trunk/src/compareCMs.java

import java.util.HashMap;

import owl.core.structure.*;
import owl.core.structure.graphs.RIGraph;
import owl.core.util.MySQLConnection;


public class compareCMs {

        /**
         * @param args
         */
        public static void main(String[] args) throws Exception {
                
                String onlyIn1File="onlyin1.graph";
                String onlyIn2File="onlyin2.graph";
                String commonFile="common.graph";
                
                
                String pdbcode1="1ses";
                String chaincode1="A";
                String pdbcode2="1set";
                String chaincode2="A";

                
                System.out.println("loading structures from pdbase");
                PdbAsymUnit fullpdb1 = new PdbAsymUnit(pdbcode1,new MySQLConnection(),"pdbase");
                PdbChain pdb1 = fullpdb1.getChain(chaincode1);
                PdbAsymUnit fullpdb2 = new PdbAsymUnit(pdbcode2,new MySQLConnection(),"pdbase");
                PdbChain pdb2 = fullpdb2.getChain(chaincode2);

                System.out.println("getting graphs");
                RIGraph graph1 = pdb1.getRIGraph("ALL", 4.2);
                RIGraph graph2 = pdb2.getRIGraph("ALL", 4.2);

                HashMap<String,RIGraph> comparison = graph1.compare(graph2);
                
                RIGraph onlyIn1 = comparison.get("onlythis");
                RIGraph onlyIn2 = comparison.get("onlyother");
                RIGraph common = comparison.get("common");
                
                System.out.println("writing output files "+onlyIn1File+", "+onlyIn2File+", "+commonFile);
                onlyIn1.writeToFile(onlyIn1File);
                onlyIn2.writeToFile(onlyIn2File);
                common.writeToFile(commonFile);
                
                
        }

}
Revision:	1372
Committed:	Wed Mar 30 09:55:49 2011 UTC (13 years, 6 months ago) by jmduarteg
File size:	1357 byte(s)
Log Message:	MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
Line	User	Rev	File contents
1	duarte	189	import java.util.HashMap;
2
3	hstehr	1005	import owl.core.structure.*;
4	hstehr	1009	import owl.core.structure.graphs.RIGraph;
5	jmduarteg	1372	import owl.core.util.MySQLConnection;
6	duarte	189
7	hstehr	1005
8	duarte	189	public class compareCMs {
9
10			/**
11			* @param args
12			*/
13	duarte	441	public static void main(String[] args) throws Exception {
14	duarte	189
15			String onlyIn1File="onlyin1.graph";
16			String onlyIn2File="onlyin2.graph";
17			String commonFile="common.graph";
18
19
20			String pdbcode1="1ses";
21			String chaincode1="A";
22			String pdbcode2="1set";
23			String chaincode2="A";
24
25
26			System.out.println("loading structures from pdbase");
27	jmduarteg	1372	PdbAsymUnit fullpdb1 = new PdbAsymUnit(pdbcode1,new MySQLConnection(),"pdbase");
28			PdbChain pdb1 = fullpdb1.getChain(chaincode1);
29			PdbAsymUnit fullpdb2 = new PdbAsymUnit(pdbcode2,new MySQLConnection(),"pdbase");
30			PdbChain pdb2 = fullpdb2.getChain(chaincode2);
31	duarte	189
32			System.out.println("getting graphs");
33	duarte	950	RIGraph graph1 = pdb1.getRIGraph("ALL", 4.2);
34			RIGraph graph2 = pdb2.getRIGraph("ALL", 4.2);
35	duarte	189
36	duarte	423	HashMap<String,RIGraph> comparison = graph1.compare(graph2);
37	duarte	189
38	duarte	423	RIGraph onlyIn1 = comparison.get("onlythis");
39			RIGraph onlyIn2 = comparison.get("onlyother");
40			RIGraph common = comparison.get("common");
41	duarte	189
42			System.out.println("writing output files "+onlyIn1File+", "+onlyIn2File+", "+commonFile);
43	duarte	953	onlyIn1.writeToFile(onlyIn1File);
44			onlyIn2.writeToFile(onlyIn2File);
45			common.writeToFile(commonFile);
46	duarte	189
47
48
49			}
50
51			}