Re: [Joelib-help] stereochemistry in TestSmarts

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

Hi all,

o.k. bug and missing feature. Here are the details:

111. BUG (serious ! Please check the new functionality in CVS !)
joelib.smiles.JOEMol2Smi
https://sourceforge.net/tracker/?func=detail&atid=425969&aid=983990&group_id=39708

Was caused because the first atom was always detected as
recognized.
Fixed !
Furthermore i've found interchanged UP/DOWN assignments at
the end of this method. So i've changed ALL assignment types.
All users should check all kind of import/export methods
affecting SMILES and SMARTS matching methods with up/down
and cis/trans support heavily.
PLEASE !

222. Up/Down searching functionality in SMARTS was simply not activated
Fixed !
I've added the test cases to
joelib/src/resources/smartsEvaluation/evaluation.txt

Please remember, that the internal auto-detection assign ALWAYS 'up' as 
preferred case. So cis cases will be always stored as up/up. In 
trans-cases the match is inverted.

I will wait at least two weeks for a new release !!!
If anyone of you has time, please check the modified recognition, which 
affects the SMILES export.

###############################
## cis/trans detection
###############################
C\C=C/C                        a_carbon_in_abcd_with_trans 
        trans-butene#1
C/C=C\C                        a_carbon_in_abcd_with_trans 
        trans-butene#4
C/C=C/C                        a_carbon_in_abcd_with_trans 
        trans-butene
C\C=C\C                        a_carbon_in_abcd_with_trans 
        trans-butene
C\C=C\C                        a_carbon_in_abcd_with_cis 
        cis-butene#1#4
# this can not be found for MDL SDF import, because JOELib's auto-assign 
method assign C\C=C\C !!!
C/C=C/C                        a_carbon_in_abcd_with_cis 
        cis-butene
#
C/C=C\C                        a_carbon_in_abcd_with_cis 
        cis-butene
C\C=C/C                        a_carbon_in_abcd_with_cis 
        cis-butene

Kind regards, Joerg

> Thanks for your quick respose.  However, this doesn't seem to change the
> results I get for TestSmarts.
> 
> * Joerg K. Wegner <we...@in...> [2004-06-30 10:18 +0200]:
> 
>>Hi all,
>>
>>As already submitted be Gerd this is a bug in the SMARTS parser. So i 
>>opened a bug tracking task and will close it today and check in to CVS.
>>
>>
>>>Bugs item #982570, was opened at 2004-06-30 08:09
>>>You can respond by visiting:
>>>
>>
>>https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708
>>
>>>Initial Comment:
>>>The SMARTS encoder writes Stereo-Up as '\' and
>>>Stereo-Down as '/' but the specs says it vise versa.
>>>----------------------------------------------------------------------
>>>You can respond by visiting:
>>>
>>
>>https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708
>>
>>If you want a quick fix change line
>>-2467- case ('/'):
>>with
>>-2479- case ('\\'):
>>
>>Kind regards, Joerg
>>
>>
>>>Hi everyone, I'm new to Joelib and need a little help.
>>>
>>>I'm having trouble getting the TestSmarts[1] program to recognize
>>>stereochemistry.  For example, the SMARTS "C\C=C/C" won't match a
>>>molecule made with that same SMILES string.  I've tried several releases,
>>>including the 2004-06-21, on Solaris.  SMARTSEvaluationDefault.sh runs
>>>with no mismatches.
>>>
>>>I run: 
>>>
>>>
>>>>java joelib.test.TestSmarts butene.trans.sdf C\\C=C/C
>>>
>>>where butene.trans.sdf is:
>>> 4  3  0  0  1  0            999 V2000
>>>   0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>  -0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>  -0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>>> 1  2  1  0  0  0  0
>>> 2  3  2  0  0  0  0
>>> 3  4  1  0  0  0  0
>>>M  END
>>>$$$$
>>>
>>>Any suggestions on what I may be doing wrong or what the problem is?
>>>
>>> 1. 
>>> http://www-ra.informatik.uni-tuebingen.de/software/joelib/api/joelib/test/TestSmarts.html
>>
>>
>>-- 
>>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
>>--
>>Never mistake motion for action.
>>                                    (E. Hemingway)
>>
>>Never mistake action for meaningful action.
>>                               (Hugo Kubinyi,2004)
>>
>>
>>
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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
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)