trunk/src/calcVolsAndSurfs.java

import java.io.File;

import proteinstructure.Pdb;
import proteinstructure.PdbasePdb;
import proteinstructure.TemplateList;
import tools.MySQLConnection;

/**
 * Executable class to calculate volumes and surfaces for a list of pdb codes 
 * using the calc-volume and calc-surface programs
 * @author duarte
 *
 */
public class calcVolsAndSurfs {

        
        private static final String LIST = "/project/StruPPi/jose/optimal_reconstruction/model_pdbs.txt";
        private static final String CALCSURF_EXE = "/project/StruPPi/Software/libproteingeometry-2.3.1/bin/calc-surface";
        private static final String CALCVOL_EXE = "/project/StruPPi/Software/libproteingeometry-2.3.1/bin/calc-volume";
        
        public static void main(String[] args) throws Exception {
                
                MySQLConnection conn = new MySQLConnection();
                
                String[] pdbIds = TemplateList.readIdsListFile(new File(LIST));

                for (String pdbId:pdbIds) {
                        System.out.print(pdbId+"\t");
                        String pdbCode = pdbId.substring(0,4);
                        String pdbChainCode = pdbId.substring(4,5);
                        Pdb pdb = new PdbasePdb(pdbCode, "pdbase", conn);
                        pdb.load(pdbChainCode);
                        System.out.printf("%10.3f\t",pdb.calcVolume(CALCVOL_EXE, ""));
                        System.out.printf("%10.3f\n",pdb.calcSurface(CALCSURF_EXE, ""));
                }
                        

        }

}
Revision:	957
Committed:	Fri Feb 12 15:06:04 2010 UTC (14 years, 8 months ago) by duarte
File size:	1239 byte(s)
Log Message:	Added some useful tools to the default package from my workspace. More clean up.
Line	File contents
1	import java.io.File;
2
3	import proteinstructure.Pdb;
4	import proteinstructure.PdbasePdb;
5	import proteinstructure.TemplateList;
6	import tools.MySQLConnection;
7
8	/**
9	* Executable class to calculate volumes and surfaces for a list of pdb codes
10	* using the calc-volume and calc-surface programs
11	* @author duarte
12	*
13	*/
14	public class calcVolsAndSurfs {
15
16
17	private static final String LIST = "/project/StruPPi/jose/optimal_reconstruction/model_pdbs.txt";
18	private static final String CALCSURF_EXE = "/project/StruPPi/Software/libproteingeometry-2.3.1/bin/calc-surface";
19	private static final String CALCVOL_EXE = "/project/StruPPi/Software/libproteingeometry-2.3.1/bin/calc-volume";
20
21	public static void main(String[] args) throws Exception {
22
23	MySQLConnection conn = new MySQLConnection();
24
25	String[] pdbIds = TemplateList.readIdsListFile(new File(LIST));
26
27	for (String pdbId:pdbIds) {
28	System.out.print(pdbId+"\t");
29	String pdbCode = pdbId.substring(0,4);
30	String pdbChainCode = pdbId.substring(4,5);
31	Pdb pdb = new PdbasePdb(pdbCode, "pdbase", conn);
32	pdb.load(pdbChainCode);
33	System.out.printf("%10.3f\t",pdb.calcVolume(CALCVOL_EXE, ""));
34	System.out.printf("%10.3f\n",pdb.calcSurface(CALCSURF_EXE, ""));
35	}
36
37
38	}
39
40	}