owl/trunk/testPdb.java

import java.sql.SQLException;
//import java.util.ArrayList;

import proteinstructure.*;

//import java.util.TreeMap;

public class testPdb {

        /**
         * Test class for classes in aglappe.proteinstructure package (Pdb, Graph, AA, Contact) 
         * Loads structure data from pdbase, msdsd and pdb file and calculates graph dumping contacts to file
         * Also gets contact map object and some common neighbours from it
         * @throws SQLException 
         */
        
        public static void main(String[] args) 
                throws Exception{
                
                String accode="1bxy";
                String chaincode="A";
                // data from pdbase
                System.out.println("loading structure from pdbase");
                Pdb pdb = new PdbasePdb(accode); // by default it goes to database "pdbase", a name for another pdbase database + a MySQLConnection can also be passed
                pdb.load(chaincode);
                System.out.println("dumping structure to pdb file");
                pdb.dump2pdbfile("testpdb.txt");
                String chain = pdb.getChainCode();
                System.out.println("getting graph");
                RIGraph graph = pdb.get_graph("ALL", 4.1);
                System.out.println("dumping contacts to file");
                graph.write_graph_to_file("test.txt");
                System.out.println("getting start of contact map matrix from graph");

                // data from msdsd
                System.out.println("loading structure from msdsd");
                Pdb pdb2 = new MsdsdPdb(accode); // by default it goes to database "msdsd_00_07_a", a name for another msdsd database + a MySQLConnection can also be passed
                pdb2.load(chaincode);
                System.out.println("dumping structure to pdb file");
                pdb2.dump2pdbfile("testpdb2.txt");
                System.out.println("getting graph");
                RIGraph graph2 = pdb2.get_graph("ALL", 4.1);
                System.out.println("dumping contacts to file");
                graph2.write_graph_to_file("test2.txt");

                // data from pdb
                System.out.println("reading from dumped pdb file");
                Pdb pdb3 = new PdbfilePdb("testpdb.txt"); // we read from the file dumped from pdbase, note that dumped file contains internal chain identifier
                pdb3.load(chain);
                System.out.println("getting graph");
                RIGraph graph3 = pdb3.get_graph("ALL", 4.1);
                System.out.println("dumping contacts to file");
                graph3.write_graph_to_file("test3.txt");
        }

}
Revision:	492
Committed:	Wed Jan 2 13:18:57 2008 UTC (17 years, 1 month ago) by duarte
File size:	2135 byte(s)
Log Message:	Copied the aglappe-jung branch into trunk.
Line	User	Rev	File contents
1	duarte	202	import java.sql.SQLException;
2			//import java.util.ArrayList;
3	duarte	125
4	duarte	132	import proteinstructure.*;
5
6	duarte	202	//import java.util.TreeMap;
7	duarte	132
8	duarte	125	public class testPdb {
9
10			/**
11			* Test class for classes in aglappe.proteinstructure package (Pdb, Graph, AA, Contact)
12	duarte	132	* Loads structure data from pdbase, msdsd and pdb file and calculates graph dumping contacts to file
13			* Also gets contact map object and some common neighbours from it
14	duarte	202	* @throws SQLException
15	duarte	125	*/
16
17	duarte	208	public static void main(String[] args)
18	duarte	441	throws Exception{
19	duarte	208
20	duarte	162	String accode="1bxy";
21			String chaincode="A";
22	duarte	132	// data from pdbase
23			System.out.println("loading structure from pdbase");
24	duarte	441	Pdb pdb = new PdbasePdb(accode); // by default it goes to database "pdbase", a name for another pdbase database + a MySQLConnection can also be passed
25			pdb.load(chaincode);
26	duarte	127	System.out.println("dumping structure to pdb file");
27			pdb.dump2pdbfile("testpdb.txt");
28	duarte	206	String chain = pdb.getChainCode();
29	duarte	125	System.out.println("getting graph");
30	duarte	420	RIGraph graph = pdb.get_graph("ALL", 4.1);
31	duarte	125	System.out.println("dumping contacts to file");
32	duarte	424	graph.write_graph_to_file("test.txt");
33	duarte	162	System.out.println("getting start of contact map matrix from graph");
34	duarte	132
35			// data from msdsd
36			System.out.println("loading structure from msdsd");
37	duarte	441	Pdb pdb2 = new MsdsdPdb(accode); // by default it goes to database "msdsd_00_07_a", a name for another msdsd database + a MySQLConnection can also be passed
38			pdb2.load(chaincode);
39	duarte	132	System.out.println("dumping structure to pdb file");
40			pdb2.dump2pdbfile("testpdb2.txt");
41			System.out.println("getting graph");
42	duarte	420	RIGraph graph2 = pdb2.get_graph("ALL", 4.1);
43	duarte	132	System.out.println("dumping contacts to file");
44	duarte	424	graph2.write_graph_to_file("test2.txt");
45	duarte	132
46			// data from pdb
47	duarte	127	System.out.println("reading from dumped pdb file");
48	duarte	441	Pdb pdb3 = new PdbfilePdb("testpdb.txt"); // we read from the file dumped from pdbase, note that dumped file contains internal chain identifier
49			pdb3.load(chain);
50	duarte	127	System.out.println("getting graph");
51	duarte	420	RIGraph graph3 = pdb3.get_graph("ALL", 4.1);
52	duarte	127	System.out.println("dumping contacts to file");
53	duarte	424	graph3.write_graph_to_file("test3.txt");
54	duarte	125	}
55
56			}