Hi, currently molecules cannot be aligned properly from scratch. When you have a known common substructure, do substructure search and use the Kabsch Alignment with the given substructure match. This alignment only works for very similar molecules, but should be enough to align at least the substructures and with them the rest of the molecules. But no guaranty for success,
best regards Christian -------- Original-Nachricht -------- Datum: Mon, 27 Nov 2006 22:16:44 -0800 (PST) Von: richard apodaca <[EMAIL PROTECTED]> An: [EMAIL PROTECTED] Betreff: [Cdk-user] Kabsch Alignment > I have a group of molecules, some of which contain a > common substructure. I want to display the molecules > with common substructures using the same orientation > for each. How can I do this in CDK? > > I had a look at Kabsch Alignment: > > http://cdk.sourceforge.net/api/org/openscience/cdk/geometry/alignment/KabschAlignment.html > > but I'm not sure it's what I'm looking for. If not, > does CDK have the capability I described? > > thanks, > Rich > > ____________________________ > Richard Apodaca > Blog: http://depth-first.com > > > > ____________________________________________________________________________________ > Yahoo! Music Unlimited > Access over 1 million songs. > http://music.yahoo.com/unlimited > > ------------------------------------------------------------------------- > 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 -- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer ------------------------------------------------------------------------- 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
