Hi, > Another example: You have > c1cc(ccc1C(=O)Nc2ccc3c(c2)nc(o3)c4ccncc4)F ZINC00037772 > > Visually this should have 3 frameworks - but you list one. > > It seems that all combinations of ring systems and linkers are valid > frameworks - or maybe I have misunderstood. > > Could you explain how you arrived at these examples?
To my understanding, there is only one Murcko framework for one molecule (if at least one cycle is present). Here are the definitions from the publication: Linker Atoms. Atoms that are on the direct path connecting two ring systems are defined as linker atoms. [as already said, could have "zero atom linker"] Side Chain Atoms. Any nonring, nonlinker atoms are defined as side chain atoms. [--> Not included in the framework] Framework. The framework is defined as the union of ring systems and linkers in a molecule. I understand the framework definition as the union of _all_ ring systems, and linkers are present only if there is at least two ring systems. As shown in Charts 1 and 2, the framework could consist of just one cycle (e.g. benzene), without linker. And the number of "cyclohexane" graph occurence (chart 1) doesn't include the number of the other graph with cyclohexane (606 < 195+119+108+55+57+47+45...). What do you think about this interpretation? Of course, listing all combinations of ring systems and linkers could be interesting too. But it could lead to a great number of frameworks (many molecules have 6 ring systems or more). 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
