Hi Christian, Just checked and you're right. For a zero-atom linker Murcko draws 2 atoms. For one-atom linker 3 and so on. So he's including the atom of the ring as well. Currently the code is only doing this for the zero-atom linker, which is why I was confused. If it would be implemented like (so including the ring-atom) then it would also solve the inconsistency of the exocyclicDoubleBonds parameter. I agree on keeping the double bonds attached. By the way, in part 2 of Murcko's article he's doing the same for the side-chains but he puts a lable on it (Augmented side chains).
Kind Regards, Peter -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Tuesday, July 17, 2007 8:45 AM To: Peter Maas; [email protected] Subject: Re: [Cdk-user] Murcko Frameworks Hi, > That is, for zero-atom linkers I found 2 atoms. Yes, these are the two ring atoms. In the Murcko paper a linker is defined as the atoms between two ring systems + the ring atoms. I think I have to check if also for the other linkers the ring atoms are included...I am not sure. > 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. I will have to change the documentation. I wanted to keep double bonds on ring systems and linkers, better on the Murcko fragment.In some newer studies these Murcko-like fragments (chemotypes) shows a greater usefullness in classifying compounds, see e.g. studies of G.M.Maggiora (and in-house). So I implemented this instead of the "simple" Murcko scaffold. I will put it on the to do list. best regards Christian -------- Original-Nachricht -------- Datum: Mon, 16 Jul 2007 17:02:06 +0200 Von: "Peter Maas" <[EMAIL PROTECTED]> An: [email protected] CC: [EMAIL PROTECTED] Betreff: Re: [Cdk-user] Murcko Frameworks > > 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 -- GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS. 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