Re: [Joelib-help] SimpleReader performance

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Hi,

this is interesting :-)

1. A profiling is recommended.
I will be happy if you've time for this, after you've found a good and=20
free Java profiling tool.

2. Only the CVS can help. Around this time i've added all the descriptors=
,
so the bottleneck could be the parsing process using the regular
expression patterns in joelib/src/joelib/data/plain/knownResults.txt
So replacing this file with a file without regular expressions can be a
solution.

As already tested by myself the descriptors are the first bottleneck,
eventually a SDF reader class without converting them can help, because i=
n
the previous version they were tored as uparsed entries, but i've changed
this to avoid problems with CML2 export.
Try your own MyMDLSD.java (removed descriptor parsing) and replace the
current MDLSD reader in
joelib.properties.

Kind regards, Joerg

On Thu, 3 Jun 2004, Oliva, Ambrogio wrote:

> Hi.
>=20
> I've found big differences in the performance of SimpleReader from olde=
r and newer versions of the joelib library. Running a simple application =
that counts the number of molecules in a SDF file with different versions=
 of joelib I've got the following results.
>=20
> - with version 20040116:
>=20
> C:\eclipse\workspace\MolCounter>java -cp .;log4j.jar;itext-0.94.jar;joe=
lib-20040116.jar  MolCounter sample.sdf
> 16:04:49 [INFO ] joelib.data.JOEElementTable              - Using eleme=
nt table: joelib/data/plain/element.txt
> 16:04:49 [INFO ] joelib.io.IOTypeHolder                   - 13 input/ou=
tput types loaded.
> 16:04:50 [INFO ] joelib.io.SimpleReader                   - ... 500 mol=
ecules successful loaded in 922 ms.
> Done: 500 found
>=20
> - with version 20040323:
> C:\eclipse\workspace\MolCounter>java -cp .;log4j.jar;itext-0.94.jar;joe=
lib-20040323.jar  MolCounter sample.sdf
> 16:04:37 [INFO ] joelib.data.JOEElementTable              - Using eleme=
nt table: joelib/data/plain/element.txt
> 16:04:37 [INFO ] joelib.io.IOTypeHolder                   - 22 input/ou=
tput types loaded.
> 16:04:38 [INFO ] joelib.desc.DescriptorHelper             - 78 descript=
or informations loaded.
> 16:04:38 [INFO ] joelib.data.JOEAtomTyper                 - Using atom =
type model: joelib/data/plain/atomtype.txt
> 16:04:38 [INFO ] joelib.data.JOEPhModel                   - Using pH va=
lue correction model: joelib/data/plain/phmodel.txt
> 16:04:42 [INFO ] joelib.io.SimpleReader                   - ... 500 mol=
ecules successful loaded in 4844 ms.
> Done: 500 found
>=20
> Could someone explain me the different behaviour of the two libraries, =
and how to speed up the process using the newer versions?
>=20
> The source code of MolCounter is below
>=20
> // Imports
> import org.apache.log4j.*;
> import joelib.io.*;
> import joelib.molecule.*;
> import java.io.*;
>=20
> public class MolCounter {
> =09
> //Obtain a suitable logger.
> private static Category logger =3D Category.getInstance("MolCounter");
>=20
> public static void main(String[] args) {
> 	=09
> 	SimpleReader reader =3D null;  //input SDF file
> 	IOType inputType =3D IOTypeHolder.instance().getIOType("SDF");
> 	try {
> 		reader =3D new SimpleReader(new FileInputStream(args[0]), inputType);
> 	} catch (Exception ex) {
> 		ex.printStackTrace();
> 	}
> 	JOEMol mol =3D new JOEMol(inputType, inputType);
> 	long lCounter =3D 0;
> 	try {=09
> 			while (reader.readNext(mol)) {
> 			lCounter++;
> 			}
> 		}=09
> 		catch (IOException ex) {
> 		// occurs if file can not be found
> 		ex.printStackTrace();
> 		}
> 		catch (MoleculeIOException ex) {
> 		// occurs if molecule entry is invalid
> 		 ex.printStackTrace();		=09
> 		}
> 		reader.close();=09
>=20
> 		System.out.println("Done: "+ lCounter + " found");
> 		System.exit(0);
> 	}
> =09
> }
>=20
>=20
>=20
> Thanks in advance.
>=20
> Ambrogio
>=20
>=20
>=20
>=20
>=20
>=20
>=20
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Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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