Re: [Joelib-devel] going chiral?

[<we...@in...>]

Hello henrik,

> * uniqueness of the SMILES patterns
> do you think here about a 'normalization' like the one in daylight?
I mean that generated SMILES patterns should be always independent from 
the numeration of the given molecule (e.g. from SDF file). This will 
then allow to use the UNIQUE SMILES String as specific ID in a database 
or something. Or you can calculate the hash code for a molecule using 
atom types and unique numeration for getting (hopefully) a unique ID, ...
> 
> Can give me a hint where to look at in the SMARTS-parser where the chiral-information is read in?
joelib/src/joelib/smart/ParseSmart:375

> Regards,
> henrik
Regards, Joerg


> dr. henrik kuhn
> new technologies
> morphochem AG
> gmunder str. 37-37a
> 81379 muenchen
> 
> tel. ++49-89-78005-0
> fax  ++49-89-78005-555
> 
> hen...@mo...
> http://www.morphochem.de
> 
> -----Original Message-----
> From:	Jörg K. Wegner [SMTP:we...@in...]
> Sent:	Monday, December 02, 2002 10:24 AM
> To:	hen...@mo...; joe...@li...
> Subject:	Re: [Joelib-devel] going chiral?
> 
> Hello Henrik,
> 
>>are you thinking about implementing chiral-capabilities into joelib as soon as possible? You need help for that purpose?
> 
> Any help would be great ! I've an long additional wish list :-)
> 
> Some parts are already available --> Take a look at:
> 
> 1. joelib/src/joelib/smiles/SmilesParser:1056
> for @ and @@
> 
> 2. joelib/src/joelib/molecule/JOEMol:2767 in method findChiralCenters()
> uses GraphPotentials (see API docu under joelib/src/joelib/desc/types)
> 
> 3. joelib/src/joelib/molecule/JOEAtom:1980 in method isChiral()
> 
> Mail to the developer mailing list, if you have further questions. 
> Because i can not handle all open fronts, i would be glad if you would
> adapt JOELib for your needs and if you would help me with the development.
> 
> Now some additional comments:
> 1. JOELib has no direct 2D layout facility. It uses the CDK layout tool, 
> but this could be eventually a problem with chiral centers (i've never 
> evaluated that).
> 
> 2. I'm not sure about the uniqueness of the SMILES patterns generated by 
> JOELib (must be evaluated). If you need a unique (re)numbering i could 
> offer you the Morgan-Agorithm code WITH solving renumbering ties (some 
> students work) !!!
> 
> 
>>Regards,
>>henrik
> 
> Regards, Joerg
> 
> 


-- 
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
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