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
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