Hi Christian, Thanks for you quick fix. Obviously I got the same warnings as Egon got but I am able to compile the code within the CDK. It does seem to work as intended like this.
I did find some unexpected results in the linkers. That is, for zero-atom linkers I found 2 atoms. Another confusing result is: when exocyclicDoubleBonds = true And the is an one-atom linker with a double bond it will give you a 2 atom linker back. When exocyclicDoubleBonds = false it will give you a 1 atom linker back. I assumed the exocyclicDoubleBond was intended for keeping double bonds on a ring fragment in stead of the linkers. Thanks again, Peter -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Monday, July 16, 2007 10:21 AM To: Peter Maas; [email protected] Subject: Re: [Cdk-user] Murcko Frameworks Hi, I checked your remarks and corrected the linker related problems. I cannot submit the changes, because I don't have an actual svn checkout. I attached the revised GenerateFragment class, maybe Egon or someone else could commit this please? I didn't add Murcko side chains and in the moment I don't plan to do it. best regards Christian -------- Original-Nachricht -------- Datum: Wed, 11 Jul 2007 17:13:30 +0200 Von: "Peter Maas" <[EMAIL PROTECTED]> An: [email protected] Betreff: [Cdk-user] Murcko Frameworks > 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 > > > > > ---------------------------------------------------------------------- > --- This SF.net email is sponsored by DB2 Express Download DB2 Express > C - the FREE version of DB2 express and take control of your XML. No > limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user -- GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS. Alle Infos und kostenlose Anmeldung: http://www.gmx.net/de/go/freemail ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
