Hi Aziz, I used the following approach: 1) apply generateMurckoFragments 2) retrieve fragments using getMurckoFrameworksAsSmileArray() 3) I differentiated by size. By definition the MurckoFragment will be the largest.
Cheers, Peter > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of > [EMAIL PROTECTED] > Sent: Wednesday, December 12, 2007 21:14 > To: [email protected] > Subject: Cdk-user Digest, Vol 19, Issue 5 > > 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. Re : Cdk-user Digest, Vol 19, Issue 4 (aziz yasri) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Dec 2007 00:33:05 -0800 (PST) > From: aziz yasri <[EMAIL PROTECTED]> > Subject: [Cdk-user] Re : Cdk-user Digest, Vol 19, Issue 4 > To: [email protected] > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=iso-8859-1 > > Hi, > > I read your answer to Alban concerning the murcko fragments > and I was interested by what you said about geting the > "chemotype" from the routine. Which method returns : > - the murcko fragment > - the chemotype fragment > > If the same method is returning both, how to filter out to > get them separatly ? > > Thanks, > > Aziz > > > > ----- Message d'origine ---- > De : "[EMAIL PROTECTED]" > <[EMAIL PROTECTED]> > ? : [email protected] > Envoy? le : Mardi, 11 D?cembre 2007, 21h04mn 32s Objet : > Cdk-user Digest, Vol 19, Issue 4 > > 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. Murcko fragments (Peter Maas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Dec 2007 10:17:43 +0100 > From: "Peter Maas" <[EMAIL PROTECTED]> > Subject: [Cdk-user] Murcko fragments > To: <[EMAIL PROTECTED]> > Cc: [email protected] > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="us-ascii" > > 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 > > > End of Cdk-user Digest, Vol 19, Issue 4 > *************************************** > > > > > > > ______________________________________________________________ > _______________ > Ne gardez plus qu'une seule adresse mail ! Copiez vos mails > vers Yahoo! Mail http://mail.yahoo.fr > > > > ------------------------------ > > -------------------------------------------------------------- > ----------- > 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://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.n > et/marketplace > > ------------------------------ > > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > End of Cdk-user Digest, Vol 19, Issue 5 > *************************************** > > ------------------------------------------------------------------------- SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. 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