
     }
   }
-
+  
   NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
     std::vector<std::string> keys;
     keys.push_back(at1);
@@ -390,15 +490,27 @@ namespace oopse {
     keys.push_back(at4);   
     return torsionTypeCont_.find(keys);
   }
-
+  
+  InversionType* ForceField::getExactInversionType(const std::string &at1, 
+						   const std::string &at2,
+						   const std::string &at3, 
+						   const std::string &at4){ 
+    std::vector<std::string> keys;
+    keys.push_back(at1);
+    keys.push_back(at2);    
+    keys.push_back(at3);    
+    keys.push_back(at4);   
+    return inversionTypeCont_.find(keys);
+  }
+  
   NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){ 
     std::vector<std::string> keys;
     keys.push_back(at1);
     keys.push_back(at2);    
     return nonBondedInteractionTypeCont_.find(keys);
   }
+  
 
-
   bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
     std::vector<std::string> keys;
     keys.push_back(at);
@@ -435,6 +547,19 @@ namespace oopse {
     return torsionTypeCont_.add(keys, torsionType);
   }
 
+  bool ForceField::addInversionType(const std::string &at1, 
+				    const std::string &at2,
+				    const std::string &at3, 
+				    const std::string &at4, 
+				    InversionType* inversionType) {
+    std::vector<std::string> keys;
+    keys.push_back(at1);
+    keys.push_back(at2);    
+    keys.push_back(at3);    
+    keys.push_back(at4);    
+    return inversionTypeCont_.add(keys, inversionType);
+  }
+  
   bool ForceField::addNonBondedInteractionType(const std::string &at1, 
 					       const std::string &at2, 
 					       NonBondedInteractionType* nbiType) {