Hi Francois, If it helps, this is what Ive been using while playing with atom types: https://github.com/ljmartin/snippets/blob/master/snippet_atom_typing.ipynb
The SMARTS codes were taken from down the bottom of this page https://www.rdkit.org/docs/GettingStartedInPython.html#chemical-features-and-pharmacophores I tried using rdkit.Chem.rdMolDescriptors.GetFeatureInvariants() but it appears to give more than the 6 listed atom types from the Gobbi paper. For ECFP, I don't know any other way to describe an atom other than the obscure integer, but you can visualize the bits using: http://rdkit.blogspot.com/2018/10/using-new-fingerprint-bit-rendering-code.html cheers lewis On Fri, Feb 1, 2019 at 2:09 PM Francois Berenger <mli...@ligand.eu> wrote: > Hi, > > I have a related question: > how to output the type of an atom in a molecule, > if possible in a human-readable format; i.e. a human > readable/understandable string rather than some (obscure) integer. > > I am interested to look at the atom types used by the ECFP > and the FCFP fingerprints. > > Thanks a lot, > Francois. > > On 31/01/2019 08:49, Lewis Martin 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 > > [3] > > 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 > >>> [1] > >>> > >>> Thanks for your time! > >>> lewis > >>> > >>> _______________________________________________ > >>> Rdkit-discuss mailing list > >>> Rdkit-discuss@lists.sourceforge.net > >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss [2] > > > > > > Links: > > ------ > > [1] > > > https://github.com/ljmartin/snippets/blob/master/atom_typing_snippet.ipynb > > [2] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > [3] > > > https://github.com/ljmartin/snippets/blob/master/snippet_fp_with_invariants.ipynb > > > > _______________________________________________ > > Rdkit-discuss mailing list > > Rdkit-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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