Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Unable to load some SDFs with RDKit backend #1909

Closed
j-wags opened this issue Jul 17, 2024 · 3 comments
Closed

Unable to load some SDFs with RDKit backend #1909

j-wags opened this issue Jul 17, 2024 · 3 comments

Comments

@j-wags
Copy link
Member

j-wags commented Jul 17, 2024 •
edited
Loading

Describe the bug
Using the RDKit backend (2024.03.4), trying to load this molecule (from the bespokefit test suite) crashes python.

bace.sdf.tgz

This only happens with the RDKit backend.

To Reproduce

from openff.toolkit import Molecule
Molecule.from_file("bace.sdf")

Output
zsh: illegal hardware instruction python

Computing environment (please complete the following information):

  • Mac OSX 14
Output of running `conda list` 
# packages in environment at /Users/jeffreywagner/conda/envs/temp:
#
# Name                    Version                   Build  Channel
ambertools                23.6            cuda_None_nompi_py311h9ef6679_105    conda-forge
amberutils                21.0                     pypi_0    pypi
amqp                      5.2.0              pyhd8ed1ab_1    conda-forge
annotated-types           0.7.0              pyhd8ed1ab_0    conda-forge
anyio                     4.4.0              pyhd8ed1ab_0    conda-forge
appnope                   0.1.4              pyhd8ed1ab_0    conda-forge
argcomplete               3.4.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py311h2725bcf_4    conda-forge
arpack                    3.9.1           nompi_hf81eadf_101    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
async-timeout             4.0.3              pyhd8ed1ab_0    conda-forge
attrs                     23.2.0             pyh71513ae_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
backports.zoneinfo        0.2.1           py311h6eed73b_8    conda-forge
basis_set_exchange        0.10               pyhd8ed1ab_1    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
billiard                  4.2.0           py311he705e18_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.6               h7d75f6d_0    conda-forge
boto3                     1.34.144           pyhd8ed1ab_0    conda-forge
botocore                  1.34.144        pyge310_1234567_0    conda-forge
brotli                    1.1.0                h0dc2134_1    conda-forge
brotli-bin                1.1.0                h0dc2134_1    conda-forge
brotli-python             1.1.0           py311hdf8f085_1    conda-forge
bson                      0.5.9                      py_0    conda-forge
bzip2                     1.0.8                hfdf4475_7    conda-forge
c-ares                    1.32.2               h51dda26_0    conda-forge
c-blosc2                  2.15.0               hb9356d3_1    conda-forge
ca-certificates           2024.7.4             h8857fd0_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.4.0              pyhd8ed1ab_0    conda-forge
cairo                     1.18.0               h9f650ed_2    conda-forge
celery                    5.3.6              pyhd8ed1ab_0    conda-forge
certifi                   2024.7.4           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py311hc0b63fd_0    conda-forge
chardet                   5.2.0           py311h6eed73b_1    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
chemper                   1.0.1              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
click-didyoumean          0.3.1              pyhd8ed1ab_0    conda-forge
click-option-group        0.5.6              pyhd8ed1ab_0    conda-forge
click-plugins             1.1.1                      py_0    conda-forge
click-repl                0.3.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.1           py311h1d816ee_0    conda-forge
coverage                  7.6.0           py311h72ae277_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
debugpy                   1.8.2           py311hbafa61a_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dnspython                 2.6.1              pyhd8ed1ab_1    conda-forge
edgembar                  0.2                      pypi_0    pypi
email-validator           2.2.0              pyhd8ed1ab_0    conda-forge
email_validator           2.2.0                hd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_0    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
expat                     2.6.2                h73e2aa4_0    conda-forge
fastapi                   0.111.1            pyhd8ed1ab_0    conda-forge
fastapi-cli               0.0.4              pyhd8ed1ab_0    conda-forge
fftw                      3.3.10          nompi_h292e606_110    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                 h77eed37_2    conda-forge
fontconfig                2.14.2               h5bb23bf_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.53.1          py311h72ae277_0    conda-forge
forcebalance              1.9.6           py311h7c2fe40_2    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               h60636b9_2    conda-forge
freetype-py               2.3.0              pyhd8ed1ab_0    conda-forge
future                    1.0.0              pyhd8ed1ab_0    conda-forge
geometric                 1.0.2              pyhd8ed1ab_0    conda-forge
greenlet                  3.0.3           py311hdd0406b_0    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
hdf4                      4.2.15               h8138101_7    conda-forge
hdf5                      1.14.3          nompi_h687a608_105    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.5              pyhd8ed1ab_0    conda-forge
httpx                     0.27.0             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       73.2                 hf5e326d_0    conda-forge
idna                      3.7                pyhd8ed1ab_0    conda-forge
importlib-metadata        8.0.0              pyha770c72_0    conda-forge
importlib_metadata        8.0.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.0              pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.5             pyh57ce528_0    conda-forge
ipython                   8.26.0             pyh707e725_0    conda-forge
ipywidgets                8.1.3              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
jmespath                  1.0.1              pyhd8ed1ab_0    conda-forge
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
json5                     0.9.25             pyhd8ed1ab_0    conda-forge
jsonpointer               3.0.0           py311h6eed73b_0    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.23.0               hd8ed1ab_0    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.2              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2           py311h6eed73b_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.14.2             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.2.3              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.27.3             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.11             pyhd8ed1ab_0    conda-forge
khronos-opencl-icd-loader 2023.04.17           h37ebe6b_1    conda-forge
kiwisolver                1.4.5           py311h5fe6e05_1    conda-forge
kombu                     5.3.7           py311h6eed73b_0    conda-forge
krb5                      1.21.3               h37d8d59_0    conda-forge
lcms2                     2.16                 ha2f27b4_0    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libaec                    1.1.3                h73e2aa4_0    conda-forge
libblas                   3.9.0           22_osx64_openblas    conda-forge
libboost                  1.84.0               h739af76_3    conda-forge
libboost-python           1.84.0          py311h49c5ead_3    conda-forge
libbrotlicommon           1.1.0                h0dc2134_1    conda-forge
libbrotlidec              1.1.0                h0dc2134_1    conda-forge
libbrotlienc              1.1.0                h0dc2134_1    conda-forge
libcblas                  3.9.0           22_osx64_openblas    conda-forge
libcurl                   8.8.0                hf9fcc65_1    conda-forge
libcxx                    18.1.8               hef8daea_0    conda-forge
libdeflate                1.20                 h49d49c5_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 h10d778d_2    conda-forge
libexpat                  2.6.2                h73e2aa4_0    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           13_2_0_h97931a8_3    conda-forge
libgfortran5              13.2.0               h2873a65_3    conda-forge
libglib                   2.80.3               h736d271_1    conda-forge
libiconv                  1.17                 hd75f5a5_2    conda-forge
libintl                   0.22.5               h5ff76d1_2    conda-forge
libjpeg-turbo             3.0.0                h0dc2134_1    conda-forge
liblapack                 3.9.0           22_osx64_openblas    conda-forge
libnetcdf                 4.9.2           nompi_h7334405_114    conda-forge
libnghttp2                1.58.0               h64cf6d3_1    conda-forge
libopenblas               0.3.27          openmp_h8869122_1    conda-forge
libpng                    1.6.43               h92b6c6a_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsqlite                 3.46.0               h1b8f9f3_0    conda-forge
libssh2                   1.11.0               hd019ec5_0    conda-forge
libtiff                   4.6.0                h129831d_3    conda-forge
libwebp-base              1.4.0                h10d778d_0    conda-forge
libxcb                    1.16                 h0dc2134_0    conda-forge
libxml2                   2.12.7               hc603aa4_3    conda-forge
libxslt                   1.1.39               h03b04e6_0    conda-forge
libzip                    1.10.1               hc158999_3    conda-forge
libzlib                   1.3.1                h87427d6_1    conda-forge
llvm-openmp               18.1.8               h15ab845_0    conda-forge
lxml                      5.2.2           py311hf8c4076_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.5           py311he705e18_0    conda-forge
matplotlib-base           3.9.1           py311hf31e254_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mctc-lib                  0.3.1                h5f0aba5_0    conda-forge
mda-xdrlib                0.2.0              pyhd8ed1ab_0    conda-forge
mdtraj                    1.10.0          py311hd77083e_0    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
msgpack-python            1.0.8           py311h46c8309_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.5                  h5846eda_0    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.1           nompi_h3a6982b_104    conda-forge
networkx                  3.3                pyhd8ed1ab_1    conda-forge
notebook                  7.2.1              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
numexpr                   2.10.0          py311hfdcbad3_0    conda-forge
numpy                     1.26.4          py311hc43a94b_0    conda-forge
ocl_icd_wrapper_apple     1.0.0                hbcb3906_0    conda-forge
openff-amber-ff-ports     0.0.4              pyhca7485f_0    conda-forge
openff-bespokefit         0.3.0+10.g1d5d98a           dev_0    <develop>
openff-forcefields        2024.04.0          pyhca7485f_0    conda-forge
openff-fragmenter-base    0.2.2              pyhd8ed1ab_0    conda-forge
openff-interchange        0.3.27             pyhd8ed1ab_0    conda-forge
openff-interchange-base   0.3.27             pyhd8ed1ab_0    conda-forge
openff-models             0.1.2              pyhca7485f_0    conda-forge
openff-qcsubmit           0.50.3             pyhd8ed1ab_0    conda-forge
openff-toolkit            0.15.2             pyhd8ed1ab_0    conda-forge
openff-toolkit-base       0.15.2             pyhd8ed1ab_0    conda-forge
openff-units              0.2.2              pyhca7485f_0    conda-forge
openff-utilities          0.1.12             pyhd8ed1ab_0    conda-forge
openjpeg                  2.5.2                h7310d3a_0    conda-forge
openmm                    8.1.1           py311h2827df7_1_khronos    conda-forge
openssl                   3.3.1                h87427d6_1    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
packmol-memgen            2024.2.9                 pypi_0    pypi
pandas                    2.2.2           py311hfdcbad3_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
panedr                    0.8.0              pyhd8ed1ab_0    conda-forge
parmed                    4.2.2           py311hd39e593_1    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
pcre2                     10.44                h7634a1b_0    conda-forge
pdb4amber                 22.0                     pypi_0    pypi
perl                      5.32.1          7_h10d778d_perl5    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.4.0          py311h2755ac0_0    conda-forge
pint                      0.23               pyhd8ed1ab_1    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pixman                    0.43.4               h73e2aa4_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.2.2              pyhd8ed1ab_0    conda-forge
pluggy                    1.5.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.20.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.47             pyha770c72_0    conda-forge
prompt_toolkit            3.0.47               hd8ed1ab_0    conda-forge
psutil                    6.0.0           py311h72ae277_0    conda-forge
pthread-stubs             0.4               hc929b4f_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                   1.26.1          py311hb544ce8_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pydantic                  2.8.2              pyhd8ed1ab_0    conda-forge
pydantic-core             2.20.1          py311h295b1db_0    conda-forge
pyedr                     0.8.0              pyhd8ed1ab_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.8.0              pyhd8ed1ab_1    conda-forge
pymbar                    3.1.1           py311he5d6b3b_3    conda-forge
pymsmt                    22.0                     pypi_0    pypi
pyobjc-core               10.3.1          py311h9d23797_0    conda-forge
pyobjc-framework-cocoa    10.3.1          py311h9d23797_0    conda-forge
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.9.2           py311h85db115_3    conda-forge
pytest                    7.4.4              pyhd8ed1ab_0    conda-forge
pytest-asyncio            0.23.7             pyhd8ed1ab_0    conda-forge
pytest-celery             0.0.0a1            pyh9f0ad1d_1    conda-forge
pytest-cov                5.0.0              pyhd8ed1ab_0    conda-forge
python                    3.11.9          h657bba9_0_cpython    conda-forge
python-constraint         1.4.0                      py_0    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.20.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-multipart          0.0.9              pyhd8ed1ab_0    conda-forge
python-tzdata             2024.1             pyhd8ed1ab_0    conda-forge
python_abi                3.11                    4_cp311    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py311h2725bcf_1    conda-forge
pyzmq                     26.0.3          py311h89e2aaa_0    conda-forge
qcelemental               0.28.0             pyhd8ed1ab_0    conda-forge
qcengine                  0.30.0             pyhd8ed1ab_0    conda-forge
qcportal                  0.53               pyhd8ed1ab_0    conda-forge
qhull                     2020.2               h3c5361c_5    conda-forge
rdkit                     2024.03.4       py311ha2b1ff4_1    conda-forge
readline                  8.2                  h9e318b2_1    conda-forge
redis-py                  5.0.7              pyhd8ed1ab_0    conda-forge
redis-server              7.2.5                h2d65c12_0    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
regex                     2024.5.15       py311h72ae277_0    conda-forge
reportlab                 4.2.2           py311h72ae277_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
requests-mock             1.12.1             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rich                      13.7.1             pyhd8ed1ab_0    conda-forge
rlpycairo                 0.2.0              pyhd8ed1ab_0    conda-forge
rpds-py                   0.19.0          py311h295b1db_0    conda-forge
s3transfer                0.10.2             pyhd8ed1ab_0    conda-forge
sander                    22.0                     pypi_0    pypi
scipy                     1.14.0          py311h40a1ab3_1    conda-forge
send2trash                1.8.3              pyh31c8845_0    conda-forge
setuptools                70.3.0             pyhd8ed1ab_0    conda-forge
shellingham               1.5.4              pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smirnoff99frosst          1.1.0              pyh44b312d_0    conda-forge
snappy                    1.2.1                he1e6707_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sqlalchemy                2.0.31          py311h72ae277_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
starlette                 0.37.2             pyhd8ed1ab_0    conda-forge
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
terminado                 0.18.1             pyh31c8845_0    conda-forge
tinycss2                  1.3.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h1abcd95_1    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.4.1           py311h72ae277_0    conda-forge
torsiondrive              1.1.0              pyhd8ed1ab_0    conda-forge
tqdm                      4.66.4             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
typer                     0.12.3             pyhd8ed1ab_0    conda-forge
typer-slim                0.12.3             pyhd8ed1ab_0    conda-forge
typer-slim-standard       0.12.3               hd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316     pyhd8ed1ab_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
unidecode                 1.3.8              pyhd8ed1ab_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.2              pyhd8ed1ab_1    conda-forge
uvicorn                   0.30.1          py311h6eed73b_0    conda-forge
vine                      5.1.0              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.6.0             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        4.0.11             pyhd8ed1ab_0    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h35c211d_1002    conda-forge
xorg-libice               1.1.1                h0dc2134_0    conda-forge
xorg-libsm                1.2.4                h0dc2134_0    conda-forge
xorg-libx11               1.8.9                h7022169_1    conda-forge
xorg-libxau               1.0.11               h0dc2134_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xorg-libxext              1.3.4                hb7f2c08_2    conda-forge
xorg-libxt                1.3.0                h0dc2134_1    conda-forge
xorg-xextproto            7.3.0             hb7f2c08_1003    conda-forge
xorg-xproto               7.0.31            h35c211d_1007    conda-forge
xtb                       6.5.1                h5bf119a_1    conda-forge
xtb-python                22.1            py311h5547dcb_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
zeromq                    4.3.5                hde137ed_4    conda-forge
zipp                      3.19.2             pyhd8ed1ab_0    conda-forge
zlib                      1.3.1                h87427d6_1    conda-forge
zlib-ng                   2.2.1                hf036a51_0    conda-forge
zstandard                 0.23.0          py311h51fa951_0    conda-forge
zstd                      1.5.6                h915ae27_0    conda-forge
@j-wags j-wags mentioned this issue Jul 17, 2024
Closed
@j-wags
Copy link
Member Author

j-wags commented Jul 17, 2024

I'm able to load it successfully by downgrading to rdkit=2024.03.3

@j-wags
Copy link
Member Author

j-wags commented Jul 17, 2024 •
edited
Loading

I'm able to reproduce the error using pure RDKit code, will open an issue on their tracker.

from rdkit import Chem

suppl = Chem.SDMolSupplier('bace.sdf')
for mol in suppl:
   print(Chem.MolToSmiles(mol))

zsh: illegal hardware instruction python

@j-wags
Copy link
Member Author

j-wags commented Jul 17, 2024

RDKit issue at rdkit/rdkit#7619

@j-wags j-wags closed this as completed Aug 22, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@j-wags