Hi Vincent, I had good results using: org.openscience.cdk.tools.GenerateFragments.
Good luck, Peter ------------------------------------------------------ Specs Kluyverweg 6 2629 HT DELFT The Netherlands p +31 15 2518111 (office) p +31 15 2518139 (direct) f +31 15 2518181 [email protected] www.specs.net ------------------------------------------------------ > -----Original Message----- > From: [email protected] [mailto:cdk-user- > [email protected]] > Sent: Monday, 27 April, 2009 14:02 > To: [email protected] > Subject: Cdk-user Digest, Vol 35, Issue 12 > > Send Cdk-user mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/cdk-user > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Cdk-user digest..." > > > Today's Topics: > > 1. Scaffold generator (Vincent Le Guilloux) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 27 Apr 2009 13:04:38 +0200 > From: Vincent Le Guilloux <[email protected]> > Subject: [Cdk-user] Scaffold generator > To: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hello, > > Is there any class/methods that could generate a scaffold from a given > molecule? > > By scaffold, I mean any existing definition of it (Murcko, ring > assemblies, ring system...) > > Just asking so I don't code something already existing :) currently I > haven't found such method/class in the test repository/documentation... > > And just a question for my curiosity: in the feature list of the cdk > is indicated " active site detection " in protein structures. Could > you tell me a few words about that ? Just what (existing?) algorithm > do you use, and if there is a publication :) > > Thanks in advance. > Best regards ;) > > -- > Vincent Le Guilloux > > Phd Student - ICOA - UMR CNRS 6005 > Div. of chemoinformatic and molecular modeling. > University of Orl?ans > Phone: ++33 2 38 49 45 77 > Fax : ++33 2 38 41 72 81 > > > > > > ------------------------------ > > ---------------------------------------------------------------------------- -- > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensign option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > > ------------------------------ > > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > End of Cdk-user Digest, Vol 35, Issue 12 > **************************************** ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensign option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
