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, 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:	208
Committed:	Wed Jun 27 14:42:12 2007 UTC (17 years, 3 months ago) by duarte
File size:	2433 byte(s)
Log Message:	FIXED BUGS: - directed was not set when reading from cm file - pdbChainCode not set when reading from db given pdbCode - filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file - using "A" as chainCode when reading from pdb file - some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
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	208	public static void main(String[] args)
19			throws IOException, PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError,
20			MsdsdInconsistentResidueNumbersError, SQLException, PdbfileFormatError{
21
22	duarte	162	String accode="1bxy";
23			String chaincode="A";
24	duarte	132	// data from pdbase
25			System.out.println("loading structure from pdbase");
26	duarte	207	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	duarte	127	System.out.println("dumping structure to pdb file");
28			pdb.dump2pdbfile("testpdb.txt");
29	duarte	206	String chain = pdb.getChainCode();
30	duarte	125	System.out.println("getting graph");
31	duarte	132	Graph graph = pdb.get_graph("ALL", 4.1);
32	duarte	125	System.out.println("dumping contacts to file");
33	duarte	208	graph.write_graph_to_file("test.txt");
34	duarte	162	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	duarte	132	}
40	duarte	162	System.out.println();
41	duarte	132	}
42
43			// data from msdsd
44			System.out.println("loading structure from msdsd");
45	duarte	207	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	duarte	132	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	duarte	208	graph2.write_graph_to_file("test2.txt");
52	duarte	132
53			// data from pdb
54	duarte	127	System.out.println("reading from dumped pdb file");
55	duarte	207	Pdb pdb3 = new PdbfilePdb("testpdb.txt",chain); // we read from the file dumped from pdbase, note that dumped file contains internal chain identifier
56	duarte	127	System.out.println("getting graph");
57	duarte	132	Graph graph3 = pdb3.get_graph("ALL", 4.1);
58	duarte	127	System.out.println("dumping contacts to file");
59	duarte	208	graph3.write_graph_to_file("test3.txt");
60	duarte	125	}
61
62			}