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)
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