Calculating distances

Question

Hi,
i need some guidance, i need to calculate the distances between two atoms (all combinations). Each atom as x, y and z axis points e.g.
x y z
ATOM 5 CA PHE 1 113.142 75.993 130.862
ATOM 25 CA ARG 2 113.940 72.288 131.419
ATOM 49 CA TYR 3 116.236 72.885 134.471
i have used the following code to reference these values
this.x = (double)(new Double(line.substring(30,38).trim()).doubleValue());
this.y = (double)(new Double(line.substring(38,46).trim()).doubleValue());
this.z = (double)(new Double(line.substring(46,54).trim()).doubleValue());
but my question is how do i; setup x1, x2 etc to calculate the distances based on the co-ordinate information for two atoms
i plan on using the squareroot-method from java.lang.Math to calculate the distance s in Angstroms'.

Answer 1

I wouldn't be using the substring since the length seems to vary. Is this perhaps what you need?import java.util.*;
import java.io.*;
public class AtomDistanceTest {
     public static void main(String[] args) {
          new AtomDistanceTest();
     public AtomDistanceTest() {
          Vector atomArray = new Vector();
          String line;
          try{
               System.out.println("Enter file for distance chek-up");
               BufferedReader inputDistance = new BufferedReader (new InputStreamReader(System.in));
               while ((line = inputDistance.readLine()) !=null && !line.equals("")) {
                    Atom atom = new Atom(line);
                    atomArray.addElement(atom);
               for (int j=0; j<atomArray.size(); j++) {
                    for (int k=j+1; k<atomArray.size(); k++) {
                         Atom a = (Atom) atomArray.elementAt(j);
                         Atom b = (Atom) atomArray.elementAt(k);
                         Atom.printDistance (a,b);
          } catch (IOException e) {
               System.out.println("Input file problem");
          } catch (Exception ex) {
               System.out.println (ex);
class Atom {
     public double x, y, z;
     public String name;
     public Atom(String s) throws IllegalArgumentException {
          try {
               StringTokenizer t = new StringTokenizer (s, " ");
               t.nextToken();
               this.name = t.nextToken();
               for (int j=0; j<3; j++) t.nextToken();
               this.x = new Double(t.nextToken()).doubleValue();
               this.y = new Double(t.nextToken()).doubleValue();
               this.z = new Double(t.nextToken()).doubleValue();
          } catch (Exception ex) {
               throw new IllegalArgumentException ("Illegal atom description");
     public String toString() {
          return "atom : " + name + "(x=" + x + " y=" + y + " z=" + z + ")";
     public double distanceFrom (Atom other) {
          return calculateDistance (x, y, z, other.x, other.y, other.z);
     public static double calculateDistance (double x1, double y1, double z1, double x2, double y2, double z2) {
          return Math.sqrt(Math.sqrt(Math.pow(Math.abs(x1-x2),2)+Math.pow(Math.abs(y1-y2),2))+Math.pow(Math.abs(z1-z2),2));
     public static void printDistance (Atom a, Atom b) {
          System.out.println ("Distance between " + a.toString() + " and " + b.toString() + " is " + a.distanceFrom(b));
}