Hi Found the 'Fragmenting a molecule' section on the Snippets website very useful: http://cheminfo.informatics.indiana.edu/~rguha/code/java/
I tried it on some molecules with aromatic rings but did not cleave certain bonds as expected from your comments. 'The side effect of this approach is that a molecule like 2,3-dimethyl benzene will not be split into any fragments. On the other hand if the molecule is split on terminal bonds, we would only include the large fragment (and not the single atom at the end of the terminal bond). A side effect of this approach is that a group like NO2 would get split up into a N=O and O which may not be appropriate.' Would it be possible to cleave TERMINAL bonds the code was changed. Tried to change the code without success. Also cyclohexane is not cleaved even though it does not have terminal bonds. CSL Bioinformatics Internet Pages at http://bioinformatics.csl.gov.uk ---------------------------------------------------------------------- Robert Stones MRes, BSc Phone: +44 (0)1904 462675 Higher Bioinformatics Specialist GTN: 5129 2675 Central Science Laboratory Fax: +44 (0)1904 462111 Sand Hutton Email: [EMAIL PROTECTED] York YO41 1LZ Web: http://www.csl.gov.uk ---------------------------------------------------------------------- ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
