On Wed, Oct 6, 2010 at 4:03 PM, gilleain torrance <[email protected]> wrote: > Hi, > > This isn't really relevant to fragments as defined in the Murko paper, > but it could be interesting to fragment ring systems and linkers in > other ways. > > Say we label the rings as A-D. Then you're asking if the ring systems > should be (A, B, C, D) or (A, (B, C), D) - where B and C are the > central 5 ring and the phenyl directly attached to it. Seems like > there are other fragmentations, like ((A, B), C, D) or (A, (B, D), C) > - where brackets indicate grouping.
Using the Murcko terminology, they are pretty clear that the ring systems would be A, B, C and D - the single bond between the phenyl and cyclopentane is considered a zero atom linker and so the two rings on either side are separate ring systems Given that a framework is a combination of ring systems and linkers, I there are quite a few frameworks - (ABCD), (AB) (ABC) (ABD) (CBD) > > It might be hard to do, but I could imagine trying to find the > commonest frameworks like this. Of course, the assumption is that > linkers are chemically more cleavable, so maybe it doesn't make sense > to include them in frameworks. Just a thought, anyway. > > gilleain > > On Wed, Oct 6, 2010 at 8:35 PM, Rajarshi Guha <[email protected]> wrote: >> Hi, I've been debugging some of my code and I could you determine how >> many frameworks should be identified from >> >> C1(c2ccccc2)(CC(CC1)CCc1ccccc1)CC1C=CC=C1 >> >> I know that that the 6-ring and 5-ring joined by a single bond (zero >> atom linker) correspond to 2 separate ring systems, but would the >> combination be a distinct framework? >> >> On Wed, Oct 6, 2010 at 4:14 AM, Pascal Muller >> <[email protected]> wrote: >>> Hi, >>> >>>>>> If I remember correctly the Murcko framework code in the CDK is broken. >>>> >>>> I would be *very* useful if the people interested in this >>>> functionality could set up (e.g. in the wiki) a set if molecules with >>>> the expected murcko hits for those molecules... >>> >>> Done: >>> https://sourceforge.net/apps/mediawiki/cdk/index.php?title=Murcko >>> >>> If something need to be modified or corrected, just say it :) >>> >>> By the way, I wrote a small script with OpenBabel (pybel actually) for >>> generating Murcko framework (although not with the same options than >>> the generateMurckoFragments function). >>> >>> Regards, >>> Pascal >>> >>> ------------------------------------------------------------------------------ >>> Beautiful is writing same markup. Internet Explorer 9 supports >>> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. >>> Spend less time writing and rewriting code and more time creating great >>> experiences on the web. Be a part of the beta today. >>> http://p.sf.net/sfu/beautyoftheweb >>> _______________________________________________ >>> Cdk-user mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>> >> >> >> >> -- >> Rajarshi Guha >> NIH Chemical Genomics Center >> >> ------------------------------------------------------------------------------ >> Beautiful is writing same markup. Internet Explorer 9 supports >> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. >> Spend less time writing and rewriting code and more time creating great >> experiences on the web. Be a part of the beta today. >> http://p.sf.net/sfu/beautyoftheweb >> _______________________________________________ >> Cdk-user mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> > -- Rajarshi Guha NIH Chemical Genomics Center ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
