> > Dear RDKitters, > > I'm using Jameed's wonderful code for a matched pair analysis. > > Given such a transformation string "[*:1]C>>[*:1][H]" > => How do I check if [*:1] is an aromatic or an aliphatic atom? > > > I fear that this can only be done by going back into the original > data/output, or am I wrong ? > > > Cheers & Thanks, > Paul > >
Hi Paul, I think you're right, since Jameed's MMP algorithm does not cut ring systems and does not capture the environment at the cutting point. Two solutions come into my mind: - either you go back to the original data, or - you search for more specific replacements, i.e. [*:1]CC>>[*:1]C[H], [*:1]c1ccccc1C>>[*:1]c1ccccc1[H] etc. In LUCID for each fragment I calculate and store circular fingerprints centered at the dummy atom ([*]) of different sizes, which allow me to filter the results very easily (exactly for the kind of questions you wanted to answer). Cheers, Grégori ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
