Re: [Rdkit-devel] bivariate_normal deprecation

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

Thanks Kiran!

On Fri, May 4, 2018 at 5:08 PM Kiran Telukunta <
kir...@in...> wrote:

> Hello Greg,
>
> I have created the ticket <https://github.com/rdkit/rdkit/issues/1851>.
>
> Thanks,
> Kiran
>
> On 4 May 2018 at 09:13, Greg Landrum <gre...@gm...> wrote:
>
>> 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
>>>
>>>
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>>
>
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