--- trunk/SHAPES/shaper.cpp	2004/06/26 15:32:12	1312
+++ trunk/SHAPES/shaper.cpp	2004/07/20 20:02:15	1360
@@ -94,10 +94,10 @@ int main(int argc, char* argv[]){
   if (cmdline_parser (argc, argv, &args_info) != 0)
     exit(1) ;
 
-  if (args_info.input_given){
-    fileName = args_info.input_arg;
-  }
-  else{
+
+  if (args_info.inputs_num > 0) {
+      fileName = args_info.inputs[0];
+  } else {
     std::cerr << "Does not have input file name" << endl;
     exit(1);
   }
@@ -110,7 +110,6 @@ int main(int argc, char* argv[]){
   strcpy(shapeName, token);
   strcat(xyzFile, "Ref.xyz");
   strcat(shapeFile, ".shape");
-  strcat(shapeName, "_RB_0");
   ofstream xfiles(xyzFile);
   
   //the bandwidth has a default value (default=16), so it is always given
@@ -224,7 +223,7 @@ int main(int argc, char* argv[]){
   strcpy(structureFileName, fileName.c_str() );
 
   PDBReader* PDBread = new PDBReader();
-  PDBread->setPDBfile(structureFileName);
+  PDBread->setPDBfileName(structureFileName);
   theAtoms = PDBread->getAtomList();
   printf("Found %d atoms\n", theAtoms.size());
 
@@ -304,11 +303,11 @@ int main(int argc, char* argv[]){
   printf("Doing SHAPE calculations and outputting results...\n");
   //do the transforms and write to the shapes file
   harmonize->doTransforms(sigmaGrid);
-  harmonize->printToShapesFile(shapeFile, 0);
+  harmonize->printToShapesFile(shapeFile, 0, tolerance);
   harmonize->doTransforms(sGrid);
-  harmonize->printToShapesFile(shapeFile, 1);
+  harmonize->printToShapesFile(shapeFile, 1, tolerance);
   harmonize->doTransforms(epsGrid);
-  harmonize->printToShapesFile(shapeFile, 2);
+  harmonize->printToShapesFile(shapeFile, 2, tolerance);
   
   //clean everything up
   harmonize->~SphereHarm();