KeyError in HYBRIDIZATION_RDKIT

[nezix]

I get a dictionary KeyError when calling espaloma_charge -i "GPC_1RDS.mol2":

"espaloma_charge/utils.py", line 55, in fp_rdkit
HYBRIDIZATION_RDKIT[atom.GetHybridization()]
KeyError: rdkit.Chem.rdchem.HybridizationType.SP2D

It looks like SP2D is indeed not in the HYBRIDIZATION_RDKIT.

https://github.com/choderalab/espaloma_charge/blob/59c6bccb9c86e15434dfeff280e6d79845ba5c89/espaloma_charge/utils.py#L11
GPC_1RDS.zip

[jchodera]

@nezix : It looks like the SP2D hybridization type was added last year. Which version of rdkit do you have installed, and have you tried a version more recent than 20 May 2022?

[mikemhenry]

We don't have an rdkit pin explicitly in our conda-forge package https://github.com/conda-forge/espaloma-feedstock/blob/main/recipe/meta.yaml#L21-L36

Once we identify the minimum version of rdkit we support, I can add it.

[jchodera]

Looks like it should be 2022.09.1 or later.

[nezix]

Sorry for the delay.
rdBase.rdkitVersion returns '2023.03.3'

[jchodera]

Can you dump your whole conda or pip environment to help us track down the issue, as well as a complete stack trace of the error? And can you share the input molecule to help us reproduce? Thanks!

[nezix]

The input molecule is in the first post.

This is the stacktrace:

espaloma_charge -i "/mnt/d/PDBs/GPC_1RDS.mol2"
/home/me/micromamba/envs/mpy310/lib/python3.11/site-packages/dgl/heterograph.py:92: DGLWarning: Recommend creating graphs by dgl.graph(data) instead of dgl.DGLGraph(data).
dgl_warning(
Traceback (most recent call last):
File "/home/me/micromamba/envs/mpy310/bin/espaloma_charge", line 8, in
sys.exit(espaloma_charge())
^^^^^^^^^^^^^^^^^
File "/home/me/micromamba/envs/mpy310/lib/python3.11/site-packages/espaloma_charge/cli.py", line 13, in espaloma_charge
charge_mol2(args.i, args.o)
File "/home/me/micromamba/envs/mpy310/lib/python3.11/site-packages/espaloma_charge/antechamber_utils.py", line 22, in charge_mol2
charges = charge(molecule)
^^^^^^^^^^^^^^^^
File "/home/me/micromamba/envs/mpy310/lib/python3.11/site-packages/espaloma_charge/app.py", line 54, in charge
graph = from_rdkit_mol(molecule)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/me/micromamba/envs/mpy310/lib/python3.11/site-packages/espaloma_charge/utils.py", line 84, in from_rdkit_mol
h_v_fp = torch.stack([fp_rdkit(atom) for atom in mol.GetAtoms()], axis=0)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/me/micromamba/envs/mpy310/lib/python3.11/site-packages/espaloma_charge/utils.py", line 84, in
h_v_fp = torch.stack([fp_rdkit(atom) for atom in mol.GetAtoms()], axis=0)
^^^^^^^^^^^^^^
File "/home/me/micromamba/envs/mpy310/lib/python3.11/site-packages/espaloma_charge/utils.py", line 55, in fp_rdkit
HYBRIDIZATION_RDKIT[atom.GetHybridization()],
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: rdkit.Chem.rdchem.HybridizationType.SP2D

This is my "mamba list" result:

Name Version Build Channel
─────────────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
ambertools 23.3 py311hbcc7a2f_1 conda-forge
anyio 3.7.1 pyhd8ed1ab_0 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py311hd4cff14_3 conda-forge
arpack 3.7.0 hdefa2d7_2 conda-forge
arrow 1.2.3 pyhd8ed1ab_0 conda-forge
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-lru 2.0.3 pyhd8ed1ab_0 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
aws-c-auth 0.7.0 hf8751d9_2 conda-forge
aws-c-cal 0.6.0 h93469e0_0 conda-forge
aws-c-common 0.8.23 hd590300_0 conda-forge
aws-c-compression 0.2.17 h862ab75_1 conda-forge
aws-c-event-stream 0.3.1 h9599702_1 conda-forge
aws-c-http 0.7.11 hbe98c3e_0 conda-forge
aws-c-io 0.13.28 h3870b5a_0 conda-forge
aws-c-mqtt 0.8.14 h2e270ba_2 conda-forge
aws-c-s3 0.3.13 heb0bb06_2 conda-forge
aws-c-sdkutils 0.1.11 h862ab75_1 conda-forge
aws-checksums 0.1.16 h862ab75_1 conda-forge
aws-crt-cpp 0.20.3 he9c0e7f_4 conda-forge
aws-sdk-cpp 1.10.57 hbc2ea52_17 conda-forge
babel 2.12.1 pyhd8ed1ab_1 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
biopython 1.81 py311h2582759_0 conda-forge
biotite 0.37.0 py311h1f0f07a_0 conda-forge
bleach 6.0.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.4 h0f2a231_0 conda-forge
boost 1.78.0 py311h59ea3da_4 conda-forge
boost-cpp 1.78.0 h6582d0a_3 conda-forge
brotli 1.0.9 h166bdaf_9 conda-forge
brotli-bin 1.0.9 h166bdaf_9 conda-forge
brotli-python 1.0.9 py311ha362b79_9 conda-forge
bson 0.5.9 py_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.19.1 hd590300_0 conda-forge
c-blosc2 2.10.0 hb4ffafa_0 conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.1 pyhd8ed1ab_0 conda-forge
cairo 1.16.0 hbbf8b49_1016 conda-forge
certifi 2023.7.22 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py311h409f033_3 conda-forge
cftime 1.6.2 py311h4c7f6c3_1 conda-forge
charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.1.3 pyhd8ed1ab_0 conda-forge
contourpy 1.1.0 py311h9547e67_0 conda-forge
cudatoolkit 11.8.0 h37601d7_11 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 3.0.0 py311hb755f60_0 conda-forge
debugpy 1.6.7 py311hcafe171_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.1.2 pyhd8ed1ab_0 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
fftw 3.3.10 nompi_hc118613_108 conda-forge
flit-core 3.9.0 pyhd8ed1ab_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 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.41.1 py311h459d7ec_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 hca18f0e_1 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
greenlet 2.0.2 py311hb755f60_1 conda-forge
griddataformats 1.0.1 pyhd8ed1ab_0 conda-forge
gsd 2.9.0 py311h1f0f07a_0 conda-forge
h5py 3.9.0 nompi_py311he78b9b8_101 conda-forge
hdf4 4.2.15 h501b40f_6 conda-forge
hdf5 1.14.1 nompi_h4f84152_100 conda-forge
hydride 1.1.2 py311hcb2cf0a_0 conda-forge
icu 72.1 hcb278e6_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
importlib-metadata 6.8.0 pyha770c72_0 conda-forge
importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge
importlib_resources 6.0.0 pyhd8ed1ab_1 conda-forge
ipykernel 6.25.0 pyh71e2992_0 conda-forge
ipython 8.14.0 pyh41d4057_0 conda-forge
ipywidgets 8.0.7 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jedi 0.18.2 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.3.0 pyhd8ed1ab_1 conda-forge
json5 0.9.14 pyhd8ed1ab_0 conda-forge
jsonpointer 2.0 py_0 conda-forge
jsonschema 4.18.4 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.18.4 pyhd8ed1ab_0 conda-forge
jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge
jupyter_client 8.3.0 pyhd8ed1ab_0 conda-forge
jupyter_core 5.3.1 py311h38be061_0 conda-forge
jupyter_events 0.6.3 pyhd8ed1ab_1 conda-forge
jupyter_server 2.7.0 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge
jupyterlab 4.0.3 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.24.0 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.8 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py311h4dd048b_1 conda-forge
krb5 1.21.1 h659d440_0 conda-forge
lcms2 2.15 haa2dc70_1 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.0.6 hcb278e6_1 conda-forge
libblas 3.9.0 17_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_9 conda-forge
libbrotlidec 1.0.9 h166bdaf_9 conda-forge
libbrotlienc 1.0.9 h166bdaf_9 conda-forge
libcblas 3.9.0 17_linux64_openblas conda-forge
libcurl 8.2.0 hca28451_0 conda-forge
libdeflate 1.18 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.1.0 he5830b7_0 conda-forge
libgfortran-ng 13.1.0 h69a702a_0 conda-forge
libgfortran5 13.1.0 h15d22d2_0 conda-forge
libglib 2.76.4 hebfc3b9_0 conda-forge
libgomp 13.1.0 he5830b7_0 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libjpeg-turbo 2.1.5.1 h0b41bf4_0 conda-forge
liblapack 3.9.0 17_linux64_openblas conda-forge
libnetcdf 4.9.2 nompi_h7e745eb_109 conda-forge
libnghttp2 1.52.0 h61bc06f_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.23 pthreads_h80387f5_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.42.0 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge
libtiff 4.5.1 h8b53f26_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.3.1 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxml2 2.11.4 h0d562d8_0 conda-forge
libxslt 1.1.37 h0054252_1 conda-forge
libzip 1.9.2 hc929e4a_1 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lxml 4.9.3 py311h1a07684_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h516909a_1000 conda-forge
markupsafe 2.1.3 py311h459d7ec_0 conda-forge
matplotlib-base 3.7.2 py311h54ef318_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdanalysis 2.5.0 py311h320fe9a_1 conda-forge
mdtraj 1.9.9 py311h90fe790_0 conda-forge
mistune 3.0.0 pyhd8ed1ab_0 conda-forge
mmtf-python 1.1.3 pyhd8ed1ab_0 conda-forge
mrcfile 1.4.3 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.5 py311ha3edf6b_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.7.3 pyhd8ed1ab_0 conda-forge
nbformat 5.9.1 pyhd8ed1ab_0 conda-forge
ncurses 6.4 hcb278e6_0 conda-forge
nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
netcdf-fortran 4.6.1 nompi_hec59055_101 conda-forge
netcdf4 1.6.4 nompi_py311h9a7c333_101 conda-forge
networkx 3.1 pyhd8ed1ab_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
notebook 7.0.0 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
numexpr 2.8.4 py311h039bad6_101 conda-forge
numpy 1.25.1 py311h64a7726_0 conda-forge
ocl-icd 2.3.1 h7f98852_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openff-amber-ff-ports 0.0.3 pyh6c4a22f_0 conda-forge
openff-forcefields 2023.06.0 pyh1a96a4e_0 conda-forge
openff-interchange 0.3.9 pyhd8ed1ab_0 conda-forge
openff-interchange-base 0.3.9 pyhd8ed1ab_0 conda-forge
openff-models 0.0.5 pyh1a96a4e_1 conda-forge
openff-toolkit 0.14.0 pyhd8ed1ab_3 conda-forge
openff-toolkit-base 0.14.0 pyhd8ed1ab_3 conda-forge
openff-units 0.2.1 pyh1a96a4e_0 conda-forge
openff-utilities 0.1.9 pyh1a96a4e_0 conda-forge
openjpeg 2.5.0 hfec8fc6_2 conda-forge
openmm 8.0.0 py311h59c6c42_1 conda-forge
openmmforcefields 0.11.2 pyhd8ed1ab_1 conda-forge
openssl 3.1.1 hd590300_1 conda-forge
overrides 7.3.1 pyhd8ed1ab_0 conda-forge
packaging 23.1 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
pandas 2.0.3 py311h320fe9a_1 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panedr 0.7.1 pyhd8ed1ab_0 conda-forge
parmed 4.1.0 py311hcafe171_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
patsy 0.5.3 pyhd8ed1ab_0 conda-forge
pbr 5.11.1 pyhd8ed1ab_0 conda-forge
pcre2 10.40 hc3806b6_0 conda-forge
pdbfixer 1.9 pyh1a96a4e_0 conda-forge
perl 5.32.1 4_hd590300_perl5 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.0.0 py311h0b84326_0 conda-forge
pint 0.21 pyhd8ed1ab_0 conda-forge
pip 23.2.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
platformdirs 3.9.1 pyhd8ed1ab_0 conda-forge
pooch 1.7.0 pyha770c72_3 conda-forge
prometheus_client 0.17.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.39 pyha770c72_0 conda-forge
prompt_toolkit 3.0.39 hd8ed1ab_0 conda-forge
psutil 5.9.5 py311h2582759_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge
pycairo 1.24.0 py311h8feb60e_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydantic 1.10.11 py311h459d7ec_0 conda-forge
pyedr 0.7.1 pyhd8ed1ab_0 conda-forge
pygments 2.15.1 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytables 3.8.0 py311h504fbfb_2 conda-forge
python 3.11.4 hab00c5b_0_cpython conda-forge
python-constraint 1.4.0 py_0 conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.18.0 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.11 3_cp311 conda-forge
pytng 0.3.0 py311h48d25d0_0 conda-forge
pytz 2023.3 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py311hd4cff14_5 conda-forge
pyzmq 25.1.0 py311h75c88c4_0 conda-forge
rdkit 2023.03.2 py311hc21844d_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.30.0 pyhd8ed1ab_0 conda-forge
reportlab 4.0.4 py311h459d7ec_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.9.2 py311h46250e7_0 conda-forge
s2n 1.3.46 h06160fa_0 conda-forge
scikit-learn 1.3.0 py311hc009520_0 conda-forge
scipy 1.11.1 py311h64a7726_0 conda-forge
seaborn 0.12.2 hd8ed1ab_0 conda-forge
seaborn-base 0.12.2 pyhd8ed1ab_0 conda-forge
send2trash 1.8.2 pyh41d4057_0 conda-forge
setuptools 68.0.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
sqlalchemy 2.0.19 py311h459d7ec_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
statsmodels 0.14.0 py311h1f0f07a_1 conda-forge
terminado 0.17.1 pyh41d4057_0 conda-forge
threadpoolctl 3.2.0 pyha21a80b_0 conda-forge
tidynamics 1.1.2 pyhd8ed1ab_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tinydb 4.8.0 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.3.2 py311h459d7ec_0 conda-forge
tqdm 4.65.0 pyhd8ed1ab_1 conda-forge
traitlets 5.9.0 pyhd8ed1ab_0 conda-forge
typing-extensions 4.7.1 hd8ed1ab_0 conda-forge
typing_extensions 4.7.1 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.0.4 pyhd8ed1ab_0 conda-forge
validators 0.20.0 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.6.1 pyhd8ed1ab_0 conda-forge
wheel 0.41.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.8 pyhd8ed1ab_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.6 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.16.2 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstd 1.5.2 hfc55251_7 conda-forge

This is pip freeze:

AmberUtils==21.0
anyio @ file:///home/conda/feedstock_root/build_artifacts/anyio_1688651106312/work/dist
argon2-cffi @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi_1640817743617/work
argon2-cffi-bindings @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi-bindings_1666850842190/work
arrow @ file:///home/conda/feedstock_root/build_artifacts/arrow_1662382474514/work
asttokens @ file:///home/conda/feedstock_root/build_artifacts/asttokens_1670263926556/work
astunparse @ file:///home/conda/feedstock_root/build_artifacts/astunparse_1610696312422/work
async-lru @ file:///home/conda/feedstock_root/build_artifacts/async-lru_1688997201545/work
attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1683424013410/work
Babel @ file:///home/conda/feedstock_root/build_artifacts/babel_1677767029043/work
backcall @ file:///home/conda/feedstock_root/build_artifacts/backcall_1592338393461/work
backports.functools-lru-cache @ file:///home/conda/feedstock_root/build_artifacts/backports.functools_lru_cache_1687772187254/work
beautifulsoup4 @ file:///home/conda/feedstock_root/build_artifacts/beautifulsoup4_1680888073205/work
biopython @ file:///home/conda/feedstock_root/build_artifacts/biopython_1676639086886/work
biotite @ file:///home/conda/feedstock_root/build_artifacts/biotite_1684073136582/work
bleach @ file:///home/conda/feedstock_root/build_artifacts/bleach_1674535352125/work
Brotli @ file:///home/conda/feedstock_root/build_artifacts/brotli-split_1687884021435/work
bson==0.5.9
cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work
cachetools @ file:///home/conda/feedstock_root/build_artifacts/cachetools_1688227447901/work
certifi==2023.7.22
cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1671179355965/work
cftime @ file:///home/conda/feedstock_root/build_artifacts/cftime_1666833839601/work
charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1688813409104/work
colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work
comm @ file:///home/conda/feedstock_root/build_artifacts/comm_1679481329611/work
contourpy @ file:///home/conda/feedstock_root/build_artifacts/contourpy_1686733806710/work
cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1635519461629/work
Cython @ file:///home/conda/feedstock_root/build_artifacts/cython_1689612348085/work
debugpy @ file:///home/conda/feedstock_root/build_artifacts/debugpy_1680755454898/work
decorator @ file:///home/conda/feedstock_root/build_artifacts/decorator_1641555617451/work
defusedxml @ file:///home/conda/feedstock_root/build_artifacts/defusedxml_1615232257335/work
dgl==1.1.2
edgembar==0.2
entrypoints @ file:///home/conda/feedstock_root/build_artifacts/entrypoints_1643888246732/work
espaloma-charge==0.0.8
exceptiongroup @ file:///home/conda/feedstock_root/build_artifacts/exceptiongroup_1688381075899/work
executing @ file:///home/conda/feedstock_root/build_artifacts/executing_1667317341051/work
fasteners @ file:///home/conda/feedstock_root/build_artifacts/fasteners_1643971550063/work
fastjsonschema @ file:///home/conda/feedstock_root/build_artifacts/python-fastjsonschema_1690055433477/work/dist
filelock==3.12.4
flit_core @ file:///home/conda/feedstock_root/build_artifacts/flit-core_1684084314667/work/source/flit_core
fonttools @ file:///home/conda/feedstock_root/build_artifacts/fonttools_1689965455159/work
fqdn @ file:///home/conda/feedstock_root/build_artifacts/fqdn_1638810296540/work/dist
freetype-py @ file:///home/conda/feedstock_root/build_artifacts/freetype-py_1650983368720/work
fsspec==2023.9.2
graypy==2.1.0
greenlet @ file:///home/conda/feedstock_root/build_artifacts/greenlet_1684082930824/work
GridDataFormats @ file:///home/conda/feedstock_root/build_artifacts/griddataformats_1653584770598/work
gsd @ file:///home/conda/feedstock_root/build_artifacts/gsd_1684751375488/work
h5py @ file:///home/conda/feedstock_root/build_artifacts/h5py_1687827978030/work
hydride @ file:///home/conda/feedstock_root/build_artifacts/hydride_1680070433457/work
idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1663625384323/work
importlib-metadata @ file:///home/conda/feedstock_root/build_artifacts/importlib-metadata_1688754491823/work
importlib-resources @ file:///home/conda/feedstock_root/build_artifacts/importlib_resources_1689017639396/work
ipykernel @ file:///home/conda/feedstock_root/build_artifacts/ipykernel_1690311270420/work
ipython @ file:///home/conda/feedstock_root/build_artifacts/ipython_1685727741709/work
ipywidgets @ file:///home/conda/feedstock_root/build_artifacts/ipywidgets_1688489611428/work
isoduration @ file:///home/conda/feedstock_root/build_artifacts/isoduration_1638811571363/work/dist
jedi @ file:///home/conda/feedstock_root/build_artifacts/jedi_1669134318875/work
Jinja2 @ file:///home/conda/feedstock_root/build_artifacts/jinja2_1654302431367/work
joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1688155275339/work
json5 @ file:///home/conda/feedstock_root/build_artifacts/json5_1688248289187/work
jsonpointer==2.0
jsonschema @ file:///home/conda/feedstock_root/build_artifacts/jsonschema-meta_1689687135513/work
jsonschema-specifications @ file:///home/conda/feedstock_root/build_artifacts/jsonschema-specifications_1689701150890/work
jupyter-events @ file:///home/conda/feedstock_root/build_artifacts/jupyter_events_1690301630599/work
jupyter-lsp @ file:///home/conda/feedstock_root/build_artifacts/jupyter-lsp-meta_1685453365113/work/jupyter-lsp
jupyter_client @ file:///home/conda/feedstock_root/build_artifacts/jupyter_client_1687700988094/work
jupyter_core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_core_1686775603054/work
jupyter_server @ file:///home/conda/feedstock_root/build_artifacts/jupyter_server_1687869799272/work
jupyter_server_terminals @ file:///home/conda/feedstock_root/build_artifacts/jupyter_server_terminals_1673491454549/work
jupyterlab @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_1689253413907/work
jupyterlab-pygments @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_pygments_1649936611996/work
jupyterlab-widgets @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_widgets_1688489450369/work
jupyterlab_server @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_server_1690205927615/work
kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/kiwisolver_1666805746048/work
lxml @ file:///home/conda/feedstock_root/build_artifacts/lxml_1688564718715/work
MarkupSafe @ file:///home/conda/feedstock_root/build_artifacts/markupsafe_1685769042879/work
matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1688684873414/work
matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1660814786464/work
MDAnalysis @ file:///home/conda/feedstock_root/build_artifacts/mdanalysis_1687093257719/work
mdtraj @ file:///home/conda/feedstock_root/build_artifacts/mdtraj_1690062486135/work
mistune @ file:///home/conda/feedstock_root/build_artifacts/mistune_1686313613819/work/dist
MMPBSA.py==16.0
mmtf-python @ file:///home/conda/feedstock_root/build_artifacts/mmtf-python_1657095270742/work
mpmath==1.3.0
mrcfile @ file:///home/conda/feedstock_root/build_artifacts/mrcfile_1663870629802/work
msgpack @ file:///home/conda/feedstock_root/build_artifacts/msgpack-python_1678312711771/work
munkres==1.1.4
nanome==0.40.5
nbclient @ file:///home/conda/feedstock_root/build_artifacts/nbclient_1684790896106/work
nbconvert @ file:///home/conda/feedstock_root/build_artifacts/nbconvert-meta_1690313290323/work
nbformat @ file:///home/conda/feedstock_root/build_artifacts/nbformat_1688996247388/work
ndfes==1.8
nest-asyncio @ file:///home/conda/feedstock_root/build_artifacts/nest-asyncio_1664684991461/work
netCDF4 @ file:///home/conda/feedstock_root/build_artifacts/netcdf4_1687961117129/work
networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1680692919326/work
notebook @ file:///home/conda/feedstock_root/build_artifacts/notebook_1689782914785/work
notebook_shim @ file:///home/conda/feedstock_root/build_artifacts/notebook-shim_1682360583588/work
numexpr @ file:///home/conda/feedstock_root/build_artifacts/numexpr_1689950413703/work
numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1688887041365/work
nvidia-cublas-cu12==12.1.3.1
nvidia-cuda-cupti-cu12==12.1.105
nvidia-cuda-nvrtc-cu12==12.1.105
nvidia-cuda-runtime-cu12==12.1.105
nvidia-cudnn-cu12==8.9.2.26
nvidia-cufft-cu12==11.0.2.54
nvidia-curand-cu12==10.3.2.106
nvidia-cusolver-cu12==11.4.5.107
nvidia-cusparse-cu12==12.1.0.106
nvidia-nccl-cu12==2.18.1
nvidia-nvjitlink-cu12==12.2.140
nvidia-nvtx-cu12==12.1.105
openff-amber-ff-ports @ file:///home/conda/feedstock_root/build_artifacts/openff-amber-ff-ports_1655128401762/work
openff-interchange @ file:///home/conda/feedstock_root/build_artifacts/openff-interchange-split_1690322666132/work
openff-models @ file:///home/conda/feedstock_root/build_artifacts/openff-models_1689355190664/work
openff-toolkit @ file:///home/conda/feedstock_root/build_artifacts/openff-toolkit-split_1689355146349/work
openff-units @ file:///home/conda/feedstock_root/build_artifacts/openff-units_1686799508759/work
openff-utilities @ file:///home/conda/feedstock_root/build_artifacts/openff-utilities_1689347316053/work
openforcefields @ file:///home/conda/feedstock_root/build_artifacts/openff-forcefields_1686950394063/work
OpenMM==8.0.0
openmmforcefields @ file:///home/conda/feedstock_root/build_artifacts/openmmforcefields_1664226607868/work
overrides @ file:///home/conda/feedstock_root/build_artifacts/overrides_1666057828264/work
packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1681337016113/work
packmol-memgen==2023.2.24
pandas @ file:///home/conda/feedstock_root/build_artifacts/pandas_1688740512823/work
pandocfilters @ file:///home/conda/feedstock_root/build_artifacts/pandocfilters_1631603243851/work
panedr @ file:///home/conda/feedstock_root/build_artifacts/panedr_1672953016377/work
ParmEd @ file:///home/conda/feedstock_root/build_artifacts/parmed_1681216004601/work
parso @ file:///home/conda/feedstock_root/build_artifacts/parso_1638334955874/work
patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1665356157073/work
pbr @ file:///home/conda/feedstock_root/build_artifacts/pbr_1673485161019/work
pdb4amber==22.0
pdbfixer @ file:///home/conda/feedstock_root/build_artifacts/pdbfixer_1684358331657/work
pexpect @ file:///home/conda/feedstock_root/build_artifacts/pexpect_1667297516076/work
pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work
Pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1688255851102/work
Pint @ file:///home/conda/feedstock_root/build_artifacts/pint_1683140320592/work
pkgutil_resolve_name @ file:///home/conda/feedstock_root/build_artifacts/pkgutil-resolve-name_1633981968097/work
platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1689538620473/work
pooch @ file:///home/conda/feedstock_root/build_artifacts/pooch_1679580333621/work
prometheus-client @ file:///home/conda/feedstock_root/build_artifacts/prometheus_client_1689032443210/work
prompt-toolkit @ file:///home/conda/feedstock_root/build_artifacts/prompt-toolkit_1688565951714/work
psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1681775010077/work
ptyprocess @ file:///home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
pure-eval @ file:///home/conda/feedstock_root/build_artifacts/pure_eval_1642875951954/work
py-cpuinfo @ file:///home/conda/feedstock_root/build_artifacts/py-cpuinfo_1666774466606/work
pycairo==1.24.0
pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1636257122734/work
pydantic @ file:///home/conda/feedstock_root/build_artifacts/pydantic_1689225027416/work
pyedr @ file:///home/conda/feedstock_root/build_artifacts/pyedr_1671541325533/work
Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1681904169130/work
pyMSMT==22.0
pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1652235407899/work
PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1661604839144/work
python-constraint==1.4.0
python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work
python-json-logger @ file:///home/conda/feedstock_root/build_artifacts/python-json-logger_1677079630776/work
pytng @ file:///home/conda/feedstock_root/build_artifacts/pytng_1671537646388/work
pytraj==2.0.6
pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1680088766131/work
PyYAML @ file:///home/conda/feedstock_root/build_artifacts/pyyaml_1666772382226/work
pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1685519251831/work
rdkit==2023.3.3
referencing @ file:///home/conda/feedstock_root/build_artifacts/referencing_1689701127998/work
reportlab @ file:///home/conda/feedstock_root/build_artifacts/reportlab_1688076703819/work
requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1684774241324/work
rfc3339-validator @ file:///home/conda/feedstock_root/build_artifacts/rfc3339-validator_1638811747357/work
rfc3986-validator @ file:///home/conda/feedstock_root/build_artifacts/rfc3986-validator_1598024191506/work
rlPyCairo @ file:///home/conda/feedstock_root/build_artifacts/rlpycairo_1687519531733/work
rpds-py @ file:///home/conda/feedstock_root/build_artifacts/rpds-py_1689705080364/work
sander==22.0
scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1688116542774/work
scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy-split_1687995550978/work/base/dist/scipy-1.11.1-cp311-cp311-linux_x86_64.whl#sha256=c0479f8a06a309e2c519a2da071412cb0e8b44464ffedffd29c463a7fcdabfa4
seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1672497695270/work
Send2Trash @ file:///home/conda/feedstock_root/build_artifacts/send2trash_1682601222253/work
six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work
smirnoff99frosst @ file:///home/conda/feedstock_root/build_artifacts/smirnoff99frosst_1610626268593/work
sniffio @ file:///home/conda/feedstock_root/build_artifacts/sniffio_1662051266223/work
soupsieve @ file:///home/conda/feedstock_root/build_artifacts/soupsieve_1658207591808/work
SQLAlchemy @ file:///home/conda/feedstock_root/build_artifacts/sqlalchemy_1689437294783/work
stack-data @ file:///home/conda/feedstock_root/build_artifacts/stack_data_1669632077133/work
statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1683305554499/work
sympy==1.12
tables @ file:///home/conda/feedstock_root/build_artifacts/pytables_1687843143673/work
tblib==1.7.0
terminado @ file:///home/conda/feedstock_root/build_artifacts/terminado_1670253674810/work
threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1689261241048/work
tidynamics @ file:///home/conda/feedstock_root/build_artifacts/tidynamics_1689080725019/work
tinycss2 @ file:///home/conda/feedstock_root/build_artifacts/tinycss2_1666100256010/work
tinydb @ file:///home/conda/feedstock_root/build_artifacts/tinydb_1686607385119/work
tomli @ file:///home/conda/feedstock_root/build_artifacts/tomli_1644342247877/work
torch==2.1.0
tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1684150209296/work
tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1677948868469/work
traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1675110562325/work
triton==2.1.0
typing-utils @ file:///home/conda/feedstock_root/build_artifacts/typing_utils_1622899189314/work
typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1688315532570/work
tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1680081134351/work
uri-template @ file:///home/conda/feedstock_root/build_artifacts/uri-template_1688655812972/work/dist
urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1689789803562/work
validators @ file:///home/conda/feedstock_root/build_artifacts/validators_1676837160772/work
wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1673864653149/work
webcolors @ file:///home/conda/feedstock_root/build_artifacts/webcolors_1679900785843/work
webencodings==0.5.1
websocket-client @ file:///home/conda/feedstock_root/build_artifacts/websocket-client_1687789148259/work
widgetsnbextension @ file:///home/conda/feedstock_root/build_artifacts/widgetsnbextension_1688504439014/work
xmltodict @ file:///home/conda/feedstock_root/build_artifacts/xmltodict_1652020822199/work
zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1689374466814/work

[nezix]

Should I install a rdkit package older than 2022 then ?