trunk/src/checkChirality.java

import java.io.File;

import owl.core.structure.Pdb;
import owl.core.structure.PdbfilePdb;
import owl.core.structure.Residue;


/**
 * Executable class to check the chirality of amino acids of a given PDB file
 * @author duarte
 *
 */
public class checkChirality {

        public static void main(String[] args) throws Exception {
                if (args.length==0) {
                        System.err.println("Usage: checkChirality <pdb_file_name>");
                        System.exit(1);
                }
                
                File file = new File(args[0]);
                Pdb pdb = new PdbfilePdb(file.getAbsolutePath());
                String[] chains = pdb.getChains();
                
                for (String chain:chains) {
                        System.out.println("Chain "+chain+". D-form residues:");
                        pdb.load(chain);
                        int dcount=0;
                        int lcount=0;
                        int ucount=0;
                        for (int resser:pdb.getAllSortedResSerials()) {
                                Residue res = pdb.getResidue(resser);
                                Residue.Chirality chir = res.getChirality();
                                if (chir == Residue.Chirality.D) {
                                        //System.out.println(res+" "+chir.getAbbrev());
                                        dcount++;
                                } else if (chir == Residue.Chirality.L) {
                                        lcount++;
                                } else if (chir == Residue.Chirality.U) {
                                        ucount++;
                                }
                        }
                        System.out.println("L-form: "+lcount+" D-form: "+dcount+" Undetermined: "+ucount);
                }

        }

}
Revision:	1005
Committed:	Wed Mar 31 12:29:26 2010 UTC (14 years, 6 months ago) by hstehr
File size:	1204 byte(s)
Log Message:	refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Line	User	Rev	File contents
1	duarte	957	import java.io.File;
2
3	hstehr	1005	import owl.core.structure.Pdb;
4			import owl.core.structure.PdbfilePdb;
5			import owl.core.structure.Residue;
6	duarte	957
7	hstehr	1005
8	duarte	957	/**
9			* Executable class to check the chirality of amino acids of a given PDB file
10			* @author duarte
11			*
12			*/
13			public class checkChirality {
14
15			public static void main(String[] args) throws Exception {
16			if (args.length==0) {
17			System.err.println("Usage: checkChirality <pdb_file_name>");
18			System.exit(1);
19			}
20
21			File file = new File(args[0]);
22			Pdb pdb = new PdbfilePdb(file.getAbsolutePath());
23			String[] chains = pdb.getChains();
24
25			for (String chain:chains) {
26			System.out.println("Chain "+chain+". D-form residues:");
27			pdb.load(chain);
28			int dcount=0;
29			int lcount=0;
30			int ucount=0;
31			for (int resser:pdb.getAllSortedResSerials()) {
32			Residue res = pdb.getResidue(resser);
33			Residue.Chirality chir = res.getChirality();
34			if (chir == Residue.Chirality.D) {
35			//System.out.println(res+" "+chir.getAbbrev());
36			dcount++;
37			} else if (chir == Residue.Chirality.L) {
38			lcount++;
39			} else if (chir == Residue.Chirality.U) {
40			ucount++;
41			}
42			}
43			System.out.println("L-form: "+lcount+" D-form: "+dcount+" Undetermined: "+ucount);
44			}
45
46			}
47
48			}