--- trunk/OOPSE/shapes/forcer.cpp	2004/05/21 15:58:48	1183
+++ trunk/OOPSE/shapes/forcer.cpp	2004/05/21 18:34:52	1184
@@ -43,8 +43,14 @@ int main(int argc, char* argv[]){
 int main(int argc, char* argv[]){
 
   gengetopt_args_info args_info;
-  vector<Atype*> vdwAtypes;
-  vector<Atype*>::iterator iter;
+
+  vector<Atype*>   vdwAtypes;
+  vector<Atype*>::iterator i;
+  Atype* at;
+  vector<VDWAtom*> theAtoms;
+  vector<VDWAtom*>::iterator j;
+  VDWAtom* atom;
+
   double mass, rpar, eps;
   string fileName;  
   char vdwFileName[2002];
@@ -56,11 +62,12 @@ int main(int argc, char* argv[]){
   char* ffPath;
   char* eof_test;
   char* foo;
+  char* myType;
+  char* vType;
   int lineNum;
   int nTokens;
-  Atype* at;
   int FF;
-  vector <VDWAtom*> theAtoms;
+  short int gotMatch;
 
   //parse the command line options
   if (cmdline_parser (argc, argv, &args_info) != 0)
@@ -177,7 +184,49 @@ int main(int argc, char* argv[]){
   PDBread->setPDBfile(structureFileName);
   theAtoms = PDBread->getAtomList();
   printf("Found %d atoms\n", theAtoms.size());
-  
+
+  for( j = theAtoms.begin(); j !=  theAtoms.end(); ++j){
+    atom = *j;
+    myType = atom->getType();
+    gotMatch = 0;
+
+    for( i = vdwAtypes.begin(); i !=  vdwAtypes.end(); ++i){
+      at = *i;
+      vType = at->getType();
+      
+      if (!strcasecmp(myType, vType)) {
+        atom->setMass(at->getMass());
+        atom->setRpar(at->getRpar());
+        atom->setEps(at->getEps());
+        gotMatch = 1;        
+      }
+    }
+    if (!gotMatch) {      
+      printf("No matches found for %s, ", myType);
+      myType = atom->getBase();
+      printf("trying with BaseType %s\n", myType);
+      for( i = vdwAtypes.begin(); i !=  vdwAtypes.end(); ++i){
+        at = *i;
+        vType = at->getType();        
+        if (!strcasecmp(myType, vType)) {
+          atom->setMass(at->getMass());
+          atom->setRpar(at->getRpar());
+          atom->setEps(at->getEps());
+          gotMatch = 1;
+        }
+      }
+    }
+
+    if (!gotMatch) {
+      printf("No matches found with BaseType!\n");
+    }
+  }
+
+  //GridBuilder gb = new GridBuilder();
+  //gb->findAxesAndOrigin(theAtoms);
+  //gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid);
+ 
+
 }
 
 int count_tokens(char *line, char *delimiters) {