Thanks so much Greg! If I catch your drift, you are talking about the new fingerprint generators from the google summer of code. I took a look myself since I was curious.
Here's a notebook demonstrating how I think it works: https://github.com/ljmartin/snippets/blob/master/snippet_fp_with_invariants.ipynb This downloads some bioactivity data from chembl and then compares standard AP or TT fingerprints with same using the atom invariants associated with the MorganFP "Feature" atom typing, which is actually the feature types from the Gobbi/Poppinger paper. As expected, the invariant versions have higher similarity! It's not CATS but this seems equivalent for my purposes - thanks! Hopefully it's close to the mark - looking forward to seeing other examples too. cheers lewis On Thu, Jan 31, 2019 at 12:03 AM Greg Landrum <greg.land...@gmail.com> wrote: > Hi Lewis, > > This is a great chance to demonstrate some of the things that can be done > with the new fingerprint generation code. It's going to take me a bit to > put this together (it's all new enough that I'm still not quite "fluent"), > but I will try to get an example put together over the next couple of days. > > -greg > > > On Wed, Jan 30, 2019 at 4:59 AM Lewis Martin <lewis.marti...@gmail.com> > wrote: > >> Hi rdkitters, >> I'd like to compare the similarity of torsion/atom pair FPs using >> standard atomic numbering with those using pharmacophore types, like the >> 'CATS' atom typing developed by Gisbert Schneider, and hoped someone has >> some advice here. *CATS* is a pharmacophore atom typing system with >> these types: H-bond donor, H-bond acceptor, positive, negative, lipophilic, >> and CATS2 has 'aromatic'. These are described in: *“Scaffold‐Hopping” by >> Topological Pharmacophore Search: A Contribution to Virtual Screening. *It >> seems pretty close to the Gobbi 2D pharmacophore typing, or the features >> used in FCFP. >> >> Ive no problem detecting the atom types - I borrowed code from the open >> source PyBioMed - but I'm stuck at the next step. How to change the atoms >> into their pharmacophore types to then make a torsion or atom pair >> fingerprint using RDKit? What I've tried so far is to just set the atomic >> number to some series of 5 atoms not normally seen in drug like molecules, >> like 40-44. This is silly but it seems to work. The only issue is trouble >> kekulizing the molecules for display. Is there a better way? >> >> >> Here's a snippet to demonstrate what I mean, it's adapted from PyBioMed >> and any errors are probably mine: >> https://github.com/ljmartin/snippets/blob/master/atom_typing_snippet.ipynb >> >> Thanks for your time! >> lewis >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
