Molecule.from_file() causes segmentation fault when used alongside ccdc modules

[whmidgley]

Describe the bug
openff.toolkit Molecule.from_file() causes segmentation fault when used alongside ccdc modules

To Reproduce
from openff.toolkit import Molecule
from ccdc.protein import Protein

mol = Molecule.from_file("mol.sdf")

Output
Segmentation fault

Python quits

Computing environment (please complete the following information):

• Debian

• Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 2.1.0 pyhd8ed1ab_1 conda-forge
aiohappyeyeballs 2.4.4 pyhd8ed1ab_1 conda-forge
aiohttp 3.11.9 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
amberlite 22.0 pypi_0 pypi
ambertools 22.5 py39h9e491d2_0 conda-forge
amberutils 21.0 pypi_0 pypi
annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge
anyio 4.8.0 pyhd8ed1ab_0 conda-forge
apsw 3.45.2.0 py39h21eaaa1_1 conda-forge
archspec 0.2.3 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_1 conda-forge
argon2-cffi-bindings 21.2.0 py39h8cd3c5a_5 conda-forge
arpack 3.7.0 hdefa2d7_2 conda-forge
arrow 1.3.0 pyhd8ed1ab_1 conda-forge
asttokens 3.0.0 pyhd8ed1ab_1 conda-forge
astunparse 1.6.3 pyhd8ed1ab_3 conda-forge
async-lru 2.0.4 pyhd8ed1ab_1 conda-forge
async-timeout 5.0.1 pyhd8ed1ab_1 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 24.2.0 pypi_0 pypi
aws-c-auth 0.7.11 h0b4cabd_1 conda-forge
aws-c-cal 0.6.9 h14ec70c_3 conda-forge
aws-c-common 0.9.12 hd590300_0 conda-forge
aws-c-compression 0.2.17 h572eabf_8 conda-forge
aws-c-event-stream 0.4.1 h97bb272_2 conda-forge
aws-c-http 0.8.0 h9129f04_2 conda-forge
aws-c-io 0.14.0 hf8f278a_1 conda-forge
aws-c-mqtt 0.10.1 h2b97f5f_0 conda-forge
aws-c-s3 0.4.9 hca09fc5_0 conda-forge
aws-c-sdkutils 0.1.13 h572eabf_1 conda-forge
aws-checksums 0.1.17 h572eabf_7 conda-forge
aws-crt-cpp 0.26.0 h04327c0_8 conda-forge
aws-sdk-cpp 1.11.210 hba3e011_10 conda-forge
babel 2.16.0 pyhd8ed1ab_1 conda-forge
beautifulsoup4 4.12.3 pyha770c72_1 conda-forge
biopython 1.84 pypi_0 pypi
bleach 6.2.0 pyhd8ed1ab_3 conda-forge
bleach-with-css 6.2.0 hd8ed1ab_3 conda-forge
blinker 1.9.0 pyhff2d567_0 conda-forge
blosc 1.21.5 h0f2a231_0 conda-forge
boltons 24.0.0 pyhd8ed1ab_1 conda-forge
boost 1.78.0 py39hda80f44_5 conda-forge
boost-cpp 1.78.0 h2c5509c_4 conda-forge
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py39hf88036b_2 conda-forge
bson 0.5.10 pyhd8ed1ab_0 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.4 hb9d3cd8_0 conda-forge
c-blosc2 2.15.2 h68e2383_0 conda-forge
ca-certificates 2024.12.31 h06a4308_0
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.5.0 pyhd8ed1ab_1 conda-forge
cairo 1.18.0 hbb29018_2 conda-forge
certifi 2024.12.14 py39h06a4308_0
cffi 1.17.1 py39h15c3d72_0 conda-forge
chardet 5.2.0 py39hf3d152e_2 conda-forge
charset-normalizer 3.4.0 pypi_0 pypi
click 8.1.7 pypi_0 pypi
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comm 0.2.2 pyhd8ed1ab_1 conda-forge
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ipykernel 6.29.5 pyh3099207_0 conda-forge
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ipywidgets 8.1.5 pyhd8ed1ab_1 conda-forge
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jedi 0.19.2 pyhd8ed1ab_1 conda-forge
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pytraj 2.0.6 pypi_0 pypi
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_1 conda-forge
pyyaml 6.0.2 py39h8cd3c5a_1 conda-forge
pyzmq 26.2.0 py39h4e4fb57_3 conda-forge
qcelemental 0.28.0 pyhd8ed1ab_1 conda-forge
qcengine 0.30.0 pyhd8ed1ab_0 conda-forge
qcportal 0.57 pyhd8ed1ab_0 conda-forge
qhull 2020.2 h434a139_5 conda-forge
rdkit 2023.03.3 py39h55a5abb_0 conda-forge
rdma-core 55.0 h5888daf_0 conda-forge
re2 2023.09.01 h7f4b329_1 conda-forge
readline 8.2 h5eee18b_0
referencing 0.35.1 pyhd8ed1ab_1 conda-forge
reportlab 4.2.5 py39h8cd3c5a_0 conda-forge
reproc 14.2.5.post0 hb9d3cd8_0 conda-forge
reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
requests-oauthlib 2.0.0 pyhd8ed1ab_1 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_1 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rich 13.9.4 pyhd8ed1ab_1 conda-forge
rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.22.3 py39he612d8f_0 conda-forge
rsa 4.9 pyhd8ed1ab_1 conda-forge
ruamel-yaml 0.17.40 pypi_0 pypi
ruamel.yaml 0.18.10 py39h8cd3c5a_0 conda-forge
ruamel.yaml.clib 0.2.8 py39h8cd3c5a_1 conda-forge
s2n 1.4.1 h06160fa_0 conda-forge
sander 22.0 pypi_0 pypi
scikit-learn 1.5.1 pypi_0 pypi
scipy 1.13.1 py39haf93ffa_0 conda-forge
send2trash 1.8.3 pyh0d859eb_1 conda-forge
setuptools 75.6.0 pypi_0 pypi
simdjson 3.11.5 h84d6215_0 conda-forge
six 1.16.0 pypi_0 pypi
sleef 3.7 h1b44611_2 conda-forge
smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge
snappy 1.1.10 hdb0a2a9_1 conda-forge
sniffio 1.3.1 pyhd8ed1ab_1 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
spdlog 1.15.0 h10c9db5_0 conda-forge
sqlalchemy 2.0.37 py39h8cd3c5a_0 conda-forge
sqlite 3.45.2 h2c6b66d_0 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
sympy 1.13.3 pypyh2585a3b_103 conda-forge
sysroot_linux-64 2.17 h0157908_18 conda-forge
tabulate 0.9.0 pyhd8ed1ab_2 conda-forge
tblib 3.0.0 pyhd8ed1ab_1 conda-forge
tensorboard 2.9.0 pypi_0 pypi
tensorboard-data-server 0.6.1 pypi_0 pypi
tensorboard-plugin-wit 1.8.1 pypi_0 pypi
tensorflow 2.9.1 pypi_0 pypi
tensorflow-base 2.15.0 cpu_py39he1df281_2 conda-forge
tensorflow-estimator 2.9.0 pypi_0 pypi
termcolor 2.5.0 pyhd8ed1ab_1 conda-forge
terminado 0.18.1 pyh0d859eb_0 conda-forge
threadpoolctl 3.5.0 pypi_0 pypi
tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tinydb 4.8.2 pyhd8ed1ab_1 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
toolz 1.0.0 pyhd8ed1ab_1 conda-forge
torchdata 0.7.1 py39h881704f_1 conda-forge
torchmetrics 1.6.1 pyhd8ed1ab_0 conda-forge
tornado 6.4.2 py39h8cd3c5a_0 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
types-python-dateutil 2.9.0.20241206 pyhd8ed1ab_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_1 conda-forge
typing_extensions 4.12.2 pyha770c72_1 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2024b h04d1e81_0
ucx 1.15.0 ha691c75_8 conda-forge
unicodedata2 15.1.0 pypi_0 pypi
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
urllib3 2.2.3 pypi_0 pypi
validators 0.34.0 pyhd8ed1ab_1 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webcolors 24.11.1 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
werkzeug 3.1.3 pyhd8ed1ab_1 conda-forge
wheel 0.45.1 pypi_0 pypi
widgetsnbextension 4.0.13 pyhd8ed1ab_1 conda-forge
wrapt 1.17.0 pypi_0 pypi
xgboost 2.1.1 pypi_0 pypi
xlsxwriter 3.2.0 pypi_0 pypi
xmltodict 0.14.2 pyhd8ed1ab_1 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.5 he73a12e_0 conda-forge
xorg-libx11 1.8.10 h4f16b4b_1 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xz 5.4.6 h5eee18b_1
yaml 0.2.5 h7f98852_2 conda-forge
yaml-cpp 0.8.0 h59595ed_0 conda-forge
yarl 1.18.0 pypi_0 pypi
zeromq 4.3.5 h3b0a872_7 conda-forge
zict 3.0.0 pyhd8ed1ab_1 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.2.3 h7955e40_0 conda-forge
zstandard 0.23.0 py39h08a7858_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge

Additional context
If you load the file before importing ccdc, it works fine and can be run again after loading ccdc

[j-wags]

Thanks for writing in @whmidgley. I tried to reproduce this issue but I don't have a CCDC license, so while I could install the conda package the python import wouldn't work. I'm contacting the CCDC developers to coordinate a fix and will post updates here.