Dear Jean-Paul, On Tue, Mar 13, 2012 at 3:03 PM, JP <[email protected]> wrote: > > Hi there everyone, > > A high level question. > > Can anyone highlight the main advantages/disadvantages of fragmenting > molecules using FragmentCatalog (Chap 1.9, RDKit documentation) vs > RDKit.Chem.Recap ? > Probably the fragmenting rules are different, but what are the use cases for > these two different methodologies? > > I would like to "find common fragments" between molecules. How should I go > about the problem of a fragment in one molecule being a subtly different > from another in a second molecule (e.g. has an extra C) ? >
RECAP fragments molecules along a set of bonds that are, theoretically, experimentally accessible. One intent is to provide something useful for a retrosynthetic analysis. The fragment catalog code in the RDKit just identifies all subgraphs in a particular size range. So you'll get fragments like "cc(C)c" that could never actually exist on their own. The results are potentially more useful for identifying common fragments, as long as you don't care if those fragments are something that could ever be "free standing". -greg ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
