Combining two answers into one: On Fri, Nov 6, 2009 at 7:59 AM, Evgueni Kolossov <ekolos...@gmail.com> wrote: > Hi Greg, > > Yes, this is solution I been thinking about as well but there is 2 problems: > 1. It will slow dawn mapping process which is slow already > 2. What atom to use for replacement?
I'm not sure I understand what you mean about slowing down the mapping process. If you replace the dummies in your fragments with query atoms, as I proposed in the sample code in my earlier message, the substructure search should not be substantially slower. The replacement itself also won't take that long, unless you really have a *lot* of fragments. On Fri, Nov 6, 2009 at 9:03 AM, Evgueni Kolossov <ekolos...@gmail.com> wrote: > > I think you should distinguish between dummy atoms and connection points - > for fragments it is connection points we are talking about. The code doesn't understand anything about connection points... it just has atoms. Dummy atoms are atoms with atomic number zero. The substructure matching code applied to normal Atoms (i.e. not QueryAtoms) compares two atoms by checking to see if their atomic numbers match, so dummies match dummies. Additionally, when isotopes are specified, it checks that the specified isotopes match. QueryAtoms, on the other had, allow client code to specify the function that's used for matching. The example I provided showed how to use a function that matches any atom; which I think is what you are looking for. > So, it suppose > to ignore this atom (but not bond!) during matching process. May be just add > another bool flag to allow user select different behavior? The substructure matching uses atoms and bonds, and returns the results as lists of atom indices; how (and why) would you propose to ignore an atom but not a bond? -greg ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
