Re: [Joelib-help] SMARTS matching problem

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

Please use JOELib2.
What are you trying to match? Amine?
Have you also cross-checked the protonation model of JOELib2?

Testing SMARTS pattern is a pain, so you can and should use the testing 
class joelib2.smarts.test.SMARTSEvaluation with scripot 
joelibSMARTSEvaluation.sh
with properties in
joelib2\src\resources\smartsEvaluation

All mismatches are shown also, so you can find out whats going wrong.
Create a SDF file for your SMILES, which must contain a unique molecule 
name !

See analogue examples in add your entry to
joelib2\src\resources\smartsEvaluation\evaluation.txt

J.


> Hi, I have a SDF file whose SMILES representation generated by Joelib2
> is 
> 
> CCCCNC(=O)n1c(nc2ccccc12)NC(=O)OC
> 
> I'm running the  SMARTSMatchingExample.java code  from the JOELib
> distribution and searching for the pattern: [$([H][NX3H1])]
> 
> This should give me two hits but instead I the program says that the
> pattern is not in found in the file. 
> 
> (I set joelib2.smarts.SMARTSParser.anyRecognizesExpliciteHydrogens
> property to true and recompiled JOELib )
> 
> Does anybody have any pointers as to what might be wrong?
> -------------------------------------------------------------------
> Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net>
> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
> -------------------------------------------------------------------
> How I wish I were what I was when I wished I were what I am.
> 
> 
> 
> 
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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...
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