Hi Geoff,
Congrats to you and co-authors on the paper and thanks for offering to
contribute to the RDKit.
Given the dependence on py_rdl, this probably isn't currently a good match
for the core RDKit (we try to minimize adding additional external
dependencies), but it would be great to have it available in the RDKit
Contrib directory. The only real requirement there is to have a README.md
file describing what the contribution is and linking to the original
publication.
You can take a look at a couple of recent contributions to use as examples:
https://github.com/rdkit/rdkit/tree/master/Contrib/CalcLigRMSD
https://github.com/rdkit/rdkit/tree/master/Contrib/NIBRSubstructureFilters
A quick aside on RDL: the RDKit can optionally use the RDL library, but it
looks like it doesn't currently expose everything RingEntropy.py needs to
Python. If the code is available in Contrib, we can take a look at doing a
C++ re-implementation of the new descriptor(s) and putting that in the
core. The advantage of the C++ implementation is that it would make
the descriptor more broadly accessible. We've done this a couple of times
in the past with code from Contrib.
Best,
-greg
On Mon, Mar 29, 2021 at 9:37 PM Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> Hi Greg,
>
> We just published a paper with a linear model predicting conformational
> entropies:
> https://pubs.acs.org/doi/10.1021/acs.jctc.0c01213
> https://github.com/hutchisonlab/molecular-entropies
>
> We built the notebooks on top of RDKit - and of course would like to
> contribute the descriptor back to RDKit.
>
> Is there a contribution guide (e.g., how to structure the code before a
> pull request)? In particular, this one has a few components that might
> prove useful as separate calls (e.g., the ring flexibility measure).
>
> Thanks,
> -Geoff
>
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geo...@pitt.edu
> twitter: @ghutchis
> web: https://hutchison.chem.pitt.edu/
>
>
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