[Rdkit-devel] bivariate_normal deprecation

[Kiran T. <kir...@in...>]

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