Dear Evgueni, On Thu, Sep 11, 2008 at 9:40 AM, Evgueni Kolossov <[email protected]> wrote: > > Can you please describe (or forward me to description) what rules you > applied for fragmentation process. Can they be modified, etc.
I'm not 100% sure which fragmentation process you are talking about, but I guess you mean the Fragment catalog stuff that's in $RDBASE/Code/GraphMol/FragCatalog and that is discussed on page 16 here: http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Docs/Book/GettingStartedInPython.pdf The basic idea is that functional groups (as defined when the fragment catalog generator is constructed; these are loaded from a text file) are removed and then all unique fragments in a particular size range are identified. Fragments are distinguished from each other based on their topology and the attached functional groups. If you have more specific questions, I'm happy to answer them if I can. -greg
