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Grep a string from pdb file

This is a discussion on Grep a string from pdb file within the C Programming forums, part of the General Programming Boards category; Hi, Im new to c programming. I have one pdb file. i want to extract a string starting with ATOM ...

  1. #1
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    Grep a string from pdb file

    Hi,
    Im new to c programming.
    I have one pdb file. i want to extract a string starting with ATOM and store it in a text file.

    here is my program,
    Code:
    #include<stdio.h>
    #include<string.h>
    #include<stdlib.h>
    #include<fcntl.h>
    #define size 50
    main()
    {
    char temp[300],*ptr;
    char sname[50],ws[50],buf[50],buf1[50],field[32];
    FILE *file,*file1;
    int n;
    printf("Enter the Filename\n");
    scanf("%s",sname);
    file=fopen(sname,"r");
    printf("Enter the Word to Search\n");
    scanf("%s",ws);
    file1=fopen("grep.txt","w");
    while(fgets(temp,200,file)!=NULL)
    {
    ptr=strstr(temp,ws);
    if(ptr!=NULL)
    fprintf(file1,"%s",ptr);
    }
    fclose(file);
    strstr function extract the intermediate ATOM and ATOMS too. but i want a string staring with ATOM.

    Thanks in advance..

  2. #2
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    Have you tried strnstr()? Then you can restrict the length.

  3. #3
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    Quote Originally Posted by Subsonics View Post
    Have you tried strnstr()? Then you can restrict the length.
    when i use strnstr() it gives the following error
    (.text+0xbd): undefined reference to `strnstr'
    collect2: ld returned 1 exit status

  4. #4
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    Hm, yeah it's not a standard C function I noticed your fcntl.h and thought it belonged to POSIX but apparently it's a BSD extension. That leaves you to implement a simple parsing function yourself, either as a second step to what strstr catches or make something from scratch that scans the lines from fgets.

    BTW, you should indent the code, that way you might get more responses here.
    Last edited by Subsonics; 04-07-2011 at 01:42 AM.
    Salem likes this.

  5. #5
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    Quote Originally Posted by Subsonics View Post
    Hm, yeah it's not a standard C function I noticed your fcntl.h and thought it belonged to POSIX but apparently it's a BSD extension. That leaves you to implement a simple parsing function yourself, either as a second step to what strstr catches or make something from scratch that scans the lines from fgets.

    BTW, you should indent the code, that way you might get more responses here.
    sorry I can't understand yours plz explain it in a clear manner.

  6. #6
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    Code:
    #include<stdio.h>
    #include<string.h>
    int main()
    {
      const char filename[] = "3IL8.pdb";
      char temp[300],*ptr;
      FILE *file,*file1;
      file = fopen(filename, "r");
      file1=fopen("grep.txt","w");
      while(fgets(temp,200,file)!=NULL)
      {
        ptr=strstr(temp,"ATOM");
        if(ptr!=NULL)
        fprintf(file1,"%s",ptr);  
      }  
      fclose(file);
    }
    I want the strings starting with "ATOM". but this program output will contain "ATOMS" and "intermediate ATOM" too.

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