[PyMOL] Using PyMOL from Java

[Kristian Rother]

Dear PyMOL users,

We have written a Java class allowing to bind Java applications to use PyMOL. 
It has been developed and tested on a SuSe Linux 8.0 machine, but migration 
to other OS'es should be no problem.

It is hereby published using the Python License. Thus, You may modify and 
distribute the source code, as long as the original notices are kept in.

We hope this program will serve You well,

Kristian Rother and Christoph Gille

Institute of Biochemistry
Humboldt University Berlin

import java.util.zip.*;
import java.io.*;
import java.util.*;

/**
		Name:        Pymol.java
  Purpose:     A class that allows to start PyMOL from Java programs and to 
               ship commands to PyMOL from an application.
  Author:      Kristian Rother and Christoph Gille
               (kristian.rot...@charite.de, christoph.gi...@charite.de)

  Created:     2003/02/17
  Copyright:   (c) 2003
  Licence:     Python License

		This class was originally written to provide PyMOL support for Strap.
		Strap is an application for editing structural alignments of proteins.

*/

public class Pymol {

				public static String examples[]=	new String[] {
								"load pdb1cse.ent",
								"color blue,pdb1cse",
								"show sticks,pdb1cse",
								"hide spheres",
								"Color Molecule Atoms Specified Specification 0,255,255"
				};
				// Name of the PyMOL executable with command-line options
				public static String customize[]= new String[] {
								"pymol -p"
				};

				private static OutputStream stdin=null;
				private static Runtime rt=Runtime.getRuntime();								
				private static Process process=null;

				public Pymol() {}
				
				// ----------------------------------------
				public static boolean  launch() {
								String pymol=customize[0];
								try {
												process=rt.exec(pymol);
												stdin=process.getOutputStream();
								} catch(Exception e){
												System.err.println("Pymol.java:  Error launching Pymol");
												return false;
								}
								try{Thread.currentThread().sleep(5000);}catch (Exception e){};
								return true;
				}
				//----------------------------------------
				/**
							When loadProtein is called the first time
							process will be null;
							When process already terminated 	process.exitValue() succeeds;
							In both cases launch Pymol again.
				*/
				public boolean loadProtein(File pdb) {
								// process terminated
								try {
												process.exitValue();
												process=null;
								}
								catch(Exception e){};
								
								if (process==null) launch();
								if (process==null) {
												System.err.println("Could not launch PyMOL.\nIs  the path of the executable set right ?\nPlease type the complete path of the binary into the file "+customize[0]);
												return false;
								}
								interpret("load "+pdb+",prot");
								return true;
				}
				// -----------------------------+-----------
				public String interpret(String s) {
								System.err.println(getClass().getName()+": "+s);
								
								try {
												stdin.write(s.getBytes());
												stdin.write('\n');
												stdin.flush();
								}catch(Exception e){
												System.err.println("Error in "+getClass().getName()+".interpret("+s+") \n  "+e);
								}
								return "";								
				}				
				// ----------------------------------------
				public void dispose() {interpret("delete all");}				
				public String[] getExamples() {return examples;}
				// ----------------------------------------
								
				/** 
								Example application of Pymol.java 
				*/
				public static void main(String argv[]) {
								int n=argv.length;
								if (n<1) {
												System.err.println("Demo: loads  some proteins into pymol and renders the 2nd and 3rd residue with spheres");
												System.err.println("Usage:  java Pymol protein.pdb [protein2.pdb ...] ");
												return;
								}
								Pymol pym=null;
								for(int i=0;i<n;i++) {
												pym=new Pymol();

												boolean ret=pym.loadProtein(new File(argv[i]));
												pym.interpret("select sel2_3,(resi 2,3)");
												pym.interpret("show spheres,sel2_3");
												pym.interpret("color yellow,sel2_3");
								}
				}
}