#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <math.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <unistd.h>
#include <zlib.h>

main(){
    const char *a[5];
    int i, j ,k, ii, jj, kk;
    char str[256];
    FILE *fp, *source, *target, *fp1;
    char ch[300];
    char str1[256];
    char sbuff[300];

    printf("Start Here ...n");

    a[0] = "submit.sh";
    a[1] = "run.prm";
    a[2] =  "name.txt";
    a[3] = "prot.pdb";
    a[4] = "step2_out.pdb";

    for (i=1;i<6;i++){
        sprintf(str,"_%d", i);
        mkdir(str, 0755); // Create temporary directories

        for (j=0;j<5;j++){
            sprintf(str,"%s", a[j]);
            source = fopen(str, "r");
            if( source == NULL )
            {
                printf("Error in doStepOneAndTwo, can't open file source n");
                return -1;
            }
            sprintf(str,"_%d/%s", i, a[j]);
            target = fopen(str, "w+");
            if( target == NULL )
            {
                fclose(source);
                printf("Error in doStepOneAndTwo, can't open file target %s n",str);
                return -1;
            }
            while( (fgets(ch, sizeof(ch), source))) {
              if (j == 1){
                  if (strstr(ch, "(DO_PREMCCE)")){
                        ch[0] = 'f';
                      }
                     else if (strstr(ch, "(DO_ROTAMERS)")){
                        ch[0] = 'f';
                     }
                     else if (strstr(ch, "(DO_MONTE)")){
                         ch[0] = 'f';
                     }
                     else if (strstr(ch, "(DELPHI_STEP)")){
                        ch[0] = 'f';
                     }
                  fputs(ch, target);
              }else {
              fputs(ch, target);
              }

          }
        }
        sprintf(str1,"chmod +x _%d/submit.sh", i);
        system(str1);

        // Submiting the jobs
        if (getcwd(sbuff, sizeof(sbuff)) != NULL)
           printf("Current working dir 1: %sn", sbuff);
           else
               printf("getcwd() error");
        sprintf(str,"_%d/", i);
        chdir(str);
        system("qsub submit.sh"); // This line doesn't works, the above directories are dynamically created (str)
        chdir(sbuff);
    }

    // Submit the job
        chdir("1l2y");
        system("qsub submit.sh"); // This line works, the above directory is manually created (1l2y)
        chdir(sbuff);



    return 0;
}