On Apr 7, 2009, at 8:12 AM, Egon Willighagen wrote: > Chris, > > On Tue, Apr 7, 2009 at 1:45 PM, Egon Willighagen > <egon.willigha...@gmail.com> wrote: >> On Tue, Apr 7, 2009 at 1:25 PM, Nina Jeliazkova <n...@acad.bg> wrote: >>> Trying to reply to this thread, >>> https://sourceforge.net/mailarchive/message.php?msg_name=49C96659.2090401%40ebi.ac.uk >>> ,I have to say SmilesGenerator generates different smiles, >>> depending on >>> how the molecule was created (e.g. read from a file or by >>> SmilesParser). >> >> There is a related bug report about this in SVN, which agrees with >> this observation. The canonicalization method used by the SMILES >> generator seems somewhat sensitive. > > so you know who wrote the canonical SMILES code? I had a look at that > prior to the 1.2.0 release, but was unable to find the source of the > instability... I'm hoping the author can shed some light on this... > normally, I would have resorted to SVN history, but since this has > been around for so long, I'm asking you...
Is this related to bug 1014344 (http://sourceforge.net/tracker/?func=detail&aid=1014344&group_id=20024&atid=120024 )? if so, the problem seems to be related to some properties being set when the molecules is obtained from different sources (though I'm not sure how those properties affect SMILES output) ------------------------------------------------------------------- Rajarshi Guha <rg...@indiana.edu> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- Q: What's polite and works for the phone company? A: A deferential operator. ------------------------------------------------------------------------------ This SF.net email is sponsored by: High Quality Requirements in a Collaborative Environment. Download a free trial of Rational Requirements Composer Now! http://p.sf.net/sfu/www-ibm-com _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
