[Joelib-devel] Re: [Joelib-help] TestSmarts

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

Hi Dave,

first ... i'm going today into holiday until the end of next week.

Yes, this was a bug in the detection and:
UP is '/'
DOWN is '\\'
CIS is C/C=C\C
TRANS is C/C=C/C

I've created a (non-planned) bug fix release.
The previous changes caused also SMILES export and i hope this is now 
correct. Please let me know if not not and send a bug report via the bug 
tracking list.

I've additionally added unspecific up/down bond matching using '\\?' and 
'/?'. Please note that you need C/?C=C/?C if you plan to match plain 
butene, also.

Download:
https://sourceforge.net/projects/joelib/

Kind regards, Joerg

> First, thanks for the new release.
> 
> I've been experimenting with TestSmarts.java, using trans_butene.mol and
> cis_butene.mol in .../build/resources/smartsEvaluation/.  It seems to be
> doing the exact opposite of what I'd expect:
> 
>     trans_butene.mol(C\C=C\C) 
>       debugging output says "C\C=C/C trans-butene"
>       TestSmarts trans_butene.mol C\\C=C/C                matches
>                  trans_butene.mol C/C=C\\C                matches
>                  trans_butene.mol C\\C=C\\C               doesn't match
>                  trans_butene.mol C/C=C/C                 doesn't match
>     cis_butene.mol(C\C=C/C)
>       debugging output says "C\C=C\C cis-butene"
>       TestSmarts cis_butene.mol C\\C=C/C                  doesn't match
>                  cis_butene.mol C/C=C\\C                  doesn't match
>                  cis_butene.mol C\\C=C\\C                 matches
>                  cis_butene.mol C/C=C/C                   doesn't match *
> 
>     * There's a note about this in evaluation.txt
>     
> Notice the debugging output from the println on line 146 of TestSmarts.java.
> 


-- 
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)