joelib-devel

RE: [Joelib-devel] Convert() & PseudoAtoms in Smiles

[<nic...@sy...>]

Hi Joerg,

	I think we could associate R as an R.group, indeed. Where we can use
the R symbol is for an attachement point in a fragment or substituent in
order to respect valency. CDK currently use this notation in the
SmilesParser and SmilesGenerator methods(). But for calculation, the R
notation doesn't have any chemical sens.

Regards,

Nico 

Re: [Joelib-devel] Convert() & PseudoAtoms in Smiles

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

Hi,

was added to support request with a very low priority. If anyone has 
time this is not that difficult, if you are having a closer look at:
joelib/src/joelib/io/types/MDLSD.java
joelib/src/joelib/smiles/JOESmilesParser.java
Only 'Rnumber' entries should be parsed and stored in
'RgroupDescriptors ' as done by MDLSD.java
Then you can use e.g. the
joelib/src/joelib/molecule/generation/MolGenerationHelper.java
to attach Rgroups to this scaffold.

Support Requests item #970983, was opened at 2004-06-11 08:44
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=425970&aid=970983&group_id=39708

Category: SMARTS/SMILES
Group: None
Status: Open
Priority: 1
Submitted By: Joerg Kurt Wegner (wegner)
Assigned to: Joerg Kurt Wegner (wegner)
Summary: Allow Rgroup 'Rnumber' entry in SMILES pattern

Kind regards, Joerg

-- 
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
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