Hi Vincent, I just realized I actually reported one of the bugs.
It actually does generate "the scaffold" as part of a set with all possible scaffolds. You can actually go through the set and pick the biggest one, which will be "the scaffold". I can send you the application I wrote for it if you like. Anyway, if you decide to write your own I'm sure it would be much appreciated by many if you would submit it to the CDK. Cheers, 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: Vincent Le Guilloux [mailto:[email protected]] > Sent: Monday, 27 April, 2009 14:54 > To: Peter Maas > Subject: RE: Cdk-user Digest, Vol 35, Issue 12 > > Hi Peter, > > Egon just told me that there are also two bug reports about finding > Murcko fragments with more than two ring systems. > > Plus this function, if I understand well, generates fragments but not > the scaffold itself and that's what I'm interested in :) > > I'm going to write my own. > Thanks for your answer :) > > Quoting Peter Maas <[email protected]>: > > > 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 > >> **************************************** > > > > > > > > > > -- > Vincent Le Guilloux > > Phd Student - ICOA - UMR CNRS 6005 > Div. of chemoinformatic and molecular modeling. > University of Orléans > 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
