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
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[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
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