[Joelib-help] SMARTS testing and examples added to CVS

[Joerg K. W. <we...@in...>]

Hi all,

1. SMARTS matching test class to check cross-dependencies for the atom 
typer or simple testing purpose. So, this is the first step to be able 
to formulate a classification problem for the atom type assignment 
process. So let me know if you are interested to discuss the details for 
this idea. I think this can be published, also.

2. I'm preparing a new updated CVS version and i've added the SMARTS 
testing class
joelib/src/joelib/smarts/test/SMARTSEvaluation.java

and the examples defined in
joelib/src/resource/smartsEvaluation/evaluation.txt

and all the corresponding molecule files
joelib/src/resource/smartsEvaluation/*.mol

to the CVS of JOELib.
Please remember that the CVS checkout process has changed:
http://sourceforge.net/cvs/?group_id=39708

The included default batch testing can be started with:
SMARTSEvaluationDefault.sh

The result is stored in:
evaluationResult.txt

and should look like the following lines, if no error occured. If 
mismatches occured they will be printed first !
======================================================

Checking 73 SMARTS patterns.
----------------------------------------------
Correct matches: 315
Mismatches:      0
----------------------------------------------
Parsed SMARTS patterns:

[#8][#1] hydroxy_group_explicit_h
LEAF(ELEM,8) vb: 0
OR(SINGLE,AROM) with grow: true src: 0 dst: 1
LEAF(ELEM,1) vb: 0


----------------------------------------------
[#8;H1] hydroxy_group
ANDLO(LEAF(ELEM,8),LEAF(HCOUNT,1)) vb: 0


----------------------------------------------
[*;!#6;r3] heteroatoms_in_3-ring
ANDLO(ANDLO(LEAF(CONST,1),NOT(LEAF(ELEM,6))),LEAF(SIZE,3)) vb: 0

Kind regards, Joerg
-- 
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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