ERROR:root:Unable to make new descriptors

[alim11github]

i did install descriptastorus via pip install git+https://github.com/bp-kelley/descriptastorus , and successfully installed .but every time when i import descriptastorus , i got this error (ERROR:root:Unable to make new descriptors, descriptor generator not installed, but Process finished with exit code 0 in pycharm) .

when i try this( from descriptastorus.descriptors import rdDescriptors, rdNormalizedDescriptors) . i also got error (ValueError: RDKit2D: Failed to initialize: unable to find specified properties: fr_Al_COO fr_Al_OH fr_Al_OH_noTert fr_ArN fr_Ar_COO fr_Ar_N ) i been stuck here few days , i did try reinstall few times (f pip install git+https://github.com/bp-kelley/descriptastorus or github source) ,but it didn't work. (RDkit 2021.9.2 scikit-learn already installed)

did i miss anything during deployment? thank for any suggestion.

[bp-kelley]

It looks like these got moved in the rdkit.Chem.Fragments in rdkit 2021.9 and out of the main descriptorList, I'll patch the code to look for them there.

[bp-kelley]

Actually, I take it back, I'm unable to duplicate the issue:

>>> import rdkit
>>> rdkit.__version__
'2021.09.2'
>>> from  descriptastorus.descriptors import rdDescriptors
WARNING:root:No normalization for BCUT2D_MWHI
WARNING:root:No normalization for BCUT2D_MWLOW
WARNING:root:No normalization for BCUT2D_CHGHI
WARNING:root:No normalization for BCUT2D_CHGLO
WARNING:root:No normalization for BCUT2D_LOGPHI
WARNING:root:No normalization for BCUT2D_LOGPLOW
WARNING:root:No normalization for BCUT2D_MRHI
WARNING:root:No normalization for BCUT2D_MRLOW
>>> rdDescriptors.RDKit2D()
<descriptastorus.descriptors.rdDescriptors.RDKit2D object at 0x103d45ee0>

Could you send the contents of rdkit.Chem.Descriptors.descList ?

[bp-kelley]

Are you using Conda or did you install rdkit via pip?

[bp-kelley]

python -c 'import rdkit;print(rdkit.__version__);from rdkit.Chem import Descriptors;print(len(Descriptors.descList))'

should be 208

[alim11github]

apologize！！ i been little bit busy recent days, so i didnt reply to you.
i uninstalled new version RDKit and pip install version 2021.03.5 and it worked. len of desclist is 123 .

but i still got this error : 2021.03.5 123 WARNING:root:No normalization for BCUT2D_MWHI WARNING:root:No normalization for BCUT2D_MWLOW WARNING:root:No normalization for BCUT2D_CHGHI WARNING:root:No normalization for BCUT2D_CHGLO WARNING:root:No normalization for BCUT2D_LOGPHI WARNING:root:No normalization for BCUT2D_LOGPLOW WARNING:root:No normalization for BCUT2D_MRHI WARNING:root:No normalization for BCUT2D_MRLOW

However ,Process finished with exit code 0, so i think this error does not affect the result. anyway, thanks for your help.

[bp-kelley]

It didn’t really work, you are missing quite a few descriptors when you pip install rdkit.

I suggest using anaconda/conda for rdkit as that is the only officially supported version.

---

Brian Kelley

On Nov 6, 2021, at 2:59 AM, alim11github @.***> wrote:

 apologize！！ i been little bit busy recent days, so i didnt reply to you. i uninstalled new version RDKit and pip install version 2021.03.5 and it worked. len of desclist is 123 .

but i still got this error : 2021.03.5 123 WARNING:root:No normalization for BCUT2D_MWHI WARNING:root:No normalization for BCUT2D_MWLOW WARNING:root:No normalization for BCUT2D_CHGHI WARNING:root:No normalization for BCUT2D_CHGLO WARNING:root:No normalization for BCUT2D_LOGPHI WARNING:root:No normalization for BCUT2D_LOGPLOW WARNING:root:No normalization for BCUT2D_MRHI WARNING:root:No normalization for BCUT2D_MRLOW

However ,Process finished with exit code 0, so i think this error does not affect the result. anyway, thanks for your help.

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