Dear Alban De results for the fragments you are getting are intended. It's not just giving the Murcko Fragment but all possibilities. The Author of this packages also included later work (G.M.Maggiora) going more into Chemotypes. If you want just the true Murcko fragments just filter for the largest one in the list which is returned by the procedure. (I can provide you some java script but since I'm a beginner as well it will not be very good code). There is also some documentation in CDK-news 3.2 on this package.
I'm not sure why you get a "null" returned. I presume it's a bug in your code. Cheers, Peter ------------------------------------------------ Date: Mon, 12 Nov 2007 10:21:50 -0800 (PST) From: albangrivel <[EMAIL PROTECTED]> Subject: Re: [Cdk-user] Murcko Frameworks To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=UTF-8 Dear All, I am totally novice in java scripting (6 days ago) and I am trying to use the "generatefragments.java" to get, from a molecule, the scaffold, the ringfragments and the linkers. I noticed several points: 1? when I try to generate the scaffold of a molecule (for example, 10 successive trials), I will have 9 trials with the expected scaffold and the remaining one will be a piece of the scaffold. 2? when I try to print out the ring fragment fragments, "generatefragments.java" returns me "null". Could you help me on these issues. I attached the class I named "fragmentor.java" for more informations and also a version of the generatefragments.java Thanks by advance for your precious help. Best regards. Alban Peter Maas-8 wrote: > > Hi All, > > I'm trying to use the Murcko frameworks which are part of the > org.openscience.cdk.tools.GenerateFragments. > > getMurckoFrameworksAsSmileArray() gives me the expected frameworks. > getLinkerFragmentsAsSmileArray() does NOT give me the expected linkers. > Actually it provides some of the frameworks. It does not give all the > frameworks provided by getMurckoFrameworksAsSmileArray() but it skips > a few. > Apparently it ignores the zero-atom linker fragments. > > Is this intended behavior? > Is anybody planning to add the Murcko side chains as well? > > Thanks, > > Peter > --------------------- Specs Kluyverweg 6 2629 HT DELFT The Netherlands p +31 15 2518139 (direct) f +31 15 2518181 www.specs.net [EMAIL PROTECTED] --------------------- ------------------------------------------------------------------------- SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
