trunk/src/testPyMol.java

import java.io.FileNotFoundException;
import java.io.PrintWriter;
import java.io.OutputStream;
import java.io.FileOutputStream;

import owl.core.util.MultiOutputStream;
import owl.core.util.PyMol;
import owl.core.util.PymolServerOutputStream;


public class testPyMol {

        /**
         * Test class for the PyMol class (our java to PyMol API) 
         * @param file where PyMol script will be written
         * @author duarte
         */
        public static void main(String[] args) {
                String file = "";
                boolean server=false;
                if (args.length<1){
                        System.err.println("Give at least one file argument");
                        System.exit(1);
                }               
                file = args[0];
                if (args.length>1){ // two arguments: output both file and server
                        server=true;
                }
                
                
                String url = "http://anthrazit:9123";
                
                String pdbFileName = "/project/StruPPi/jose/tinker/benchmarking/1bxy_A.pdb";

                PrintWriter Out = null;         
                
                // to output only to server we would need the following PrintWriter
                //Out = new PrintWriter(new PymolServerOutputStream(url),true);
                
                if (server){
                        OutputStream os1 = new PymolServerOutputStream(url);
                        OutputStream os2 = null;
                        try {
                                os2 = new FileOutputStream(file);
                        } catch (FileNotFoundException e) {
                                e.printStackTrace();
                                System.exit(2);
                        }
                        OutputStream multi = new MultiOutputStream(os1, os2);
                        Out = new PrintWriter(multi, true);
                } else {
                        try {
                                Out = new PrintWriter(new FileOutputStream(file),true);
                        } catch (FileNotFoundException e) {
                                e.printStackTrace();
                                System.exit(1);
                        }
                }
                
                PyMol mypymol = new PyMol(Out);
                
                mypymol.loadPDB(pdbFileName);
                // more pymol commands

        }

}
Revision:	1005
Committed:	Wed Mar 31 12:29:26 2010 UTC (14 years, 6 months ago) by hstehr
File size:	1615 byte(s)
Log Message:	refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Line	User	Rev	File contents
1	duarte	114	import java.io.FileNotFoundException;
2			import java.io.PrintWriter;
3			import java.io.OutputStream;
4			import java.io.FileOutputStream;
5
6	hstehr	1005	import owl.core.util.MultiOutputStream;
7			import owl.core.util.PyMol;
8			import owl.core.util.PymolServerOutputStream;
9	duarte	114
10	hstehr	1005
11	duarte	114	public class testPyMol {
12
13			/**
14			* Test class for the PyMol class (our java to PyMol API)
15			* @param file where PyMol script will be written
16			* @author duarte
17			*/
18			public static void main(String[] args) {
19			String file = "";
20			boolean server=false;
21			if (args.length<1){
22			System.err.println("Give at least one file argument");
23			System.exit(1);
24			}
25			file = args[0];
26			if (args.length>1){ // two arguments: output both file and server
27			server=true;
28			}
29
30
31			String url = "http://anthrazit:9123";
32
33			String pdbFileName = "/project/StruPPi/jose/tinker/benchmarking/1bxy_A.pdb";
34
35			PrintWriter Out = null;
36
37			// to output only to server we would need the following PrintWriter
38			//Out = new PrintWriter(new PymolServerOutputStream(url),true);
39
40			if (server){
41			OutputStream os1 = new PymolServerOutputStream(url);
42			OutputStream os2 = null;
43			try {
44			os2 = new FileOutputStream(file);
45			} catch (FileNotFoundException e) {
46			e.printStackTrace();
47			System.exit(2);
48			}
49			OutputStream multi = new MultiOutputStream(os1, os2);
50			Out = new PrintWriter(multi, true);
51			} else {
52			try {
53			Out = new PrintWriter(new FileOutputStream(file),true);
54			} catch (FileNotFoundException e) {
55			e.printStackTrace();
56			System.exit(1);
57			}
58			}
59
60			PyMol mypymol = new PyMol(Out);
61
62			mypymol.loadPDB(pdbFileName);
63			// more pymol commands
64
65			}
66
67			}