This RDKit blog post uses some code from Nadine to provide SMARTS strings
corresponding to standard Morgan ("ECFP") bits:
http://rdkit.blogspot.com/2016/03/explaining-morgan-similarity.html
At the moment it's not possible to do the same thing with the new
fingerprinting code (that didn't get finis
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
wrote:
> Thanks so much Greg!
>
> If I catch your drift, you are talking
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-an
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
Yep, that's quite similar to what I'm working on. In fact, I'm probably
going to borrow some of your example for mine. :-)
On Thu, Jan 31, 2019 at 12:50 AM Lewis Martin
wrote:
> Thanks so much Greg!
>
> If I catch your drift, you are talking about the new fingerprint
> generators from the google
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_invaria
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
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
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