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 <greg.land...@gmail.com> 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 <kiran.telukunta@indiayouth.
> info> 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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