[ERROR] Runtime.ImportModuleError: Unable to import module 'app': No module named 'sascorer' Traceback (most recent call last):

[MichelML]

[ERROR] Runtime.ImportModuleError: Unable to import module 'app': No module named 'sascorer' Traceback (most recent call last):

Posting so it's logged somewhere.

Is this a new dependency for datamol? Disclaimer, I didn't update datamol in my project (lambdomics) since a couple months (I was at 0.5 before upgrading). sascorer seems to have appear in commit 8576d4b with the descriptors module, and this module is imported by default when using import datamol as dm .

sascorer seems to be a module coming from RDKit but I'm not sure. Is it just a matter of making sure to import RDKit before datamol if you use both in your project?

[hadim]

Closing here.

For the record, the issue was due to the relocation of a conda env using conda-pack. RDKit seems to hard code the absolute paths of the rdkit config folder and so during the relocation the config paths does not point to the correct folder anymore explaining the import module error.

There is no real good solution for this on the rdkit side currently since using relative paths might also causes issues on non-standard systems.

[adelenelai]

Hello @MichelML @hadim, did it work for you to just import RDKit before datamol? Did not for me..

Any recommended workaround? Should we go back to an older RDKit?

With datamol 0.7.3 and rdkit 2022.03.2, I'm getting:

import rdkit.Chem as Chem
from rdkit.Chem import AllChem
...
import datamol as dm

File ~/opt/anaconda3/envs/my-rdkit-env/lib/python3.10/site-packages/datamol/__init__.py:74, in <module>
     72 from . import actions
     73 from . import molar
---> 74 from . import descriptors
     75 from . import predictors
     77 from .convert import to_smiles

File ~/opt/anaconda3/envs/my-rdkit-env/lib/python3.10/site-packages/datamol/descriptors/__init__.py:1, in <module>
----> 1 from .descriptors import mw
      2 from .descriptors import fsp3
      3 from .descriptors import n_hba

File ~/opt/anaconda3/envs/my-rdkit-env/lib/python3.10/site-packages/datamol/descriptors/descriptors.py:15, in <module>
     12 from rdkit.Chem import Crippen
     14 sys.path.append(os.path.join(RDConfig.RDContribDir, "SA_Score"))
---> 15 import sascorer  # type:ignore
     17 from .. import Mol
     18 from ..convert import from_smarts

ModuleNotFoundError: No module named 'sascorer'

Thank you!

[hadim]

What OS are you using?

[adelenelai]

Mac 11.5.1 Thanks for helping with this!

…

On Fri, 13 May 2022, 12:30 Hadrien Mary, ***@***.***> wrote: What OS are you using? — Reply to this email directly, view it on GitHub <#83 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGBKIPKTFDOSSVTTGSKNWWTVJYVMLANCNFSM5OY4JBPQ> . You are receiving this because you commented.Message ID: ***@***.***>

[hadim]

I can't reproduce on Linux. I'll check if I can get access to an OSX machine.

[MichelML]

@adelenelai anyway we can see your conda env file? do you use pypi or conda to install rdkit and datamol?

@mercuryseries @maclandrol I think you guys have a Mac if you want to test this quickly.

[adelenelai]

For rdkit and datamol I used conda.
datamol is installed within my rdkit env.

Thanks a lot.

(my-rdkit-env) adelene.lai$ conda list
# packages in environment at .../my-rdkit-env:
#
# Name                    Version                   Build  Channel
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
appnope                   0.1.2           py310hecd8cb5_1001  
argon2-cffi               21.3.0             pyhd3eb1b0_0  
argon2-cffi-bindings      21.2.0          py310hca72f7f_0  
asttokens                 2.0.5              pyhd3eb1b0_0  
attrs                     21.4.0             pyhd3eb1b0_0  
backcall                  0.2.0              pyhd3eb1b0_0  
beautifulsoup4            4.11.1          py310hecd8cb5_0  
bleach                    4.1.0              pyhd3eb1b0_0  
boost                     1.74.0          py310h509978a_5    conda-forge
boost-cpp                 1.74.0               h8b082ac_8    conda-forge
brotli                    1.0.9                h5eb16cf_7    conda-forge
brotli-bin                1.0.9                h5eb16cf_7    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
ca-certificates           2021.10.8            h033912b_0    conda-forge
cairo                     1.16.0            h1680b09_1011    conda-forge
certifi                   2021.10.8       py310h2ec42d9_2    conda-forge
cffi                      1.15.0          py310hc55c11b_1  
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
datamol                   0.7.3              pyhd8ed1ab_0    conda-forge
debugpy                   1.5.1           py310he9d5cce_0  
decorator                 5.1.1              pyhd3eb1b0_0  
defusedxml                0.7.1              pyhd3eb1b0_0  
entrypoints               0.4             py310hecd8cb5_0  
executing                 0.8.3              pyhd3eb1b0_0  
expat                     2.4.8                h96cf925_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.0               h676cef8_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.33.3          py310h6c45266_0    conda-forge
freetype                  2.10.4               h4cff582_1    conda-forge
fsspec                    2022.3.0           pyhd8ed1ab_0    conda-forge
gettext                   0.19.8.1          hd1a6beb_1008    conda-forge
giflib                    5.2.1                hbcb3906_2    conda-forge
greenlet                  1.1.2           py310h9d931ec_2    conda-forge
icu                       70.1                 h96cf925_0    conda-forge
ipykernel                 6.9.1           py310hecd8cb5_0  
ipython                   8.3.0           py310hecd8cb5_0  
ipython_genutils          0.2.0              pyhd3eb1b0_1  
ipywidgets                7.7.0                    pypi_0    pypi
jbig                      2.1               h0d85af4_2003    conda-forge
jedi                      0.18.1          py310hecd8cb5_1  
jinja2                    3.0.3              pyhd3eb1b0_0  
joblib                    1.1.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h5eb16cf_1    conda-forge
jsonschema                4.4.0           py310hecd8cb5_0  
jupyter_client            7.2.2           py310hecd8cb5_0  
jupyter_core              4.10.0          py310hecd8cb5_0  
jupyterlab-widgets        1.1.0                    pypi_0    pypi
jupyterlab_pygments       0.1.2                      py_0  
kiwisolver                1.4.2           py310h6be76da_1    conda-forge
lcms2                     2.12                 h577c468_0    conda-forge
lerc                      3.0                  he49afe7_0    conda-forge
libblas                   3.9.0           14_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                h5eb16cf_7    conda-forge
libbrotlidec              1.0.9                h5eb16cf_7    conda-forge
libbrotlienc              1.0.9                h5eb16cf_7    conda-forge
libcblas                  3.9.0           14_osx64_openblas    conda-forge
libcxx                    13.0.1               hc203e6f_0    conda-forge
libdeflate                1.10                 h0d85af4_0    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           9_3_0_h6c81a4c_23    conda-forge
libgfortran5              9.3.0               h6c81a4c_23    conda-forge
libglib                   2.70.2               hf1fb8c0_4    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
liblapack                 3.9.0           14_osx64_openblas    conda-forge
libopenblas               0.3.20          openmp_hb3cd9ec_0    conda-forge
libpng                    1.6.37               h7cec526_2    conda-forge
libsodium                 1.0.18               h1de35cc_0  
libtiff                   4.3.0                h17f2ce3_3    conda-forge
libwebp                   1.2.2                h28dabe5_0    conda-forge
libwebp-base              1.2.2                h0d85af4_1    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libzlib                   1.2.11            h6c3fc93_1014    conda-forge
llvm-openmp               14.0.3               ha654fa7_0    conda-forge
loguru                    0.6.0           py310h2ec42d9_1    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
markupsafe                2.0.1           py310hca72f7f_0  
matplotlib-base           3.5.2           py310h4510841_0    conda-forge
matplotlib-inline         0.1.2              pyhd3eb1b0_2  
mistune                   0.8.4           py310hca72f7f_1000  
mols2grid                 0.2.2                    pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nb_conda_kernels          2.3.1           py310hecd8cb5_0  
nbclient                  0.5.13          py310hecd8cb5_0  
nbconvert                 6.4.4           py310hecd8cb5_0  
nbformat                  5.3.0           py310hecd8cb5_0  
ncurses                   6.3                  h96cf925_1    conda-forge
nest-asyncio              1.5.5           py310hecd8cb5_0  
notebook                  6.4.11          py310hecd8cb5_0  
numpy                     1.22.3          py310he1f95b8_2    conda-forge
openjpeg                  2.4.0                h6e7aa92_1    conda-forge
openssl                   3.0.3                hfe4f2af_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.2           py310h514ec25_1    conda-forge
pandocfilters             1.5.0              pyhd3eb1b0_0  
parso                     0.8.3              pyhd3eb1b0_0  
pcre                      8.45                 he49afe7_0    conda-forge
pexpect                   4.8.0              pyhd3eb1b0_3  
pickleshare               0.7.5           pyhd3eb1b0_1003  
pillow                    9.1.0           py310h382dc3b_2    conda-forge
pip                       22.0.4             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
prometheus_client         0.13.1             pyhd3eb1b0_0  
prompt-toolkit            3.0.20             pyhd3eb1b0_0  
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3eb1b0_2  
pure_eval                 0.2.2              pyhd3eb1b0_0  
pycairo                   1.21.0          py310h5138a19_1    conda-forge
pycparser                 2.21               pyhd3eb1b0_0  
pygments                  2.11.2             pyhd3eb1b0_0  
pyparsing                 3.0.8              pyhd8ed1ab_0    conda-forge
pyrsistent                0.18.0          py310hca72f7f_0  
python                    3.10.4          h1cc4136_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.15.1             pyhd3eb1b0_0  
python_abi                3.10                    2_cp310    conda-forge
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
pyzmq                     22.3.0          py310he9d5cce_2  
rdkit                     2022.03.2       py310haadc31d_0    conda-forge
rdkit-pypi                2022.3.2.1               pypi_0    pypi
readline                  8.1                  h05e3726_0    conda-forge
reportlab                 3.5.68          py310h3301372_1    conda-forge
scikit-learn              1.1.0           py310hfc06b38_0    conda-forge
scipy                     1.8.0           py310h47774c9_1    conda-forge
selfies                   2.0.0              pyhd8ed1ab_0    conda-forge
send2trash                1.8.0              pyhd3eb1b0_1  
setuptools                62.1.0          py310h2ec42d9_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
soupsieve                 2.3.1              pyhd3eb1b0_0  
sqlalchemy                1.4.36          py310h6c45266_0    conda-forge
sqlite                    3.38.4               hd9f0692_0    conda-forge
stack_data                0.2.0              pyhd3eb1b0_0  
terminado                 0.13.1          py310hecd8cb5_0  
testpath                  0.5.0              pyhd3eb1b0_0  
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
tornado                   6.1             py310hca72f7f_0  
tqdm                      4.64.0             pyhd8ed1ab_0    conda-forge
traitlets                 5.1.1              pyhd3eb1b0_0  
typing-extensions         4.1.1                hd3eb1b0_0  
typing_extensions         4.1.1              pyh06a4308_0  
tzdata                    2022a                h191b570_0    conda-forge
unicodedata2              14.0.0          py310h1961e1f_1    conda-forge
wcwidth                   0.2.5              pyhd3eb1b0_0  
webencodings              0.5.1           py310hecd8cb5_1  
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.6.0                    pypi_0    pypi
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
zeromq                    4.3.4                h23ab428_0  
zlib                      1.2.11            h6c3fc93_1014    conda-forge
zstd                      1.5.2                h582d3a0_0    conda-forge

[maclandrol]

Will test this morning, but my first guess is rdkit pypi not packaging the contrib (including sasscorer) module, since it's not part of the 'package' itself.

Can you print

from rdkit.Chem import RDConfig
In [3]: RDConfig.RDContribDir
Out[3]: '/Users/manu/.miniconda/envs/testenv/share/RDKit/Contrib'

Then check whether you see SA_Score in the RDKIT Contrib folder ?

ls /Users/manu/.miniconda/envs/testenv/share/RDKit/Contrib

[MichelML]

@adelenelai I see you have two versions of rdkit in your env:

rdkit                     2022.03.2       py310haadc31d_0    conda-forge
rdkit-pypi                2022.3.2.1               pypi_0    pypi

I would try to remove rdkit-pypi from your env as a first attempt (and try what @maclandrol suggested)

[maclandrol]

@adelenelai Confirmed. The rdkit from pypi does not package the 'Contrib' module, thus it cannot be imported.

In your case, the interpreter is picking up the rdkit-pypi over the one from conda-forge. This happens likely because you pip install 'rdkit-pypi' AFTER installing datamol.

I am not sure a simple pip uninstall 'rdkit-pypi' would work, so instead you can either create a new env, or run the following:

• pip uninstall 'rdkit-pypi'
• mamba install datamol -c conda-forge --force-reinstall
• mamba install rdkit -c conda-forge --force-reinstall

As a side note, remember that if you install datamol from conda-forge, you don't need to install rdkit anymore.

@hadim , we should remove anything that links to contrib from the __init__ for cases like this.

[adelenelai]

Hello @MichelML and @maclandrol

I did pip uninstall rdkit-pypi to leave rdkit remaining in the env as you advised.

But...things started to break and I couldn't even do import rdkit.Chem.rdchem as rdchem any more D:

So...I did a fresh install of rdkit in a new env, then conda install -c conda-forge datamol.

After that, importing datamol was no problem :)

Thanks a lot for your speedy help

[hadim]

@hadim , we should remove anything that links to contrib from the __init__ for cases like this.

Yes, we should catch the error and make it silent (or simply a warning).

[hadim]

Thank you @adelenelai for the report!

[hadim]

Fixed in >=0.7.4 now on pypi and soon on conda (a few hours).