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, PdbCodeNotFoundError, PdbChainCodeNotFoundError, 
                                MsdsdInconsistentResidueNumbersError, SQLException, PdbfileFormatError{
                
                String accode="1bxy";
                String chaincode="A";
                // data from pdbase
                System.out.println("loading structure from pdbase");
                Pdb pdb = new PdbasePdb(accode,chaincode); // by default it goes to database "pdbase", a name for another pdbase database + a MySQLConnection can also be passed
                System.out.println("dumping structure to pdb file");
                pdb.dump2pdbfile("testpdb.txt");
                String chain = pdb.getChainCode();
                System.out.println("getting graph");
                Graph 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");
                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 MsdsdPdb(accode,chaincode); // by default it goes to database "msdsd_00_07_a", a name for another msdsd database + a MySQLConnection can also be passed 
                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_graph_to_file("test2.txt");

                // data from pdb
                System.out.println("reading from dumped pdb file");
                Pdb pdb3 = new PdbfilePdb("testpdb.txt",chain); // we read from the file dumped from pdbase, note 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_graph_to_file("test3.txt");
        }

}
Revision:	215
Committed:	Thu Jun 28 15:43:04 2007 UTC (17 years, 3 months ago) by stehr
File size:	2429 byte(s)
Log Message:	some clean up of exceptions in Pdb and Graph classes: merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError, created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead
Line	File contents
1	import java.io.IOException;
2	import java.sql.SQLException;
3	//import java.util.ArrayList;
4
5	import proteinstructure.*;
6
7	//import java.util.TreeMap;
8
9	public class testPdb {
10
11	/**
12	* Test class for classes in aglappe.proteinstructure package (Pdb, Graph, AA, Contact)
13	* 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	* @throws SQLException
16	*/
17
18	public static void main(String[] args)
19	throws IOException, PdbaseInconsistencyError, PdbCodeNotFoundError, PdbChainCodeNotFoundError,
20	MsdsdInconsistentResidueNumbersError, SQLException, PdbfileFormatError{
21
22	String accode="1bxy";
23	String chaincode="A";
24	// data from pdbase
25	System.out.println("loading structure from pdbase");
26	Pdb pdb = new PdbasePdb(accode,chaincode); // by default it goes to database "pdbase", a name for another pdbase database + a MySQLConnection can also be passed
27	System.out.println("dumping structure to pdb file");
28	pdb.dump2pdbfile("testpdb.txt");
29	String chain = pdb.getChainCode();
30	System.out.println("getting graph");
31	Graph graph = pdb.get_graph("ALL", 4.1);
32	System.out.println("dumping contacts to file");
33	graph.write_graph_to_file("test.txt");
34	System.out.println("getting start of contact map matrix from graph");
35	int[][] mat = graph.getIntMatrix();
36	for (int i=0;i<10;i++){
37	for (int j=0;j<10;j++){
38	System.out.print(mat[i][j]);
39	}
40	System.out.println();
41	}
42
43	// data from msdsd
44	System.out.println("loading structure from msdsd");
45	Pdb pdb2 = new MsdsdPdb(accode,chaincode); // by default it goes to database "msdsd_00_07_a", a name for another msdsd database + a MySQLConnection can also be passed
46	System.out.println("dumping structure to pdb file");
47	pdb2.dump2pdbfile("testpdb2.txt");
48	System.out.println("getting graph");
49	Graph graph2 = pdb2.get_graph("ALL", 4.1);
50	System.out.println("dumping contacts to file");
51	graph2.write_graph_to_file("test2.txt");
52
53	// data from pdb
54	System.out.println("reading from dumped pdb file");
55	Pdb pdb3 = new PdbfilePdb("testpdb.txt",chain); // we read from the file dumped from pdbase, note that dumped file contains internal chain identifier
56	System.out.println("getting graph");
57	Graph graph3 = pdb3.get_graph("ALL", 4.1);
58	System.out.println("dumping contacts to file");
59	graph3.write_graph_to_file("test3.txt");
60	}
61
62	}