Error with pybel.readfile

[SashaErmilova]

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Hello everyone,

I've installed openbabel via conda but when I tried reading file with pybel.readfile(), I got the following error:
*** Open Babel Error in ReadFile
Cannot read from /Users/sashaermilova/Downloads/temp/ABABIP_1.xyz
Traceback (most recent call last):
File "/Users/sashaermilova/Desktop/compare_pybel.py", line 3, in
mol1 = next(pybel.readfile("xyz", "/Users/sashaermilova/Downloads/temp/ABABIP_1.xyz"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
StopIteration

Here's the code I'm running:

from openbabel import pybel

mol1 = next(pybel.readfile("xyz", "/Users/sashaermilova/Downloads/temp/ABABIP_1.xyz"))
mol2 = next(pybel.readfile("xyz", "/Users/sashaermilova/Downloads/temp/ABABIP_6.xyz"))

fp1 = mol1.calcfp()
fp2 = mol2.calcfp()

similarity = fp1 | fp2

print(similarity)

How can I solve this problem?

Installed packages

# packages in environment at /opt/anaconda3:
#
# Name                    Version                   Build  Channel
_anaconda_depends         2024.02         py311_openblas_1  
abseil-cpp                20230802.0           h313beb8_2  
aiobotocore               2.7.0           py311hca03da5_0  
aiohttp                   3.9.3           py311h80987f9_0  
aioitertools              0.7.1              pyhd3eb1b0_0  
aiosignal                 1.2.0              pyhd3eb1b0_0  
alabaster                 0.7.12             pyhd3eb1b0_0  
altair                    5.0.1           py311hca03da5_0  
anaconda-anon-usage       0.4.3           py311hd6b623d_100  
anaconda-catalogs         0.2.0           py311hca03da5_0  
anaconda-client           1.12.3          py311hca03da5_0  
anaconda-cloud-auth       0.1.4           py311hca03da5_0  
anaconda-navigator        2.5.2           py311hca03da5_0  
anaconda-project          0.11.1          py311hca03da5_0  
anyio                     4.2.0           py311hca03da5_0  
aom                       3.6.0                h313beb8_0  
appdirs                   1.4.4              pyhd3eb1b0_0  
applaunchservices         0.3.0           py311hca03da5_0  
appnope                   0.1.2           py311hca03da5_1001  
appscript                 1.1.2           py311h80987f9_0  
archspec                  0.2.1              pyhd3eb1b0_0  
argon2-cffi               21.3.0             pyhd3eb1b0_0  
argon2-cffi-bindings      21.2.0          py311h80987f9_0  
arrow                     1.2.3           py311hca03da5_1  
arrow-cpp                 14.0.2               hc7aafb3_1  
ase                       3.23.1b1                 pypi_0    pypi
ase-ext                   20.9.0                   pypi_0    pypi
astroid                   2.14.2          py311hca03da5_0  
astropy                   5.3.4           py311hb9f6ed7_0  
asttokens                 2.0.5              pyhd3eb1b0_0  
async-lru                 2.0.4           py311hca03da5_0  
atomicwrites              1.4.0                      py_0  
attrs                     23.1.0          py311hca03da5_0  
automat                   20.2.0                     py_0  
autopep8                  1.6.0              pyhd3eb1b0_1  
aws-c-auth                0.6.19               h80987f9_0  
aws-c-cal                 0.5.20               h80987f9_0  
aws-c-common              0.8.5                h80987f9_0  
aws-c-compression         0.2.16               h80987f9_0  
aws-c-event-stream        0.2.15               h313beb8_0  
aws-c-http                0.6.25               h80987f9_0  
aws-c-io                  0.13.10              h80987f9_0  
aws-c-mqtt                0.7.13               h80987f9_0  
aws-c-s3                  0.1.51               h80987f9_0  
aws-c-sdkutils            0.1.6                h80987f9_0  
aws-checksums             0.1.13               h80987f9_0  
aws-crt-cpp               0.18.16              h313beb8_0  
aws-sdk-cpp               1.10.55              h313beb8_0  
babel                     2.11.0          py311hca03da5_0  
backports                 1.1                pyhd3eb1b0_0  
backports.functools_lru_cache 1.6.4              pyhd3eb1b0_0  
backports.tempfile        1.0                pyhd3eb1b0_1  
backports.weakref         1.0.post1                  py_1  
bcrypt                    3.2.0           py311h80987f9_1  
beautifulsoup4            4.12.2          py311hca03da5_0  
bel-resources             0.0.3                    pypi_0    pypi
binaryornot               0.4.4              pyhd3eb1b0_1  
bioregistry               0.11.14                  pypi_0    pypi
black                     23.11.0         py311hca03da5_0  
blas                      1.0                    openblas  
bleach                    4.1.0              pyhd3eb1b0_0  
blinker                   1.6.2           py311hca03da5_0  
blosc                     1.21.3               h313beb8_0  
bokeh                     3.3.4           py311hb6e6a13_0  
boltons                   23.0.0          py311hca03da5_0  
boost-cpp                 1.82.0               h48ca7d4_2  
botocore                  1.31.64         py311hca03da5_0  
bottleneck                1.3.7           py311hb9f6ed7_0  
brotli                    1.0.9                h1a28f6b_7  
brotli-bin                1.0.9                h1a28f6b_7  
brotli-python             1.0.9           py311h313beb8_7  
brunsli                   0.1                  hc377ac9_1  
bzip2                     1.0.8                h620ffc9_4  
c-ares                    1.19.1               h80987f9_0  
c-blosc2                  2.12.0               h7df6c2f_0  
ca-certificates           2024.7.4             hf0a4a13_0    conda-forge
cachetools                4.2.2              pyhd3eb1b0_0  
cairo                     1.18.0               hd1e100b_0    conda-forge
cctools                   949.0.1             hc179dcd_25  
cctools_osx-arm64         949.0.1             h332cad3_25  
certifi                   2024.7.4           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py311h80987f9_0  
cfitsio                   3.470                h7f6438f_7  
chardet                   4.0.0           py311hca03da5_1003  
charls                    2.2.0                hc377ac9_0  
charset-normalizer        2.0.4              pyhd3eb1b0_0  
click                     8.1.7           py311hca03da5_0  
click-plugins             1.1.1                    pypi_0    pypi
cloudpickle               2.2.1           py311hca03da5_0  
clyent                    1.2.2           py311hca03da5_1  
colorama                  0.4.6           py311hca03da5_0  
colorcet                  3.0.1           py311hca03da5_0  
comm                      0.2.2                    pypi_0    pypi
conda                     24.1.2          py311h267d04e_0    conda-forge
conda-build               24.1.2          py311hca03da5_0  
conda-content-trust       0.2.0           py311hca03da5_0  
conda-index               0.4.0              pyhd3eb1b0_0  
conda-libmamba-solver     24.1.0             pyhd3eb1b0_0  
conda-pack                0.6.0              pyhd3eb1b0_0  
conda-package-handling    2.2.0           py311hca03da5_0  
conda-package-streaming   0.9.0           py311hca03da5_0  
conda-repo-cli            1.0.75          py311hca03da5_0  
conda-token               0.4.0              pyhd3eb1b0_0  
conda-verify              3.4.2                      py_1  
constantly                23.10.4         py311hca03da5_0  
contourpy                 1.2.0           py311h48ca7d4_0  
cookiecutter              2.5.0           py311hca03da5_0  
cryptography              42.0.2          py311hd4332d6_0  
cssselect                 1.2.0           py311hca03da5_0  
curies                    0.7.10                   pypi_0    pypi
curl                      8.5.0                h02f6b3c_0  
cycler                    0.11.0             pyhd3eb1b0_0  
cyrus-sasl                2.1.28               h9131b1a_1  
cytoolz                   0.12.2          py311h80987f9_0  
dask                      2023.11.0       py311hca03da5_0  
dask-core                 2023.11.0       py311hca03da5_0  
datashader                0.16.0          py311hca03da5_0  
dav1d                     1.2.1                h80987f9_0  
debugpy                   1.6.7           py311h313beb8_0  
decorator                 5.1.1              pyhd3eb1b0_0  
defusedxml                0.7.1              pyhd3eb1b0_0  
diff-match-patch          20200713           pyhd3eb1b0_0  
dill                      0.3.7           py311hca03da5_0  
distributed               2023.11.0       py311hca03da5_0  
distro                    1.8.0           py311hca03da5_0  
dnspython                 2.6.1                    pypi_0    pypi
docker-pycreds            0.4.0                    pypi_0    pypi
docstring-to-markdown     0.11            py311hca03da5_0  
docutils                  0.18.1          py311hca03da5_3  
entrypoints               0.4             py311hca03da5_0  
et_xmlfile                1.1.0           py311hca03da5_0  
executing                 0.8.3              pyhd3eb1b0_0  
expat                     2.6.2                hebf3989_0    conda-forge
filelock                  3.13.1          py311hca03da5_0  
flake8                    6.0.0           py311hca03da5_0  
flask                     2.2.5           py311hca03da5_0  
fmt                       9.1.0                h48ca7d4_0  
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               h82840c6_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.25.0             pyhd3eb1b0_0  
fqdn                      1.5.1                    pypi_0    pypi
freetype                  2.12.1               h1192e45_0  
frozenlist                1.4.0           py311h80987f9_0  
fsspec                    2023.10.0       py311hca03da5_0  
future                    0.18.3          py311hca03da5_0  
gensim                    4.3.0           py311h6956b77_0  
gettext                   0.22.5               h8414b35_3    conda-forge
gettext-tools             0.22.5               h8414b35_3    conda-forge
gflags                    2.2.2                h313beb8_1  
giflib                    5.2.1                h80987f9_3  
gitdb                     4.0.7              pyhd3eb1b0_0  
gitpython                 3.1.37          py311hca03da5_0  
glib                      2.78.4               h313beb8_0  
glib-tools                2.78.4               h313beb8_0  
glog                      0.5.0                h313beb8_1  
gmp                       6.2.1                hc377ac9_3  
gmpy2                     2.1.2           py311h40f64dc_0  
greenlet                  3.0.1           py311h313beb8_0  
grpc-cpp                  1.48.2               hc60591f_4  
gst-plugins-base          1.14.1               h313beb8_1  
gstreamer                 1.14.1               h80987f9_1  
gtest                     1.14.0               h48ca7d4_0  
h5py                      3.9.0           py311hba6ad2f_0  
hdf5                      1.12.1               h05c076b_3  
heapdict                  1.0.1              pyhd3eb1b0_0  
holoviews                 1.18.3          py311hca03da5_0  
humanize                  4.10.0                   pypi_0    pypi
hvplot                    0.9.2           py311hca03da5_0  
hyperlink                 21.0.0             pyhd3eb1b0_0  
icu                       73.2                 hc8870d7_0    conda-forge
idna                      3.4             py311hca03da5_0  
imagecodecs               2023.1.23       py311h5e7c512_0  
imageio                   2.33.1          py311hca03da5_0  
imagesize                 1.4.1           py311hca03da5_0  
imbalanced-learn          0.11.0          py311hca03da5_1  
importlib-metadata        7.0.1           py311hca03da5_0  
importlib_metadata        7.0.1                hd3eb1b0_0  
incremental               22.10.0            pyhd3eb1b0_0  
inflection                0.5.1           py311hca03da5_0  
iniconfig                 1.1.1              pyhd3eb1b0_0  
intake                    0.6.8           py311hca03da5_0  
intervaltree              3.1.0              pyhd3eb1b0_0  
ipykernel                 6.28.0          py311hca03da5_0  
ipython                   8.20.0          py311hca03da5_0  
ipython_genutils          0.2.0              pyhd3eb1b0_1  
ipywidgets                7.7.5                    pypi_0    pypi
isoduration               20.11.0                  pypi_0    pypi
isort                     5.9.3              pyhd3eb1b0_0  
itemadapter               0.3.0              pyhd3eb1b0_0  
itemloaders               1.1.0           py311hca03da5_0  
itsdangerous              2.0.1              pyhd3eb1b0_0  
jaraco.classes            3.2.1              pyhd3eb1b0_0  
jedi                      0.18.1          py311hca03da5_1  
jellyfish                 1.0.1           py311h15d1925_0  
jinja2                    3.1.3           py311hca03da5_0  
jmespath                  1.0.1           py311hca03da5_0  
joblib                    1.2.0           py311hca03da5_0  
jpeg                      9e                   h80987f9_1  
jq                        1.6                  h1a28f6b_1  
json5                     0.9.6              pyhd3eb1b0_0  
jsonpatch                 1.32               pyhd3eb1b0_0  
jsonpointer               2.1                pyhd3eb1b0_0  
jsonschema                4.19.2          py311hca03da5_0  
jsonschema-specifications 2023.7.1        py311hca03da5_0  
jupyter                   1.0.0           py311hca03da5_9  
jupyter-lsp               2.2.0           py311hca03da5_0  
jupyter_client            8.6.0           py311hca03da5_0  
jupyter_console           6.6.3           py311hca03da5_0  
jupyter_core              5.5.0           py311hca03da5_0  
jupyter_events            0.8.0           py311hca03da5_0  
jupyter_server            2.10.0          py311hca03da5_0  
jupyter_server_terminals  0.4.4           py311hca03da5_1  
jupyterlab                4.0.11          py311hca03da5_0  
jupyterlab-variableinspector 3.1.0           py311hca03da5_0  
jupyterlab-widgets        1.1.8                    pypi_0    pypi
jupyterlab_pygments       0.1.2                      py_0  
jupyterlab_server         2.25.1          py311hca03da5_0  
jxrlib                    1.1                  h1a28f6b_2  
keyring                   23.13.1         py311hca03da5_0  
kiwisolver                1.4.4           py311h313beb8_0  
krb5                      1.20.1               hf3e1bf2_1  
latexcodec                3.0.0                    pypi_0    pypi
lazy-object-proxy         1.6.0           py311h80987f9_0  
lazy_loader               0.3             py311hca03da5_0  
lcms2                     2.12                 hba8e193_0  
ld64                      530                 hb29bf3f_25  
ld64_osx-arm64            530                 h001ce53_25  
ldid                      2.1.5                h20b2a84_3  
lerc                      3.0                  hc377ac9_0  
libaec                    1.0.4                hc377ac9_1  
libarchive                3.6.2                h82b9b87_1    conda-forge
libasprintf               0.22.5               h8414b35_3    conda-forge
libasprintf-devel         0.22.5               h8414b35_3    conda-forge
libavif                   0.11.1               h80987f9_0  
libboost                  1.82.0               h0bc93f9_2  
libbrotlicommon           1.0.9                h1a28f6b_7  
libbrotlidec              1.0.9                h1a28f6b_7  
libbrotlienc              1.0.9                h1a28f6b_7  
libclang                  14.0.6          default_h1b80db6_1  
libclang13                14.0.6          default_h24352ff_1  
libcurl                   8.5.0                h3e2b118_0  
libcxx                    18.1.8               h5a72898_4    conda-forge
libdeflate                1.17                 h80987f9_1  
libedit                   3.1.20230828         h80987f9_0  
libev                     4.33                 h1a28f6b_1  
libevent                  2.1.12               h02f6b3c_1  
libexpat                  2.6.2                hebf3989_0    conda-forge
libffi                    3.4.4                hca03da5_0  
libgettextpo              0.22.5               h8414b35_3    conda-forge
libgettextpo-devel        0.22.5               h8414b35_3    conda-forge
libgfortran               5.0.0           11_3_0_hca03da5_28  
libgfortran5              11.3.0              h009349e_28  
libglib                   2.78.4               h0a96307_0  
libiconv                  1.17                 h0d3ecfb_2    conda-forge
libintl                   0.22.5               h8414b35_3    conda-forge
libintl-devel             0.22.5               h8414b35_3    conda-forge
liblief                   0.12.3               h313beb8_0  
libllvm14                 14.0.6               h7ec7a93_3  
libmamba                  1.5.6                h15e39b3_0  
libmambapy                1.5.6           py311h1c5506f_0  
libnghttp2                1.57.0               h62f6fdd_0  
libopenblas               0.3.21               h269037a_0  
libpng                    1.6.39               h80987f9_0  
libpq                     12.17                h02f6b3c_0  
libprotobuf               3.20.3               h514c7bf_0  
libsodium                 1.0.18               h1a28f6b_0  
libsolv                   0.7.24               h514c7bf_0  
libspatialindex           1.9.3                hc377ac9_0  
libsqlite                 3.46.0               hfb93653_0    conda-forge
libssh2                   1.10.0               h02f6b3c_2  
libthrift                 0.15.0               h73c2103_2  
libtiff                   4.5.1                h313beb8_0  
libwebp-base              1.3.2                h80987f9_0  
libxml2                   2.12.7               ha661575_1    conda-forge
libxslt                   1.1.39               h223e5b9_0    conda-forge
libzlib                   1.2.13               hfb2fe0b_6    conda-forge
libzopfli                 1.0.3                hc377ac9_0  
linkify-it-py             2.0.0           py311hca03da5_0  
llvm-openmp               14.0.6               hc6e5704_0  
llvmlite                  0.42.0          py311h313beb8_0  
locket                    1.0.0           py311hca03da5_0  
lolopy                    3.0.0                    pypi_0    pypi
lxml                      5.2.2           py311hf9a6a72_0    conda-forge
lz4                       4.3.2           py311h80987f9_0  
lz4-c                     1.9.4                h313beb8_0  
lzo                       2.10                 h1a28f6b_2  
markdown                  3.4.1           py311hca03da5_0  
markdown-it-py            2.2.0           py311hca03da5_1  
markupsafe                2.1.3           py311h80987f9_0  
matlantis-features        0.0.0                    pypi_0    pypi
matminer                  0.9.2                    pypi_0    pypi
matplotlib                3.8.0           py311hca03da5_0  
matplotlib-base           3.8.0           py311h7aedaa7_0  
matplotlib-inline         0.1.6           py311hca03da5_0  
mccabe                    0.7.0              pyhd3eb1b0_0  
mdit-py-plugins           0.3.0           py311hca03da5_0  
mdurl                     0.1.0           py311hca03da5_0  
menuinst                  2.0.2           py311hca03da5_0  
mistune                   2.0.4           py311hca03da5_0  
monty                     2024.5.24                pypi_0    pypi
more-click                0.1.2                    pypi_0    pypi
more-itertools            10.1.0          py311hca03da5_0  
mpc                       1.1.0                h8c48613_1  
mpfr                      4.0.2                h695f6f0_1  
mpmath                    1.3.0           py311hca03da5_0  
msgpack-python            1.0.3           py311h48ca7d4_0  
multidict                 6.0.4           py311h80987f9_0  
multipledispatch          0.6.0           py311hca03da5_0  
multisplitby              0.0.1                    pypi_0    pypi
munkres                   1.1.4                      py_0  
mypy                      1.8.0           py311h80987f9_0  
mypy_extensions           1.0.0           py311hca03da5_0  
mysql                     5.7.24               ha71a6ea_2  
navigator-updater         0.4.0           py311hca03da5_1  
nbclient                  0.8.0           py311hca03da5_0  
nbconvert                 7.10.0          py311hca03da5_0  
nbformat                  5.9.2           py311hca03da5_0  
ncurses                   6.4                  h313beb8_0  
nest-asyncio              1.6.0           py311hca03da5_0  
networkx                  3.1             py311hca03da5_0  
nglview                   3.1.2                    pypi_0    pypi
nltk                      3.8.1           py311hca03da5_0  
notebook                  7.0.8           py311hca03da5_0  
notebook-shim             0.2.3           py311hca03da5_0  
numba                     0.59.0          py311h7aedaa7_0  
numexpr                   2.8.7           py311h6dc990b_0  
numpy                     1.26.4          py311he598dae_0  
numpy-base                1.26.4          py311hfbfe69c_0  
numpydoc                  1.5.0           py311hca03da5_0  
oniguruma                 6.9.7.1              h1a28f6b_0  
openbabel                 3.1.1           py311h292ccdb_9    conda-forge
openjpeg                  2.3.0                h7a6adac_2  
openpyxl                  3.0.10          py311h80987f9_0  
openssl                   3.3.1                hfb2fe0b_2    conda-forge
orc                       1.7.4                hdca1487_1  
overrides                 7.4.0           py311hca03da5_0  
packaging                 23.1            py311hca03da5_0  
palettable                3.3.3                    pypi_0    pypi
pandas                    2.1.4           py311h7aedaa7_0  
pandocfilters             1.5.0              pyhd3eb1b0_0  
panel                     1.3.8           py311hca03da5_0  
param                     2.0.2           py311hca03da5_0  
parsel                    1.8.1           py311hca03da5_0  
parso                     0.8.3              pyhd3eb1b0_0  
partd                     1.4.1           py311hca03da5_0  
patch                     2.7.6             h1a28f6b_1001  
pathlib                   1.0.1              pyhd3eb1b0_1  
pathspec                  0.10.3          py311hca03da5_0  
patsy                     0.5.3           py311hca03da5_0  
pcre2                     10.42                hb066dcc_0  
pexpect                   4.8.0              pyhd3eb1b0_3  
pfp-api-client            0.0.0                    pypi_0    pypi
pickleshare               0.7.5           pyhd3eb1b0_1003  
pillow                    10.2.0          py311h80987f9_0  
pip                       23.3.1          py311hca03da5_0  
pixman                    0.43.4               hebf3989_0    conda-forge
pkce                      1.0.3           py311hca03da5_0  
pkginfo                   1.9.6           py311hca03da5_0  
platformdirs              3.10.0          py311hca03da5_0  
plotly                    5.9.0           py311hca03da5_0  
pluggy                    1.0.0           py311hca03da5_1  
ply                       3.11            py311hca03da5_0  
prometheus_client         0.14.1          py311hca03da5_0  
prompt-toolkit            3.0.43          py311hca03da5_0  
prompt_toolkit            3.0.43               hd3eb1b0_0  
protego                   0.1.16                     py_0  
protobuf                  3.20.3          py311h313beb8_0  
psutil                    5.9.0           py311h80987f9_0  
psycopg2                  2.9.9                    pypi_0    pypi
psycopg2-binary           2.9.9                    pypi_0    pypi
ptyprocess                0.7.0              pyhd3eb1b0_2  
pure_eval                 0.2.2              pyhd3eb1b0_0  
py-cpuinfo                9.0.0           py311hca03da5_0  
py-lief                   0.12.3          py311h313beb8_0  
py4j                      0.10.9.7                 pypi_0    pypi
pyamg                     5.2.1                    pypi_0    pypi
pyarrow                   14.0.2          py311ha07b5f9_0  
pyasn1                    0.4.8              pyhd3eb1b0_0  
pyasn1-modules            0.2.8                      py_0  
pybind11-abi              4                    hd3eb1b0_1  
pybtex                    0.24.0                   pypi_0    pypi
pycodestyle               2.10.0          py311hca03da5_0  
pycosat                   0.6.6           py311h80987f9_0  
pycparser                 2.21               pyhd3eb1b0_0  
pyct                      0.5.0           py311hca03da5_0  
pycurl                    7.45.2          py311h02f6b3c_1  
pydantic                  1.10.12         py311h80987f9_1  
pydeck                    0.8.0           py311hca03da5_2  
pydispatcher              2.0.5           py311hca03da5_2  
pydocstyle                6.3.0           py311hca03da5_0  
pyerfa                    2.0.0           py311h80987f9_0  
pyflakes                  3.0.1           py311hca03da5_0  
pygments                  2.15.1          py311hca03da5_1  
pyjwt                     2.4.0           py311hca03da5_0  
pylint                    2.16.2          py311hca03da5_0  
pylint-venv               2.3.0           py311hca03da5_0  
pyls-spyder               0.4.0              pyhd3eb1b0_0  
pymatgen                  2024.6.10                pypi_0    pypi
pymongo                   4.8.0                    pypi_0    pypi
pyobjc-core               9.0             py311h3eb5a62_1  
pyobjc-framework-cocoa    9.0             py311hb094c41_0  
pyobjc-framework-coreservices 9.0             py311hdd8dd1f_0  
pyobjc-framework-fsevents 9.0             py311hca03da5_0  
pyodbc                    5.0.1           py311h313beb8_0  
pyopenssl                 24.0.0          py311hca03da5_0  
pyparsing                 3.0.9           py311hca03da5_0  
pyqt                      5.15.10         py311h313beb8_0  
pyqt5-sip                 12.13.0         py311h80987f9_0  
pyqtwebengine             5.15.10         py311h313beb8_0  
pysocks                   1.7.1           py311hca03da5_0  
pystow                    0.5.4                    pypi_0    pypi
pytables                  3.9.2           py311h0326f10_0  
pytest                    7.4.0           py311hca03da5_0  
python                    3.11.8          hdf0ec26_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd3eb1b0_0  
python-dotenv             0.21.0          py311hca03da5_0  
python-fastjsonschema     2.16.2          py311hca03da5_0  
python-json-logger        2.0.7           py311hca03da5_0  
python-libarchive-c       2.9                pyhd3eb1b0_1  
python-lmdb               1.4.1           py311h313beb8_0  
python-lsp-black          1.2.1           py311hca03da5_0  
python-lsp-jsonrpc        1.0.0              pyhd3eb1b0_0  
python-lsp-server         1.7.2           py311hca03da5_0  
python-slugify            5.0.2              pyhd3eb1b0_0  
python-snappy             0.6.1           py311h313beb8_0  
python-tzdata             2023.3             pyhd3eb1b0_0  
python.app                3               py311h80987f9_0  
python_abi                3.11                    5_cp311    conda-forge
pytoolconfig              1.2.6           py311hca03da5_0  
pytrie                    0.4.0                    pypi_0    pypi
pytz                      2023.3.post1    py311hca03da5_0  
pyviz_comms               3.0.0           py311hca03da5_0  
pywavelets                1.5.0           py311hb9f6ed7_0  
pyyaml                    6.0.1           py311h80987f9_0  
pyzmq                     25.1.2          py311h313beb8_0  
qdarkstyle                3.0.2              pyhd3eb1b0_0  
qstylizer                 0.2.2           py311hca03da5_0  
qt-main                   5.15.2              h0917680_10  
qt-webengine              5.15.9               h2903aaf_7  
qtawesome                 1.2.2           py311hca03da5_0  
qtconsole                 5.4.2           py311hca03da5_0  
qtpy                      2.4.1           py311hca03da5_0  
queuelib                  1.6.2           py311hca03da5_0  
ratelimit                 2.2.1                    pypi_0    pypi
re2                       2022.04.01           hc377ac9_0  
readline                  8.2                  h1a28f6b_0  
referencing               0.30.2          py311hca03da5_0  
regex                     2023.10.3       py311h80987f9_0  
reproc                    14.2.4               hc377ac9_1  
reproc-cpp                14.2.4               hc377ac9_1  
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
requests-file             1.5.1              pyhd3eb1b0_0  
requests-toolbelt         1.0.0           py311hca03da5_0  
rfc3339-validator         0.1.4           py311hca03da5_0  
rfc3986-validator         0.1.1           py311hca03da5_0  
rich                      13.3.5          py311hca03da5_0  
rope                      1.7.0           py311hca03da5_0  
rpds-py                   0.10.6          py311hf0e4da2_0  
rtree                     1.0.1           py311hca03da5_0  
ruamel.yaml               0.17.21         py311h80987f9_0  
ruamel_yaml               0.17.21         py311h80987f9_0  
s3fs                      2023.10.0       py311hca03da5_0  
scikit-image              0.22.0          py311h7aedaa7_0  
scikit-learn              1.5.0                    pypi_0    pypi
scipy                     1.14.0                   pypi_0    pypi
scrapy                    2.8.0           py311hca03da5_0  
seaborn                   0.12.2          py311hca03da5_0  
semver                    2.13.0             pyhd3eb1b0_0  
send2trash                1.8.2           py311hca03da5_0  
sentry-sdk                2.5.1                    pypi_0    pypi
service_identity          18.1.0             pyhd3eb1b0_1  
setproctitle              1.3.3                    pypi_0    pypi
setuptools                68.2.2          py311hca03da5_0  
sip                       6.7.12          py311h313beb8_0  
six                       1.16.0             pyhd3eb1b0_1  
smart_open                5.2.1           py311hca03da5_0  
smmap                     4.0.0              pyhd3eb1b0_0  
snappy                    1.1.10               h313beb8_1  
sniffio                   1.3.0           py311hca03da5_0  
snowballstemmer           2.2.0              pyhd3eb1b0_0  
sortedcontainers          2.4.0              pyhd3eb1b0_0  
soupsieve                 2.5             py311hca03da5_0  
spglib                    2.4.0                    pypi_0    pypi
sphinx                    5.0.2           py311hca03da5_0  
sphinxcontrib-applehelp   1.0.2              pyhd3eb1b0_0  
sphinxcontrib-devhelp     1.0.2              pyhd3eb1b0_0  
sphinxcontrib-htmlhelp    2.0.0              pyhd3eb1b0_0  
sphinxcontrib-jsmath      1.0.1              pyhd3eb1b0_0  
sphinxcontrib-qthelp      1.0.3              pyhd3eb1b0_0  
sphinxcontrib-serializinghtml 1.1.5              pyhd3eb1b0_0  
spyder                    5.4.3           py311hca03da5_1  
spyder-kernels            2.4.4           py311hca03da5_0  
sqlalchemy                2.0.25          py311h80987f9_0  
sqlite                    3.41.2               h80987f9_0  
stack_data                0.2.0              pyhd3eb1b0_0  
statsmodels               0.14.0          py311hb9f6ed7_0  
streamlit                 1.30.0          py311hca03da5_0  
sympy                     1.12            py311hca03da5_0  
tabulate                  0.9.0           py311hca03da5_0  
tapi                      1100.0.11            h8754e6a_1  
tbb                       2021.8.0             h48ca7d4_0  
tblib                     1.7.0              pyhd3eb1b0_0  
tenacity                  8.2.2           py311hca03da5_0  
terminado                 0.17.1          py311hca03da5_0  
text-unidecode            1.3                pyhd3eb1b0_0  
textdistance              4.2.1              pyhd3eb1b0_0  
threadpoolctl             3.5.0                    pypi_0    pypi
three-merge               0.1.1              pyhd3eb1b0_0  
tifffile                  2023.4.12       py311hca03da5_0  
tinycss2                  1.2.1           py311hca03da5_0  
tk                        8.6.13               h5083fa2_1    conda-forge
tldextract                3.2.0              pyhd3eb1b0_0  
toml                      0.10.2             pyhd3eb1b0_0  
tomlkit                   0.11.1          py311hca03da5_0  
toolz                     0.12.0          py311hca03da5_0  
torch                     2.3.1                    pypi_0    pypi
torchvision               0.18.1                   pypi_0    pypi
tornado                   6.3.3           py311h80987f9_0  
tqdm                      4.66.4                   pypi_0    pypi
traitlets                 5.7.1           py311hca03da5_0  
truststore                0.8.0           py311hca03da5_0  
twisted                   23.10.0         py311hca03da5_0  
typing-extensions         4.9.0           py311hca03da5_1  
typing_extensions         4.9.0           py311hca03da5_1  
tzdata                    2023d                h04d1e81_0  
tzlocal                   2.1             py311hca03da5_1  
uc-micro-py               1.0.1           py311hca03da5_0  
ujson                     5.4.0           py311h313beb8_0  
uncertainties             3.2.1                    pypi_0    pypi
unidecode                 1.2.0              pyhd3eb1b0_0  
unixodbc                  2.3.11               h1a28f6b_0  
uri-template              1.3.0                    pypi_0    pypi
urllib3                   2.0.7           py311hca03da5_0  
utf8proc                  2.6.1                h80987f9_1  
validators                0.18.2             pyhd3eb1b0_0  
w3lib                     2.1.2           py311hca03da5_0  
wandb                     0.17.1                   pypi_0    pypi
watchdog                  2.1.6           py311h80987f9_0  
wcwidth                   0.2.5              pyhd3eb1b0_0  
webcolors                 24.6.0                   pypi_0    pypi
webencodings              0.5.1           py311hca03da5_1  
websocket-client          0.58.0          py311hca03da5_4  
werkzeug                  2.2.3           py311hca03da5_0  
whatthepatch              1.0.2           py311hca03da5_0  
wheel                     0.41.2          py311hca03da5_0  
widgetsnbextension        3.6.7                    pypi_0    pypi
wrapt                     1.14.1          py311h80987f9_0  
wurlitzer                 3.0.2           py311hca03da5_0  
xarray                    2023.6.0        py311hca03da5_0  
xlwings                   0.29.1          py311hca03da5_0  
xyzservices               2022.9.0        py311hca03da5_1  
xz                        5.4.5                h80987f9_0  
yaml                      0.2.5                h1a28f6b_0  
yaml-cpp                  0.8.0                h313beb8_0  
yapf                      0.31.0             pyhd3eb1b0_0  
yarl                      1.9.3           py311h80987f9_0  
zeromq                    4.3.5                h313beb8_0  
zfp                       1.0.0                h313beb8_0  
zict                      3.0.0           py311hca03da5_0  
zipp                      3.17.0          py311hca03da5_0  
zlib                      1.2.13               hfb2fe0b_6    conda-forge
zlib-ng                   2.0.7                h80987f9_0  
zope                      1.0             py311hca03da5_1  
zope.interface            5.4.0           py311h80987f9_0  
zstandard                 0.19.0          py311h80987f9_0  
zstd                      1.5.5                hd90d995_0

Environment info

Error while loading conda entry point: conda-libmamba-solver (dlopen(/opt/anaconda3/lib/python3.11/site-packages/libmambapy/bindings.cpython-311-darwin.so, 0x0002): Library not loaded: @rpath/libarchive.19.dylib
  Referenced from: <027768CD-20C9-3E75-850D-35E842A32FA5> /opt/anaconda3/lib/libmamba.2.0.0.dylib
  Reason: tried: '/opt/anaconda3/lib/libarchive.19.dylib' (no such file), '/opt/anaconda3/lib/python3.11/site-packages/libmambapy/../../../libarchive.19.dylib' (no such file), '/opt/anaconda3/lib/python3.11/site-packages/libmambapy/../../../libarchive.19.dylib' (no such file), '/opt/anaconda3/bin/../lib/libarchive.19.dylib' (no such file), '/opt/anaconda3/bin/../lib/libarchive.19.dylib' (no such file), '/usr/local/lib/libarchive.19.dylib' (no such file), '/usr/lib/libarchive.19.dylib' (no such file, not in dyld cache))

     active environment : base
    active env location : /opt/anaconda3
            shell level : 1
       user config file : /Users/sashaermilova/.condarc
 populated config files : /Users/sashaermilova/.condarc
          conda version : 24.1.2
    conda-build version : 24.1.2
         python version : 3.11.8.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=m2
                          __conda=24.1.2=0
                          __osx=13.4=0
                          __unix=0=0
       base environment : /opt/anaconda3  (writable)
      conda av data dir : /opt/anaconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/anaconda3/pkgs
                          /Users/sashaermilova/.conda/pkgs
       envs directories : /opt/anaconda3/envs
                          /Users/sashaermilova/.conda/envs
               platform : osx-arm64
             user-agent : conda/24.1.2 requests/2.32.3 CPython/3.11.8 Darwin/22.5.0 OSX/13.4 solver/libmamba aau/0.4.3 c/ZWQga7oujDNA8c9iMLewGw s/fyjyrS2PgJQ3lt1MXZ4Tcw e/_Yt9Lh-iyStuCzH7vc9M5w
                UID:GID : 501:20
             netrc file : /Users/sashaermilova/.netrc
           offline mode : False

[fredrikw]

Hi,
This issue should probably be posted to the main OpenBabel repository (https://github.com/openbabel/openbabel).
But it looks like there is a problem with the file content. Have you tried converting the file to something else in e.g. obabel to see if it is correct?
Your code would give a StopIteration error when pybel can't read any more molecules from it.