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root/group/trunk/SHAPES/shaper.cpp
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Comparing trunk/SHAPES/shaper.cpp (file contents):
Revision 1312 by chrisfen, Sat Jun 26 15:32:12 2004 UTC vs.
Revision 1360 by gezelter, Tue Jul 20 20:02:15 2004 UTC

# Line 94 | Line 94 | int main(int argc, char* argv[]){
94    if (cmdline_parser (argc, argv, &args_info) != 0)
95      exit(1) ;
96  
97 <  if (args_info.input_given){
98 <    fileName = args_info.input_arg;
99 <  }
100 <  else{
97 >
98 >  if (args_info.inputs_num > 0) {
99 >      fileName = args_info.inputs[0];
100 >  } else {
101      std::cerr << "Does not have input file name" << endl;
102      exit(1);
103    }
# Line 110 | Line 110 | int main(int argc, char* argv[]){
110    strcpy(shapeName, token);
111    strcat(xyzFile, "Ref.xyz");
112    strcat(shapeFile, ".shape");
113 –  strcat(shapeName, "_RB_0");
113    ofstream xfiles(xyzFile);
114    
115    //the bandwidth has a default value (default=16), so it is always given
# Line 224 | Line 223 | int main(int argc, char* argv[]){
223    strcpy(structureFileName, fileName.c_str() );
224  
225    PDBReader* PDBread = new PDBReader();
226 <  PDBread->setPDBfile(structureFileName);
226 >  PDBread->setPDBfileName(structureFileName);
227    theAtoms = PDBread->getAtomList();
228    printf("Found %d atoms\n", theAtoms.size());
229  
# Line 304 | Line 303 | int main(int argc, char* argv[]){
303    printf("Doing SHAPE calculations and outputting results...\n");
304    //do the transforms and write to the shapes file
305    harmonize->doTransforms(sigmaGrid);
306 <  harmonize->printToShapesFile(shapeFile, 0);
306 >  harmonize->printToShapesFile(shapeFile, 0, tolerance);
307    harmonize->doTransforms(sGrid);
308 <  harmonize->printToShapesFile(shapeFile, 1);
308 >  harmonize->printToShapesFile(shapeFile, 1, tolerance);
309    harmonize->doTransforms(epsGrid);
310 <  harmonize->printToShapesFile(shapeFile, 2);
310 >  harmonize->printToShapesFile(shapeFile, 2, tolerance);
311    
312    //clean everything up
313    harmonize->~SphereHarm();  

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