Have you looked at BioJava for reading / parsing PDB files?

I'm not a PDB guru, but if your file record is just the set of line you showed, then I would use the following trivial program:

(...)
Pattern delim=Pattern.compile("[\t]");//is it a tab or a space ?
String line;
while((line=bufferedReader.readLine())!=null)
  {
  String tokens[]=delim.split(line);
  double x= Double.parseDouble(tokens[6]);
  double y= Double.parseDouble(tokens[7]);
  double z= Double.parseDouble(tokens[8]);
  (...)
  }
(....)

if your PDB file is more complex than your snippet then, as said Khader, have a look at Biojava or at JavaCC .

Jmol and the CDK have PDB readers that allow you to do this too. A Groovy script (using Java classes) for the CDK could look like:

import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.io.*;
import org.openscience.cdk.tools.manipulator.*;
import org.openscience.cdk.io.IChemObjectReader.Mode;
import org.openscience.cdk.*;
import java.io.File;
import java.util.zip.GZIPInputStream;

reader = new PDBReader(
  new GZIPInputStream(
    new URL("http://www.pdb.org/pdb/files/1CRN.pdb.gz").openStream()
  )
);
crambin = reader.read(new ChemFile());
for (container in ChemFileManipulator.getAllAtomContainers(crambin)) {
  for (atom in container.atoms()) {
    println atom.point3d;
  }
}

How to extract the coordinates of an atom from a pdb file in c

char *substring(size_t start, size_t stop, const char *src, char *dst, size_t size)
{
    int count = stop - start;
    if ( count >= --size )
    {
        count = size;
    }

    sprintf(dst, "%.*s", count, src + start);
    return dst;
}

int main(void)
{
    const char filename[] = "cys_coord.txt";
    char x[10],y[10],z[10];
    int i,j;
    char buffer[500], *ptr;
    FILE *file = fopen(filename, "r");

    if ( file )
    {
        for ( i = 0; fgets(buffer, sizeof buffer, file); ++i )
        {
            printf("%s\n",buffer);  
            printf("x = %s\n", substring(30, 8, buffer, x, sizeof x));
            printf("y = %s\n", substring(38, 8, buffer, y, sizeof y));
            printf("z = %s\n", substring(46, 8, buffer, z, sizeof z)); 
        }
    }
    fclose(file);
}

Hey there,

I came up with this but I think I am making a mess of all the information or methods and classes. Could anybody help me to straighten my thoughts? Pleasseee... and THank you!

import java.util.*;  
import java.io.*;
import java.util.regex.Pattern; import
java.io.StreamTokenizer;

public class CoorToks {

    public StringTokenizer(String token); //invalid method declaration
    public static void main(String[] args) throws IOException {
        BufferedReader inputStream = null; // scan input line by line
        PrintWriter outputStream = null;// output aligned the same way
        Pattern delim=Pattern.compile("/s");

        String token;
        StringTokenizer tokenizer = new StringTokenizer(token);

        try {
            inputStream = new BufferedReader(new FileReader("1APB.pdb.txt"));
            outputStream = new PrintWriter(new FileWriter("characteroutput.txt"));
            while(tokenizer.hasMoreTokens())
            {
                if (token.trim().startsWith("ATOM") && !token.trim().endsWith("H")) // I need to scan for the word "ATOM" before i start tokenizing. ends at H.
                {
                    // and i only need the 7th to 9th tokens of each line.
                    // should i use a pattern delimiter instead?
                    String tokens[]=delim.split(token);
                    double x= Double.parseDouble(tokens[7]);
                    double y= Double.parseDouble(tokens[8]);
                    double z= Double.parseDouble(tokens[9]);
                    outputStream.println(token);

                    //the compiler says it can't find variable tokens. which means i have to do a declaration of variables?
                    // how do i do that when there are so many tokens coming from the text file.
                }
            }
        }//end of try

        finally {
            while ((token = inputStream.readLine()) != null)
            {
                outputStream.println(token);
            }
            if (inputStream != null) {
                inputStream.close();
            }
            if (outputStream != null) {
                outputStream.close();
            }
        }
    }
}

Do it object oriented!

You can use BioJava, check this two links:

• Read PDB
• PDB atoms

If you are using java this is the best option.