cuikatoms2samples.c

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#include "defines.h"
#include "filename.h"
#include "bioworld.h"

#include <stdlib.h>

int main(int argc, char **arg)
{ 
  if (argc>1)
    {
      Tparameters parameters;
      TBioWorld bioWorld;

      Tfilename fparam;
      Tfilename fsamples;
      Tfilename fatoms;

      boolean nv;
      double *sample;

      unsigned int na;
      double *atoms;

      unsigned int i,j,k,r;
      boolean end;
      int token;

      FILE *fin;
      FILE *fout;

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

      /* Read the problem file */
      InitBioWorld(&parameters,arg[1],NO_UINT,&sample,&bioWorld);
      free(sample);

      /* File from where to read the atoms */
      CreateFileName(NULL,arg[1],NULL,ATOM_EXT,&fatoms);
      fin=fopen(GetFileFullName(&fatoms),"r");
      if (!fin)
        Error("Can not open the input file with the atom positions");

      /* Open the file where to store the output samples */
      r=(unsigned int)(GetParameter(CT_REPRESENTATION,&parameters));
      if (r==REP_JOINTS)
        CreateFileName(NULL,arg[1],"_a2s",JOINTS_EXT,&fsamples);
      else
        CreateFileName(NULL,arg[1],"_a2s",LINKS_EXT,&fsamples);
      fprintf(stderr,"Writing samples to                : %s\n",GetFileFullName(&fsamples));

      fout=fopen(GetFileFullName(&fsamples),"w");
      if (!fout)
        Error("Could not open the file to write the samples");
 
      /* Allocate space for the atoms and the sample */
      na=BioWorldNAtoms(&bioWorld);
      NEW(atoms,3*na,double);

      /* Read one sample from the file of samples */
      end=FALSE;
      do {
        k=0;
        for(i=0;((!end)&&(i<na));i++)
          {
            for(j=0;((!end)&&(j<3));j++,k++)
              {
                token=fscanf(fin,"%lf",&(atoms[k]));
                if ((token==EOF)||(token==0))
                  end=TRUE;
              }
          }

        if (!end)
          {
            /* Deduce the conformation from the atom positions */
            nv=BioWordConformationFromAtomPositions(&parameters,atoms,&sample,&bioWorld);

            /* Save the conformation */
            for(i=0;i<nv;i++)
              fprintf(fout,"%.16f ",sample[i]);
            fprintf(fout,"\n");

            free(sample);
          }

      } while(!end);

      /* Close the files */
      fclose(fin);
      fclose(fout);

      /* Release memeory */
      free(atoms);
 
      DeleteBioWorld(&bioWorld);
      DeleteParameters(&parameters);

      DeleteFileName(&fparam);
      DeleteFileName(&fsamples);  
      DeleteFileName(&fatoms);   
    }
  else
    {
      fprintf(stderr,"  Wrong number of parameters.\n");
      fprintf(stderr,"  Use:\n");
      fprintf(stderr,"    cuikatoms2samples <problem_name>.pdb\n");
      fprintf(stderr,"  where <problem_name>.pdb contains the molecular information\n");
      fprintf(stderr,"  The '.pab' extension is required\n");
      fprintf(stderr,"  All the extensions managed by OpenBabel can be used\n");
    }
 
  return(EXIT_SUCCESS);
}