Stefan Kuhn <[EMAIL PROTECTED]> wrote: > Am Friday 30 December 2005 11:32 schrieb Nina Jeliazkova: > > Stefan Kuhn <[EMAIL PROTECTED]> wrote: > > > Am Friday 30 December 2005 11:07 schrieb Nina Jeliazkova: > > > > Hi, > > > > > > > > Stefan Kuhn <[EMAIL PROTECTED]> wrote: > > > > > > Ok, that makes the sql a lot easier than the fingerprints. Is that > > > > > > good enough to use smiles for duplicate checking? are you aure to > > > > > > find them > > > > > > > > all? > > > > > > > > > Given the smiles implemenatation is not buggy it should work for > > > > identity > > > > > > > search (and therefore for duplicate checking). Substructure search is > > > > > a > > > > > > > > Judging from my own experience, using SMILES for identity search seems > > > > simple, but could be a bit tricky. One have to decide to use stereo > > > > SMILES at least for some compounds if not for all, otherwise there will > > > > be inconsistencies. > > > > > > We do indeed use a stereo smiles. This works, but not if users do not > > > draw correct wedge bonds, but pseudo-3d-perspectives. I cannot see how to > > > handle these at all, also ismorphism checks do not use these. > > > Stefan > > > > You mean you are using stereo smiles in NmrShiftDb ? > > > > Am I right that compounds in NmrShiftDb are imported one by one and not for > > example by reading SDF file and storing the compounds? > > (I would like to know how to handle the second case, i.e. how to > > automatically decide where stereo smiles are necessary and where they are > > not) > I do not see much of a difference. When we do a bulk import, we can still > create stereo smiles, using all specified wedge bonds. The cdk smiles > generator will give the same smiles when called in "stereo mode" and without, > if there are no stereo centers in the molecule.
Yes, but I mean if wedge bonds are not explicitly specified. Nina > Stefan > > > > Regards, > > Nina > > > > > > Regards, > > > > Nina > > > > > > > > > different thing. > > > > > Stefan > > > > > > -- > > > Stefan Kuhn M. A. > > > Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) > > > Zülpicher Str. 47, 50674 Cologne > > > Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786 > > > My public PGP key is available at http://pgp.mit.edu > > > > > > > > > ------------------------------------------------------- > > > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > > > files for problems? Stop! Download the new AJAX search engine that > > > makes searching your log files as easy as surfing the web. DOWNLOAD > > > SPLUNK! http://ads.osdn.com/?ad_idv37&alloc_id865&opÌk > > > _______________________________________________ > > > Cdk-user mailing list > > > [email protected] > > > https://lists.sourceforge.net/lists/listinfo/cdk-user -- ------------------------------------------------------------------ Assoc. Prof. Dr. Nina Nikolova-Jeliazkova * * Institute for Parallel Processing * * Bulgarian Academy of Sciences * IST Foundation * Acad. G. Bonchev St 25-A * The Bulgarian NREN * 1113 Sofia, Bulgaria * * Tel: +359 886 802011 * * ICQ: 10705013 http://www.ist.bg www: http://ambit.acad.bg/nina ------------------------------------------------------------------ PGP Public Key http://cert.acad.bg/pgp-keys/keys/nina-nikolova-0xEEABA669.asc 8E99 8BAD D804 1A43 27B7 7F87 CF04 C7D1 EEAB A669 ------------------------------------------------------------------ ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_idv37&alloc_id865&op=click _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
