Re: [Rdkit-devel] bivariate_normal deprecation

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

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 <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
>>
>> ------------------------------------------------------------
>> ------------------
>> 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
>>
>