Hi Paul, The 'anchored' fingerprint by the attachment point is how I've done it in the past too. It can give you more granularity than the simple aromatic/non-aromatic classification. It's easy to do it with RDKit but I don't have the snippet at hand. Cheers, George
Sent from my gPad On 27 Aug 2014, at 13:21, [email protected] wrote: >> >> 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 ------------------------------------------------------------------------------ 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
