Re: [Rdkit-devel] bivariate_normal deprecation

[Greg L. <gre...@gm...>]

Hi Kira,

I would rather not introduce a dependency on scipy (which is rather large)
here. I think it probably makes more sense to just add an RDKit
reimplementation of the function and use that.

I need to check, but I would guess that the license on matplotlib would
probably allow us to just grab their current implementation and use that.

Regardless, there should be an RDKit GitHub ticket for this. Do you want to
create that or shall I?

Best,
-greg



On Fri, 4 May 2018 at 06:19, Kiran Telukunta <
kir...@in...> wrote:

> Hi All,
>
>
> What is the best way to rewrite in rdkit.Chem.Draw import SimilarityMaps
>
> def calcAtomGaussians(mol, a=0.03, step=0.02, weights=None):
>
> As  mlab.bivariate_normal
> <https://matplotlib.org/api/mlab_api.html#matplotlib.mlab.bivariate_normal>
> ​​
> is deprecated.
>
> Should we use scipy multivarate function
> <https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.multivariate_normal.html#scipy.stats.multivariate_normal>
> or is there any other best method?
>
> I was trying to use SimilarityMaps.GetSimilarityMapForFingerprint, and got
> the error:
>
> home/kiran/anaconda3/envs/rdkit-2018_03_1/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py:285:
> MatplotlibDeprecationWarning: The bivariate_normal function was deprecated
> in version 2.2.
>   Z = mlab.bivariate_normal(X, Y, a, a, mol._atomPs[0][0],
> mol._atomPs[0][1]) * weights[0]
> /home/kiran/anaconda3/envs/rdkit-2018_03_1/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py:287:
> MatplotlibDeprecationWarning: The bivariate_normal function was deprecated
> in version 2.2.
>   Zp = mlab.bivariate_normal(X, Y, a, a, mol._atomPs[i][0],
> mol._atomPs[i][1])
>
> I was using latest RDKit 2018.03.1.
>
> Thanks,
> Kiran
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>