trunk/src/checkChirality.java

import java.io.File;

import owl.core.structure.PdbChain;
import owl.core.structure.PdbAsymUnit;
import owl.core.structure.Residue;
import owl.core.structure.AaResidue;


/**
 * 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]);
                PdbAsymUnit pdb = new PdbAsymUnit(file);
                
                for (PdbChain chain:pdb.getPolyChains()) {
                        System.out.println("Chain "+chain+". D-form residues:");
                        int dcount=0;
                        int lcount=0;
                        int ucount=0;
                        for (Residue res : chain) {
                                if (!(res instanceof AaResidue)) continue;
                                AaResidue.Chirality chir = ((AaResidue)res).getChirality();
                                if (chir == AaResidue.Chirality.D) {
                                        //System.out.println(res+" "+chir.getAbbrev());
                                        dcount++;
                                } else if (chir == AaResidue.Chirality.L) {
                                        lcount++;
                                } else if (chir == AaResidue.Chirality.U) {
                                        ucount++;
                                }
                        }
                        System.out.println("L-form: "+lcount+" D-form: "+dcount+" Undetermined: "+ucount);
                }

        }

}
Revision:	1392
Committed:	Thu May 19 14:27:50 2011 UTC (13 years, 4 months ago) by jmduarteg
File size:	1202 byte(s)
Log Message:	MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
Line	File contents
1	import java.io.File;
2
3	import owl.core.structure.PdbChain;
4	import owl.core.structure.PdbAsymUnit;
5	import owl.core.structure.Residue;
6	import owl.core.structure.AaResidue;
7
8
9	/**
10	* Executable class to check the chirality of amino acids of a given PDB file
11	* @author duarte
12	*
13	*/
14	public class checkChirality {
15
16	public static void main(String[] args) throws Exception {
17	if (args.length==0) {
18	System.err.println("Usage: checkChirality <pdb_file_name>");
19	System.exit(1);
20	}
21
22	File file = new File(args[0]);
23	PdbAsymUnit pdb = new PdbAsymUnit(file);
24
25	for (PdbChain chain:pdb.getPolyChains()) {
26	System.out.println("Chain "+chain+". D-form residues:");
27	int dcount=0;
28	int lcount=0;
29	int ucount=0;
30	for (Residue res : chain) {
31	if (!(res instanceof AaResidue)) continue;
32	AaResidue.Chirality chir = ((AaResidue)res).getChirality();
33	if (chir == AaResidue.Chirality.D) {
34	//System.out.println(res+" "+chir.getAbbrev());
35	dcount++;
36	} else if (chir == AaResidue.Chirality.L) {
37	lcount++;
38	} else if (chir == AaResidue.Chirality.U) {
39	ucount++;
40	}
41	}
42	System.out.println("L-form: "+lcount+" D-form: "+dcount+" Undetermined: "+ucount);
43	}
44
45	}
46
47	}