owl/trunk/testPdb.java

import java.io.IOException;

import proteinstructure.Graph;
import proteinstructure.Pdb;
import proteinstructure.PdbaseAcCodeNotFoundError;
import proteinstructure.PdbaseInconsistencyError;
public class testPdb {

        /**
         * Test class for classes in aglappe.proteinstructure package (Pdb, Graph, AA, Contact) 
         * Loads structure data from db and calculates graph dumping contacts to file
         */
        
        public static void main(String[] args) throws IOException, PdbaseInconsistencyError, PdbaseAcCodeNotFoundError{
                System.out.println("loading structure");
                Pdb pdb = new Pdb("1bxy","A");          
                System.out.println("dumping structure to pdb file");
                pdb.dump2pdbfile("testpdb.txt");
                System.out.println("getting graph");
                Graph graph = pdb.get_graph("Ca", 8.0);
                System.out.println("dumping contacts to file");
                graph.write_contacts_to_file("test.txt");
                
                System.out.println("reading from dumped pdb file");
                Pdb pdb2 = new Pdb("testpdb.txt");
                System.out.println("getting graph");
                Graph graph2 = pdb2.get_graph("Ca", 8.0);
                System.out.println("dumping contacts to file");
                graph2.write_contacts_to_file("test2.txt");
        }

}
Revision:	127
Committed:	Wed May 9 14:54:02 2007 UTC (17 years, 9 months ago) by duarte
File size:	1130 byte(s)
Log Message:	Implemented read of pdb data from pdb file. FIXED BUG in dumping of pdb file. Was missing end of line in atom lines Added more tests in testPdb
Line	User	Rev	File contents
1	duarte	125	import java.io.IOException;
2
3			import proteinstructure.Graph;
4			import proteinstructure.Pdb;
5			import proteinstructure.PdbaseAcCodeNotFoundError;
6			import proteinstructure.PdbaseInconsistencyError;
7			public class testPdb {
8
9			/**
10			* Test class for classes in aglappe.proteinstructure package (Pdb, Graph, AA, Contact)
11			* Loads structure data from db and calculates graph dumping contacts to file
12			*/
13
14			public static void main(String[] args) throws IOException, PdbaseInconsistencyError, PdbaseAcCodeNotFoundError{
15			System.out.println("loading structure");
16	duarte	127	Pdb pdb = new Pdb("1bxy","A");
17			System.out.println("dumping structure to pdb file");
18			pdb.dump2pdbfile("testpdb.txt");
19	duarte	125	System.out.println("getting graph");
20			Graph graph = pdb.get_graph("Ca", 8.0);
21			System.out.println("dumping contacts to file");
22			graph.write_contacts_to_file("test.txt");
23
24	duarte	127	System.out.println("reading from dumped pdb file");
25			Pdb pdb2 = new Pdb("testpdb.txt");
26			System.out.println("getting graph");
27			Graph graph2 = pdb2.get_graph("Ca", 8.0);
28			System.out.println("dumping contacts to file");
29			graph2.write_contacts_to_file("test2.txt");
30	duarte	125	}
31
32			}