Here's a simple example that uses custom atom invariants based on the RDKit's usual pharmacophore features: https://gist.github.com/greglandrum/e28ef79e8e9f63e371de8a2c6829a691
On Thu, Jan 31, 2019 at 12:50 AM Lewis Martin <lewis.marti...@gmail.com> wrote: > 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 >
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