owl/trunk/testPdb.java

import java.io.IOException;
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 IOException, PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException{
                String accode="1bxy";
                String chaincode="A";
                // data from pdbase
                System.out.println("loading structure from pdbase");
                Pdb pdb = new Pdb(accode,chaincode); // pdbase is default source for constructor, a name for a pdbase database can also be passed
                System.out.println("dumping structure to pdb file");
                pdb.dump2pdbfile("testpdb.txt");
                String chain = pdb.chain;
                System.out.println("getting graph");
                Graph graph = pdb.get_graph("ALL", 4.1);
                System.out.println("dumping contacts to file");
                graph.write_contacts_to_file("test.txt");
                System.out.println("getting start of contact map matrix from graph");
                int[][] mat = graph.getIntMatrix();
                for (int i=0;i<10;i++){
                        for (int j=0;j<10;j++){
                                System.out.print(mat[i][j]);
                        }
                        System.out.println();
                }

                // data from msdsd
                System.out.println("loading structure from msdsd");
                Pdb pdb2 = new Pdb(accode,chaincode,"msdsd_00_07_a");
                System.out.println("dumping structure to pdb file");
                pdb2.dump2pdbfile("testpdb2.txt");
                System.out.println("getting graph");
                Graph graph2 = pdb2.get_graph("ALL", 4.1);
                System.out.println("dumping contacts to file");
                graph2.write_contacts_to_file("test2.txt");

                // data from pdb
                System.out.println("reading from dumped pdb file");
                Pdb pdb3 = new Pdb("testpdb.txt",chain,false); // we read from the file dumped from pdbase, not that dumped file contains internal chain identifier
                System.out.println("getting graph");
                Graph graph3 = pdb3.get_graph("ALL", 4.1);
                System.out.println("dumping contacts to file");
                graph3.write_contacts_to_file("test3.txt");
        }

}
Revision:	202
Committed:	Thu Jun 21 17:18:11 2007 UTC (17 years, 4 months ago) by duarte
File size:	2255 byte(s)
Log Message:	MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
Line	User	Rev	File contents
1	duarte	125	import java.io.IOException;
2	duarte	202	import java.sql.SQLException;
3			//import java.util.ArrayList;
4	duarte	125
5	duarte	132	import proteinstructure.*;
6
7	duarte	202	//import java.util.TreeMap;
8	duarte	132
9	duarte	125	public class testPdb {
10
11			/**
12			* Test class for classes in aglappe.proteinstructure package (Pdb, Graph, AA, Contact)
13	duarte	132	* Loads structure data from pdbase, msdsd and pdb file and calculates graph dumping contacts to file
14			* Also gets contact map object and some common neighbours from it
15	duarte	202	* @throws SQLException
16	duarte	125	*/
17
18	duarte	202	public static void main(String[] args) throws IOException, PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException{
19	duarte	162	String accode="1bxy";
20			String chaincode="A";
21	duarte	132	// data from pdbase
22			System.out.println("loading structure from pdbase");
23	duarte	162	Pdb pdb = new Pdb(accode,chaincode); // pdbase is default source for constructor, a name for a pdbase database can also be passed
24	duarte	127	System.out.println("dumping structure to pdb file");
25			pdb.dump2pdbfile("testpdb.txt");
26	duarte	162	String chain = pdb.chain;
27	duarte	125	System.out.println("getting graph");
28	duarte	132	Graph graph = pdb.get_graph("ALL", 4.1);
29	duarte	125	System.out.println("dumping contacts to file");
30			graph.write_contacts_to_file("test.txt");
31	duarte	162	System.out.println("getting start of contact map matrix from graph");
32			int[][] mat = graph.getIntMatrix();
33			for (int i=0;i<10;i++){
34			for (int j=0;j<10;j++){
35			System.out.print(mat[i][j]);
36	duarte	132	}
37	duarte	162	System.out.println();
38	duarte	132	}
39
40			// data from msdsd
41			System.out.println("loading structure from msdsd");
42	duarte	162	Pdb pdb2 = new Pdb(accode,chaincode,"msdsd_00_07_a");
43	duarte	132	System.out.println("dumping structure to pdb file");
44			pdb2.dump2pdbfile("testpdb2.txt");
45			System.out.println("getting graph");
46			Graph graph2 = pdb2.get_graph("ALL", 4.1);
47			System.out.println("dumping contacts to file");
48			graph2.write_contacts_to_file("test2.txt");
49
50			// data from pdb
51	duarte	127	System.out.println("reading from dumped pdb file");
52	duarte	162	Pdb pdb3 = new Pdb("testpdb.txt",chain,false); // we read from the file dumped from pdbase, not that dumped file contains internal chain identifier
53	duarte	127	System.out.println("getting graph");
54	duarte	132	Graph graph3 = pdb3.get_graph("ALL", 4.1);
55	duarte	127	System.out.println("dumping contacts to file");
56	duarte	132	graph3.write_contacts_to_file("test3.txt");
57	duarte	125	}
58
59			}