cuikbiominimize.c

Go to the documentation of this file.

#include "bioworld.h"
#include "parameters.h"

#include "atlas.h"
#include "filename.h"
#include "samples.h"

#include <stdlib.h>
#include <string.h>
#include <time.h>

int main(int argc, char **arg)
{      
  if (argc>1)
    { 
      TBioWorld bioWorld;      /* The molecular information.  */
      Tatlas atlas;            /* The atlas defined during minimization. */
      Tparameters parameters;  /* Parameters used in the Cuik process. */

      Tfilename fparam;
      Tfilename fatlas;
  
      double *s1;              /* Starting point for the minimization. */

      TAtlasBase ab;
      
      /*Init parameters*/
      CreateFileName(NULL,arg[1],NULL,PARAM_EXT,&fparam);
      fprintf(stderr,"Reading parameters from           : %s\n",GetFileFullName(&fparam));          
      InitParametersFromFile(GetFileFullName(&fparam),&parameters);

      if (!InitBioWorld(&parameters,arg[1],NO_UINT,&s1,&bioWorld))
        Error("Could not read the molecular information");
      free(s1);
      CS_WD_FROM_WORLD(BioWorldWorld(&bioWorld),&ab);

      /* Read the start sample */
      ReadOneSample(&parameters,arg[1],CS_WD_GET_NUM_SYSTEM_VARS(&ab),&s1);
     
      /* Minimize */
      MinimizeOnAtlas(&parameters,arg[1],s1,&ab,100,
                      BioWorldEnergy,(void *)(&bioWorld),NULL,&atlas);
      

      /* Save the results (the tracked paths are already saved in MinimizeOnAtlas) */
      CreateFileName(NULL,arg[1],NULL,ATLAS_EXT,&fatlas);
      fprintf(stderr,"Writing atlas to                  : %s\n",GetFileFullName(&fatlas));
      SaveAtlas(&parameters,&fatlas,&atlas);

      /* Release memory */
      free(s1);
      DeleteAtlas(&atlas);
      DeleteParameters(&parameters);
      DeleteBioWorld(&bioWorld);

      DeleteFileName(&fparam);
      DeleteFileName(&fatlas);
    }
 else
   {
     fprintf(stderr,"  Wrong number of parameters.\n");
     fprintf(stderr,"  Use:\n");   
     fprintf(stderr,"      cuikbiominimize <problem filename>.pdb\n");
     fprintf(stderr,"  where <problem filename>.pdb contains the molecular information\n");
     fprintf(stderr,"  The extension for the problem file (ex. pdb) is required.\n");
     fprintf(stderr,"  All the extensions managed by OpenBabel can be used\n");
   }
  return(EXIT_SUCCESS);
}