Try the development version (bit short on time myself right now). I'm
pretty sure I implemented this. A quick test is:
obabel -:"'F[C@H](Br)Cl" -s "'F[C@@H](Br)Cl" -osmi
...should be "0 molecules converted"
- Noel
On 9 July 2014 00:16, Craig James <cja...@emolecules.com> wrote:
> On Tue, Jul 8, 2014 at 2:05 PM, Stefano Forli <fo...@scripps.edu> wrote:
>
>> Hi all,
>> I'm having an issue with SMARTS pattern matching and chirality.
>> I'm trying to recognize one specific chiral configuration, but I get
>> unexpected answers,
>> see the following example:
>> ------------------------------
>> #!/usr/bin/env python
>> import pybel
>> ob = pybel.ob
>> patterns = [ ('p1' , '[$(*[C@@H])]'),
>> ('p2' , 'F[C@@H](Br)Cl'),
>> ('p3' , '[$(*[C@H])]'),
>> ('p4' , 'F[C@H](Br)Cl'),
>> ]
>> $ python smartest.py
>> Molecule F[C@H](Br)Cl ...
>>
> PATTERN p1 : [$(*[C@@H])] => [(1,), (3,), (4,), (5,)]
>> PATTERN p2 : F[C@@H](Br)Cl => [(1, 2, 4, 5)]
>> PATTERN p3 : [$(*[C@H])] => [(1,), (3,), (4,), (5,)]
>> PATTERN p4 : F[C@H](Br)Cl => [(1, 2, 4, 5)]
>>
>> I would expect patterns p1 and p2 to return no matches, and p3 and p4 to
>> succeed.
>>
>
> p1 and p3 should match all of the hetero atoms (1,3,4,5), and it does so
> correctly. The chiral spec is incomplete, which allows it to match
> anything. Think of it this way:
>
> p1: [$(*[C@@H](*)*)]
> p3: F[C@@H](*)*
>
> Written this way, you can see that p1 and p3 will both match either stereo
> configuration.
>
>
>
>> Although, even carbon chirality is clearly the opposite in the molecule
>> and p1, p2, the
>> script finds matches.
>>
>
> It should not match p2.
>
> Craig
>
>
> ------------------------------------------------------------------------------
> Open source business process management suite built on Java and Eclipse
> Turn processes into business applications with Bonita BPM Community Edition
> Quickly connect people, data, and systems into organized workflows
> Winner of BOSSIE, CODIE, OW2 and Gartner awards
> http://p.sf.net/sfu/Bonitasoft
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
