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Unexpected `Unspecified Stereochemistry Error` in Molecule.from_rdkit

See original GitHub issue

Describe the bug I have an rdkit molecule object in which I have to set custom SetAtomMapNum for all atoms. Whenever I want to parse that rdkit object to an openff-toolkit Molecule object, I get an UndefinedStereochemistryError. This happens for molecules who don’t even have steorecenters by construction and only if I add hydrogen atoms to them. If I set every atommap to 0 on every atom, the erroneous behaviour is not observed.

To Reproduce

from openff.toolkit.topology.molecule import Molecule
from rdkit.Chem import AllChem as Chem

### The following will crash with `UndefinedStereochemistryError`
rdmol = Chem.MolFromSmiles("CCCC")
rdmol = Chem.AddHs(rdmol)
for i, a in enumerate(rdmol.GetAtoms()):
    a.SetAtomMapNum(i)
offmol = Molecule.from_rdkit(rdmol)

### The following will not crash
rdmol = Chem.MolFromSmiles("CCCC")
rdmol = Chem.AddHs(rdmol)
for i, a in enumerate(rdmol.GetAtoms()):
    a.SetAtomMapNum(0)
offmol = Molecule.from_rdkit(rdmol)

Output

---------------------------------------------------------------------------
UndefinedStereochemistryError             Traceback (most recent call last)
Input In [54], in <cell line: 10>()
      7     a.SetAtomMapNum(i)
      8     #a.SetAtomMapNum(0)
---> 10 offmol = Molecule.from_rdkit(rdmol)

File ~/progs/miniconda3/envs/atomtyping/lib/python3.9/site-packages/openff/toolkit/utils/base_wrapper.py:51, in ToolkitWrapper.requires_toolkit.<locals>.decorator.<locals>.wrapped_function(*args, **kwargs)
     47     msg = "This function requires the {} toolkit".format(
     48         cls._toolkit_name
     49     )
     50     raise ToolkitUnavailableException(msg)
---> 51 value = func(*args, **kwargs)
     52 return value

File ~/progs/miniconda3/envs/atomtyping/lib/python3.9/site-packages/openff/toolkit/topology/molecule.py:5110, in FrozenMolecule.from_rdkit(cls, rdmol, allow_undefined_stereo, hydrogens_are_explicit)
   5079 """
   5080 Create a Molecule from an RDKit molecule.
   5081 
   (...)
   5107 
   5108 """
   5109 toolkit = RDKitToolkitWrapper()
-> 5110 molecule = toolkit.from_rdkit(
   5111     rdmol,
   5112     allow_undefined_stereo=allow_undefined_stereo,
   5113     hydrogens_are_explicit=hydrogens_are_explicit,
   5114     _cls=cls,
   5115 )
   5116 return molecule

File ~/progs/miniconda3/envs/atomtyping/lib/python3.9/site-packages/openff/toolkit/utils/rdkit_wrapper.py:1458, in RDKitToolkitWrapper.from_rdkit(self, rdmol, allow_undefined_stereo, hydrogens_are_explicit, _cls)
   1455 Chem.AssignStereochemistry(rdmol, cleanIt=False)
   1457 # Check for undefined stereochemistry.
-> 1458 self._detect_undefined_stereo(
   1459     rdmol,
   1460     raise_warning=allow_undefined_stereo,
   1461     err_msg_prefix="Unable to make OFFMol from RDMol: ",
   1462 )
   1464 # Create a new OpenFF Molecule
   1465 offmol = _cls()

File ~/progs/miniconda3/envs/atomtyping/lib/python3.9/site-packages/openff/toolkit/utils/rdkit_wrapper.py:2280, in RDKitToolkitWrapper._detect_undefined_stereo(cls, rdmol, err_msg_prefix, raise_warning)
   2278 else:
   2279     msg = "Unable to make OFFMol from RDMol: " + msg
-> 2280     raise UndefinedStereochemistryError(msg)

UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from RDMol: RDMol has unspecified stereochemistry. Undefined chiral centers are:
 - Atom C (index 0)
 - Atom C (index 1)
 - Atom C (index 2)
 - Atom C (index 3)

Computing environment (please complete the following information):

  • Operating system: 5.15.0-46-generic #49~20.04.1-Ubuntu SMP Thu Aug 4 19:15:44 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
  • Output of running conda list:
# packages in environment at /scratch/wulsdorf/progs/miniconda3/envs/atomtyping:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
abseil-cpp                20210324.2           h2531618_0  
alembic                   1.7.6              pyhd8ed1ab_0    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
amberlite                 16.0                     pypi_0    pypi
ambertools                20.9                     pypi_0    pypi
ambit                     0.5.1                hbe8a562_1    psi4
anyio                     3.5.0            py39hf3d152e_0    conda-forge
appdirs                   1.4.4              pyhd3eb1b0_0  
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39h3811e60_1    conda-forge
arpack                    3.7.0                hc6cf775_2    conda-forge
arrow-cpp                 7.0.0           py39h6409b3a_2_cpu    conda-forge
asttokens                 2.0.5              pyhd3eb1b0_0  
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
async_generator           1.10                       py_0    conda-forge
atk-1.0                   2.36.0               h3371d22_4    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
autocommand               2.2.1                    pypi_0    pypi
aws-c-cal                 0.5.11               h95a6274_0    conda-forge
aws-c-common              0.6.2                h7f98852_0    conda-forge
aws-c-event-stream        0.2.7               h3541f99_13    conda-forge
aws-c-io                  0.10.5               hfb6a706_0    conda-forge
aws-checksums             0.1.11               ha31a3da_7    conda-forge
aws-sdk-cpp               1.8.186              hb4091e7_3    conda-forge
babel                     2.9.1              pyh44b312d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.1                pyhd3eb1b0_0  
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bcrypt                    3.2.0            py39h3811e60_2    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
black                     19.10b0                    py_0  
blas                      1.0                         mkl  
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.0               h9c3ff4c_0    conda-forge
boost                     1.74.0           py39h5472131_5    conda-forge
boost-cpp                 1.74.0               h312852a_4    conda-forge
brotli                    1.0.9                h7f98852_6    conda-forge
brotli-bin                1.0.9                h7f98852_6    conda-forge
brotlipy                  0.7.0           py39h3811e60_1003    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f8727e_0  
ca-certificates           2022.9.24            ha878542_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.16.0            h6cf1ce9_1008    conda-forge
certifi                   2022.9.24          pyhd8ed1ab_0    conda-forge
cffi                      1.15.0           py39hd667e15_1  
charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge
chemper                   1.0.0              pyh9f0ad1d_0    conda-forge
chemps2                   1.8.10               hbe8a562_0    psi4
cheroot                   8.6.0                    pypi_0    pypi
cherrypy                  18.8.0                   pypi_0    pypi
click                     8.0.3                    pypi_0    pypi
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
colour                    0.1.5                    pypi_0    pypi
cryptography              36.0.1           py39h95dcef6_0    conda-forge
cudatoolkit               11.6.0              habf752d_10    conda-forge
curl                      7.81.0               h2574ce0_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.28          py39he80948d_0    conda-forge
dbus                      1.13.18              hb2f20db_0  
debugpy                   1.5.1            py39he80948d_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecated                1.2.13                   pypi_0    pypi
dftd3                     3.2.1                h84218bc_2    psi4
dkh                       1.2                  h173d85e_2    psi4
double-conversion         3.2.0                h9c3ff4c_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 0.8.3              pyhd3eb1b0_0  
expat                     2.4.4                h9c3ff4c_0    conda-forge
faerun                    0.4.2                    pypi_0    pypi
fftw                      3.3.9                h27cfd23_1  
filelock                  3.4.2                    pypi_0    pypi
flit-core                 3.6.0              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                2.13.96              ha180cfb_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.29.1           py39h3811e60_0    conda-forge
freetype                  2.11.0               h70c0345_0  
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gau2grid                  2.0.7                h7f98852_1    conda-forge
gcp                       2.0.2                he991be0_2    psi4
gdk-pixbuf                2.42.6               h04a7f16_0    conda-forge
gdma                      2.2.6                h0e1e685_6    psi4
geometric                 0.9.7.2                    py_0    conda-forge
gettext                   0.21.0               hf68c758_0  
gflags                    2.2.2             he1b5a44_1004    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
glib                      2.70.2               h780b84a_4    conda-forge
glib-tools                2.70.2               h780b84a_4    conda-forge
glog                      0.5.0                h48cff8f_0    conda-forge
gmp                       6.2.1                h2531618_2  
graphite2                 1.3.14               h23475e2_0  
graphviz                  2.50.0               h85b4f2f_1    conda-forge
grpc-cpp                  1.43.2               h9e046d8_1    conda-forge
grpcio                    1.43.0                   pypi_0    pypi
gst-plugins-base          1.18.5               hf529b03_2    conda-forge
gstreamer                 1.18.5               h9f60fe5_3    conda-forge
gtk2                      2.24.33              h539f30e_1    conda-forge
gts                       0.7.6                h64030ff_2    conda-forge
h5py                      3.6.0            py39ha0f2276_0  
harfbuzz                  3.1.1                h83ec7ef_0    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.10.6          nompi_h7c3c948_1111    conda-forge
icu                       68.2                 h9c3ff4c_0    conda-forge
idna                      3.3                pyhd3eb1b0_0  
imageio                   2.21.1             pyhfa7a67d_0    conda-forge
importlib-metadata        4.11.1           py39hf3d152e_0    conda-forge
importlib_metadata        4.11.1               hd8ed1ab_0    conda-forge
importlib_resources       5.4.0              pyhd8ed1ab_0    conda-forge
inflect                   6.0.0                    pypi_0    pypi
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
intel-openmp              2022.0.1          h06a4308_3633  
ipykernel                 6.9.1            py39hef51801_0    conda-forge
ipython                   8.3.0            py39hf3d152e_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.5              pyhd3eb1b0_1  
jaraco-classes            3.2.2                    pypi_0    pypi
jaraco-collections        3.5.2                    pypi_0    pypi
jaraco-context            4.1.2                    pypi_0    pypi
jaraco-functools          3.5.1                    pypi_0    pypi
jaraco-text               3.9.1                    pypi_0    pypi
jbig                      2.1                  hdba287a_0  
jedi                      0.18.1           py39hf3d152e_0    conda-forge
jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge
joblib                    1.1.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h7f98852_0    conda-forge
json5                     0.9.6              pyhd3eb1b0_0  
jsonschema                4.4.0              pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0            py39hf3d152e_7    conda-forge
jupyter_client            7.1.2              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.0              pyhd8ed1ab_0    conda-forge
jupyter_core              4.9.2            py39hf3d152e_0    conda-forge
jupyter_server            1.17.0             pyhd8ed1ab_0    conda-forge
jupyterlab                3.4.2              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_server         2.10.3             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.0.2              pyhd8ed1ab_0    conda-forge
kiwisolver                1.3.2            py39h1a9c180_1    conda-forge
krb5                      1.19.2               hcc1bbae_3    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h295c915_0  
libblas                   3.9.0           1_h6e990d7_netlib    conda-forge
libbrotlicommon           1.0.9                h7f98852_6    conda-forge
libbrotlidec              1.0.9                h7f98852_6    conda-forge
libbrotlienc              1.0.9                h7f98852_6    conda-forge
libcblas                  3.9.0           3_h893e4fe_netlib    conda-forge
libclang                  11.1.0          default_ha53f305_1    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcurl                   7.81.0               h2574ce0_0    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libedit                   3.1.20210910         h7f8727e_0  
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgd                     2.3.3                h695aa2c_0  
libgfortran-ng            7.5.0               h14aa051_20    conda-forge
libgfortran4              7.5.0               h14aa051_20    conda-forge
libglib                   2.70.2               h174f98d_4    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
libgoogle-cloud           1.35.0               h6945097_2    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libint2                   2.6.0                hc9558a2_9    psi4
liblapack                 3.9.0           3_h893e4fe_netlib    conda-forge
libllvm11                 11.1.0               hf817b99_3    conda-forge
libnetcdf                 4.7.4           nompi_h56d31a8_107    conda-forge
libnghttp2                1.46.0               hce63b2e_0  
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.5                h27cfd23_1  
libopenblas               0.3.17               hf726d26_1  
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     13.5                 hd57d9b9_1    conda-forge
libprotobuf               3.19.4               h780b84a_0    conda-forge
librsvg                   2.52.5               hc3c00ef_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_12    conda-forge
libthrift                 0.15.0               he6d91bd_1    conda-forge
libtiff                   4.3.0                h542a066_3    conda-forge
libtool                   2.4.6             h9c3ff4c_1008    conda-forge
libutf8proc               2.7.0                h7f98852_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libuv                     1.40.0               h7b6447c_0  
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp                   1.2.2                h3452ae3_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxc                     5.1.5                h84b9e52_1    psi4
libxcb                    1.14                 h7b6447c_0  
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libxslt                   1.1.33               h15afd5d_2    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
llvm-openmp               13.0.1               hf817b99_0    conda-forge
lxml                      4.8.0            py39h107f48f_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mako                      1.1.6              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.0            py39hb9d737c_0    conda-forge
matplotlib                3.5.1            py39hf3d152e_0    conda-forge
matplotlib-base           3.5.1            py39h2fa2bec_0    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mdtraj                    1.9.7            py39h138c130_1    conda-forge
mhfp                      1.9.2                    pypi_0    pypi
mistune                   0.8.4           py39h3811e60_1005    conda-forge
mkl                       2021.4.0           h8d4b97c_729    conda-forge
mkl-service               2.4.0            py39h7e14d7c_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
mock                      4.0.3            py39hf3d152e_2    conda-forge
more-itertools            8.14.0                   pypi_0    pypi
mpc                       1.2.1                h9f54685_0    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
msgpack-python            1.0.3            py39h1a9c180_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mypy_extensions           0.4.3            py39hf3d152e_4    conda-forge
mysql-common              8.0.28               ha770c72_0    conda-forge
mysql-libs                8.0.28               hfa10184_0    conda-forge
nb_conda                  2.2.1            py39hf3d152e_4    conda-forge
nb_conda_kernels          2.3.1            py39hf3d152e_1    conda-forge
nbclassic                 0.3.5              pyhd8ed1ab_0    conda-forge
nbclient                  0.5.11             pyhd8ed1ab_0    conda-forge
nbconvert                 6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          6.5.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.4.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h7f8727e_2  
nest-asyncio              1.5.4              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.5.3           nompi_hfef6a68_101    conda-forge
networkx                  2.6.3              pyhd8ed1ab_1    conda-forge
nglview                   3.0.3              pyh8a188c0_0    conda-forge
nlopt                     2.7.1            py39h3e08f04_0    conda-forge
nodejs                    16.13.1              hb931c9a_0  
notebook                  6.4.8              pyha770c72_0    conda-forge
nspr                      4.32                 h9c3ff4c_1    conda-forge
nss                       3.74                 hb5efdd6_0    conda-forge
numexpr                   2.8.1            py39h6abb31d_0  
numpy                     1.21.5           py39haac66dc_0    conda-forge
ocl-icd                   2.3.1                h7f98852_0    conda-forge
ocl-icd-system            1.0.0                         1    conda-forge
ogdf                      1.2.0                h2bc3f7f_0    tmap
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openeye-toolkits          2021.2.0                 py39_0    openeye
openff-forcefields        2.0.0              pyh6c4a22f_0    conda-forge
openff-toolkit            0.10.2             pyhd8ed1ab_0    conda-forge
openff-toolkit-base       0.10.2             pyhd8ed1ab_0    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openmm                    7.6.0            py39h71eca04_0    conda-forge
openmmforcefields         0.10.0             pyhd8ed1ab_0    conda-forge
openssl                   1.1.1q               h166bdaf_0    conda-forge
orc                       1.7.3                h1be678f_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
packmol-memgen            1.1.0rc0                 pypi_0    pypi
pandas                    1.4.1            py39hde0f152_0    conda-forge
pandoc                    2.17.1.1             ha770c72_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.48.10              h54213e6_2    conda-forge
parmed                    at20RC5+54.g5702a232fe.dirty          pypi_0    pypi
parquet-cpp               1.5.1                h34088ae_4  
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pathspec                  0.7.0                      py_0  
patsy                     0.5.2              pyhd8ed1ab_0    conda-forge
pcmsolver                 1.2.1.1          py39h6d17ec8_2    psi4
pcre                      8.45                 h9c3ff4c_0    conda-forge
pdb4amber                 1.7.dev0                 pypi_0    pypi
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pexpect                   4.8.0              pyhd3eb1b0_3  
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    8.4.0            py39h5aabda8_0  
pint                      0.18               pyhd8ed1ab_0    conda-forge
pip                       22.0.3             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h7f8727e_1  
plotly                    5.6.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0            py39hf3d152e_2    conda-forge
portend                   3.1.0                    pypi_0    pypi
postgresql                13.5                 h2510834_1    conda-forge
prometheus_client         0.13.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.27             pyha770c72_0    conda-forge
prompt_toolkit            3.0.27               hd8ed1ab_0    conda-forge
protobuf                  3.19.3                   pypi_0    pypi
psi4                      1.5+e9f4d6d      py39hbf93d9d_0    psi4
psutil                    5.9.0            py39h3811e60_0    conda-forge
psycopg2                  2.9.2            py39h3811e60_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3eb1b0_2  
pure_eval                 0.2.2              pyhd3eb1b0_0  
py                        1.11.0             pyh6c4a22f_0    conda-forge
py-cpuinfo                8.0.0              pyhd3eb1b0_1  
pyarrow                   7.0.0           py39hff6fa39_2_cpu    conda-forge
pycairo                   1.20.1           py39hedcb9fc_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.9.0            py39h3811e60_0    conda-forge
pygments                  2.11.2             pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.7              pyhd8ed1ab_0    conda-forge
pyqt                      5.12.3           py39hf3d152e_8    conda-forge
pyqt-impl                 5.12.3           py39hde8b62d_8    conda-forge
pyqt5-sip                 4.19.18          py39he80948d_8    conda-forge
pyqtchart                 5.12             py39h0fcd23e_8    conda-forge
pyqtwebengine             5.12.1           py39h0fcd23e_8    conda-forge
pyrsistent                0.18.1           py39h3811e60_0    conda-forge
pysocks                   1.7.1            py39hf3d152e_4    conda-forge
pytables                  3.6.1            py39hf6dc253_3    conda-forge
pytest                    7.0.1            py39hf3d152e_0    conda-forge
python                    3.9.10          h85951f9_2_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.15.3             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytraj                    2.0.5                    pypi_0    pypi
pytz                      2021.3             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py39h3811e60_3    conda-forge
pyzmq                     22.3.0           py39h295c915_2  
qcelemental               0.24.0             pyhd8ed1ab_0    conda-forge
qcengine                  0.23.0             pyhd8ed1ab_0    conda-forge
qcfractal                 0.15.8.1         py39hf3d152e_0    conda-forge
qcfractal-core            0.15.8.1         py39hf3d152e_0    conda-forge
qcportal                  0.15.8             pyhd8ed1ab_0    conda-forge
qt                        5.12.9               hda022c4_4    conda-forge
qtconsole                 5.2.2              pyhd8ed1ab_1    conda-forge
qtconsole-base            5.2.2              pyhd8ed1ab_1    conda-forge
qtpy                      2.0.1              pyhd8ed1ab_0    conda-forge
ray                       1.9.2                    pypi_0    pypi
rdkit                     2021.09.4        py39hccf6a74_0    conda-forge
re2                       2022.02.01           h9c3ff4c_0    conda-forge
readline                  8.1.2                h7f8727e_1  
redis                     4.1.0                    pypi_0    pypi
regex                     2022.3.15        py39h7f8727e_0  
reportlab                 3.5.68           py39he59360d_1    conda-forge
requests                  2.27.1             pyhd8ed1ab_0    conda-forge
s2n                       1.0.10               h9b69904_0    conda-forge
sander                    16.0                     pypi_0    pypi
scikit-learn              1.0.2            py39h51133e4_1  
scipy                     1.7.3            py39hc147768_0  
seaborn                   0.12.0               hd8ed1ab_0    conda-forge
seaborn-base              0.12.0             pyhd8ed1ab_0    conda-forge
send2trash                1.8.0              pyhd3eb1b0_1  
setuptools                60.9.3           py39hf3d152e_0    conda-forge
simint                    0.7                  h642920c_1    psi4
six                       1.16.0             pyh6c4a22f_0    conda-forge
smirnoff99frosst          1.1.0              pyh44b312d_0    conda-forge
snappy                    1.1.8                he1b5a44_3    conda-forge
sniffio                   1.2.0            py39hf3d152e_2    conda-forge
soupsieve                 2.3.1              pyhd8ed1ab_0    conda-forge
sqlalchemy                1.3.23           py39h3811e60_0    conda-forge
sqlite                    3.37.0               hc218d9a_0  
stack_data                0.2.0              pyhd3eb1b0_0  
statsmodels               0.13.2           py39hd257fcd_0    conda-forge
tbb                       2021.5.0             hd09550d_0  
tempora                   5.0.2                    pypi_0    pypi
tenacity                  8.0.1              pyhd8ed1ab_0    conda-forge
terminado                 0.13.1           py39hf3d152e_0    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tinycss2                  1.1.1              pyhd8ed1ab_0    conda-forge
tinydb                    4.7.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tmap                      1.0.6            py39h2bc3f7f_0    tmap
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     1.2.2              pyhd3eb1b0_0  
tornado                   6.1              py39h3811e60_2    conda-forge
torsiondrive              1.1.0              pyhd8ed1ab_0    conda-forge
tqdm                      4.62.3             pyhd3eb1b0_1  
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
typed-ast                 1.5.2            py39h3811e60_0    conda-forge
typing-extensions         4.1.1                hd8ed1ab_0    conda-forge
typing_extensions         4.1.1              pyha770c72_0    conda-forge
tzcode                    2021e                h7f98852_0    conda-forge
tzdata                    2021e                hda174b7_0  
ujson                     5.4.0                    pypi_0    pypi
unicodedata2              14.0.0           py39h3811e60_0    conda-forge
urllib3                   1.26.8             pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.2.3              pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd3eb1b0_0  
widgetsnbextension        3.5.2            py39h06a4308_0  
wrapt                     1.13.3                   pypi_0    pypi
xmltodict                 0.12.0                     py_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxpm               3.5.13               h7f98852_0    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zc-lockfile               2.0                      pypi_0    pypi
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.7.0              pyhd8ed1ab_1    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.5.2                ha95c52a_0    conda-forge

Additional context

Issue Analytics

  • State:open
  • Created a year ago
  • Comments:5 (3 by maintainers)

github_iconTop GitHub Comments

2reactions
wutobiascommented, Sep 29, 2022

And (whether or not this is the root cause of this issue) I’d strongly recommend upgrading from 0.10.2 to the newest OFF toolkit release (either 0.10.6 if you need the old API, or 0.11.1 if not). There have been several critical bugfixes since 0.10.2. For example, Sage doesn’t correctly apply TIP3P charges to water in 0.10.2.

Thanks. These are very useful comments. For this issue however, neither v0.10.6 nor 0.11.1 resolve the problem.

1reaction
wutobiascommented, Sep 29, 2022

Would either of these work for you in the short term, @wutobias?

Yes, that works for me in the short term. Thanks for looking into it!

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