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choderalab / espaloma_charge

Standalone charge assignment from Espaloma framework.
MIT License
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KeyError in HYBRIDIZATION_RDKIT #28

Open nezix opened 8 months ago

nezix commented 8 months ago

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 commented 8 months ago

@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 commented 8 months ago

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 commented 8 months ago

Looks like it should be 2022.09.1 or later.

nezix commented 8 months ago

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

jchodera commented 8 months ago

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 commented 8 months ago

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 commented 8 months ago

Should I install a rdkit package older than 2022 then ?