openff-toolkit: Assigning partial charges is not thread safe

Describe the bug

If I create an OpenFF Molecule object from a RDKit Molecule object, I get an error when trying to parametrize it. In the following code, if I instead create the Molecule from SMILES with

mol = Molecule.from_smiles('[H][O][C]([H])([H])[S][C]([H])([H])[H]', allow_undefined_stereo=True, hydrogens_are_explicit=True)

then it works.

To Reproduce

from openff.toolkit.typing.engines.smirnoff import ForceField
from openff.toolkit.topology import Molecule, Topology
from rdkit import Chem
forcefield = ForceField('openff_unconstrained-2.0.0.offxml')
rdmol = Chem.MolFromSmiles('[H][O][C]([H])([H])[S][C]([H])([H])[H]')
mol = Molecule.from_rdkit(rdmol, allow_undefined_stereo=True, hydrogens_are_explicit=True)
topology = Topology.from_molecules([mol])
system = forcefield.create_openmm_system(topology)

Output

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/utilities/utilities.py", line 80, in wrapper
    return function(*args, **kwargs)
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1174, in create_openmm_system
    interchange = self.create_interchange(
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/utilities/utilities.py", line 80, in wrapper
    return function(*args, **kwargs)
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1248, in create_interchange
    return Interchange.from_smirnoff(
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/interchange/components/interchange.py", line 256, in from_smirnoff
    return _create_interchange(
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/interchange/smirnoff/_create.py", line 117, in _create_interchange
    _electrostatics(
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/interchange/smirnoff/_create.py", line 263, in _electrostatics
    "Electrostatics": SMIRNOFFElectrostaticsCollection.create(
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/interchange/smirnoff/_nonbonded.py", line 371, in create
    handler.store_matches(
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/interchange/smirnoff/_nonbonded.py", line 774, in store_matches
    matches, potentials = self._find_reference_matches(
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/interchange/smirnoff/_nonbonded.py", line 629, in _find_reference_matches
    ) = cls._find_charge_model_matches(
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/interchange/smirnoff/_nonbonded.py", line 570, in _find_charge_model_matches
    partial_charges = cls._compute_partial_charges(
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/interchange/smirnoff/_nonbonded.py", line 385, in _compute_partial_charges
    molecule.assign_partial_charges(method)
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/toolkit/topology/molecule.py", line 2603, in assign_partial_charges
    toolkit_registry.call(
  File "/home/peastman/miniconda3/envs/spice/lib/python3.10/site-packages/openff/toolkit/utils/toolkit_registry.py", line 370, in call
    raise ValueError(msg)
ValueError: No registered toolkits can provide the capability "assign_partial_charges" for args "()" and kwargs "{'molecule': Molecule with name '' and SMILES '[C][S][C][O]', 'partial_charge_method': 'am1bcc', 'use_conformers': None, 'strict_n_conformers': False, 'normalize_partial_charges': True, '_cls': <class 'openff.toolkit.topology.molecule.Molecule'>}"
Available toolkits are: [ToolkitWrapper around The RDKit version 2023.03.1, ToolkitWrapper around AmberTools version 22.0, ToolkitWrapper around Built-in Toolkit version None]
 ToolkitWrapper around The RDKit version 2023.03.1 <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : partial_charge_method 'am1bcc' is not available from RDKitToolkitWrapper. Available charge methods are ['gasteiger', 'mmff94'] 
 ToolkitWrapper around AmberTools version 22.0 <class 'openff.toolkit.utils.exceptions.RadicalsNotSupportedError'> : The OpenFF Toolkit does not currently support parsing molecules with S- and P-block radicals. Found 1 radical electrons on molecule [C]S[C][O].
 ToolkitWrapper around Built-in Toolkit version None <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : Partial charge method "am1bcc"" is not supported by the Built-in toolkit. Available charge methods are ['zeros', 'formal_charge']

Computing environment (please complete the following information):

• Operating system

Ubuntu 22.04

• Output of running conda list

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
ambertools                23.0            py310he275f01_1    conda-forge
amberutils                21.0                     pypi_0    pypi
anyio                     3.7.0              pyhd8ed1ab_1    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h5764c6d_3    conda-forge
arpack                    3.7.0                hdefa2d7_2    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.4               h0f2a231_0    conda-forge
boost                     1.78.0          py310hc4a4660_4    conda-forge
boost-cpp                 1.78.0               h6582d0a_3    conda-forge
brotli                    1.0.9                h166bdaf_8    conda-forge
brotli-bin                1.0.9                h166bdaf_8    conda-forge
bzip2                     1.0.8                h7b6447c_0  
c-ares                    1.19.1               hd590300_0    conda-forge
c-blosc2                  2.9.2                hb4ffafa_0    conda-forge
ca-certificates           2023.05.30           h06a4308_0  
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.3.0              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            hbbf8b49_1016    conda-forge
certifi                   2023.5.7           pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_3    conda-forge
charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.3              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7           py310hdf3cbec_0    conda-forge
cudatoolkit               11.8.0              h37601d7_11    conda-forge
curl                      8.1.2                h409715c_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.35         py310hc6cd4ac_0    conda-forge
debugpy                   1.6.7           py310heca2aa9_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
edgembar                  0.2                      pypi_0    pypi
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.1.1              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
fftw                      3.3.10          nompi_hc118613_108    conda-forge
flit-core                 3.9.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.40.0          py310h2372a71_0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
greenlet                  2.0.2           py310hc6cd4ac_1    conda-forge
h5py                      3.8.0           nompi_py310ha66b2ad_101    conda-forge
hdf4                      4.2.15               h501b40f_6    conda-forge
hdf5                      1.14.0          nompi_hb72d44e_103    conda-forge
icu                       72.1                 hcb278e6_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.6.0              pyha770c72_0    conda-forge
importlib_metadata        6.6.0                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.23.1             pyh210e3f2_0    conda-forge
ipython                   8.14.0             pyh41d4057_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.7.5              pyhd8ed1ab_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.2.0              pyhd8ed1ab_0    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            8.2.0              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.0           py310hff52083_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.6.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.1.4              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4           py310hbf28c38_1    conda-forge
krb5                      1.20.1               h81ceb04_0    conda-forge
lcms2                     2.15                 haa2dc70_1    conda-forge
ld_impl_linux-64          2.38                 h1181459_1  
lerc                      4.0.0                h27087fc_0    conda-forge
libaec                    1.0.6                hcb278e6_1    conda-forge
libblas                   3.9.0           17_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_8    conda-forge
libbrotlidec              1.0.9                h166bdaf_8    conda-forge
libbrotlienc              1.0.9                h166bdaf_8    conda-forge
libcblas                  3.9.0           17_linux64_openblas    conda-forge
libcurl                   8.1.2                h409715c_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.4                h6a678d5_0  
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgfortran-ng            13.1.0               h69a702a_0    conda-forge
libgfortran5              13.1.0               h15d22d2_0    conda-forge
libglib                   2.76.3               hebfc3b9_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libjpeg-turbo             2.1.5.1              h0b41bf4_0    conda-forge
liblapack                 3.9.0           17_linux64_openblas    conda-forge
libnetcdf                 4.9.2           nompi_h0f3d0bb_105    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.23          pthreads_h80387f5_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.42.0               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.1.0               hfd8a6a1_0    conda-forge
libtiff                   4.5.0                ha587672_6    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.3.0                h0b41bf4_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxml2                   2.11.4               h0d562d8_0    conda-forge
libzip                    1.9.2                hc929e4a_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markupsafe                2.1.3           py310h2372a71_0    conda-forge
matplotlib-base           3.7.1           py310he60537e_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mctc-lib                  0.3.1                h74f4db8_0    conda-forge
mdtraj                    1.9.7           py310h902c554_4    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclassic                 1.0.0              pyhb4ecaf3_1    conda-forge
nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge
nbconvert                 7.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.5.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.9.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  h6a678d5_0  
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.1           nompi_h4f3791c_100    conda-forge
networkx                  3.1                pyhd8ed1ab_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
notebook                  6.5.4              pyha770c72_0    conda-forge
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
numexpr                   2.8.4           py310h690d005_100    conda-forge
numpy                     1.24.3          py310ha4c1d20_0    conda-forge
ocl-icd                   2.3.1                h7f98852_0    conda-forge
ocl-icd-system            1.0.0                         1    conda-forge
openbabel                 3.1.1           py310h956b46e_7    conda-forge
openff-amber-ff-ports     0.0.3              pyh6c4a22f_0    conda-forge
openff-forcefields        2023.05.1          pyh1a96a4e_1    conda-forge
openff-interchange        0.3.4              pyhd8ed1ab_2    conda-forge
openff-interchange-base   0.3.4              pyhd8ed1ab_2    conda-forge
openff-models             0.0.5              pyh1a96a4e_0    conda-forge
openff-toolkit            0.13.1             pyhd8ed1ab_0    conda-forge
openff-toolkit-base       0.13.1             pyhd8ed1ab_0    conda-forge
openff-units              0.2.0              pyh1a96a4e_2    conda-forge
openff-utilities          0.1.8              pyh1a96a4e_0    conda-forge
openjpeg                  2.5.0                hfec8fc6_2    conda-forge
openmm                    8.0.0           py310h5728c26_1    conda-forge
openssl                   3.1.1                hd590300_1    conda-forge
overrides                 7.3.1              pyhd8ed1ab_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h86c2bf4_0    conda-forge
packmol-memgen            2023.2.24                pypi_0    pypi
pandas                    2.0.2           py310h7cbd5c2_0    conda-forge
pandoc                    3.1.3                h32600fe_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
panedr                    0.7.1              pyhd8ed1ab_0    conda-forge
parmed                    4.1.0           py310heca2aa9_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pbr                       5.11.1             pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
pdb4amber                 22.0                     pypi_0    pypi
pdbfixer                  1.9                pyh1a96a4e_0    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.5.0           py310h582fbeb_1    conda-forge
pint                      0.21               pyhd8ed1ab_0    conda-forge
pip                       23.1.2          py310h06a4308_0  
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.5.3              pyhd8ed1ab_0    conda-forge
pooch                     1.7.0              pyha770c72_3    conda-forge
prometheus_client         0.17.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.38             pyha770c72_0    conda-forge
prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
psutil                    5.9.5           py310h1fa729e_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge
pycairo                   1.23.0          py310hb8a676c_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.9          py310h2372a71_0    conda-forge
pyedr                     0.7.1              pyhd8ed1ab_0    conda-forge
pygments                  2.15.1             pyhd8ed1ab_0    conda-forge
pymsmt                    22.0                     pypi_0    pypi
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3          py310h1fa729e_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.8.0           py310hde6a235_1    conda-forge
python                    3.10.11         he550d4f_0_cpython    conda-forge
python-constraint         1.4.0                      py_0    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.17.1             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0             py310h5764c6d_5    conda-forge
pyzmq                     25.1.0          py310h5bbb5d0_0    conda-forge
rdkit                     2023.03.1       py310h399bcf7_0    conda-forge
readline                  8.2                  h5eee18b_0  
reportlab                 3.6.13          py310h1a56a1c_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
sander                    22.0                     pypi_0    pypi
scipy                     1.10.1          py310ha4c1d20_3    conda-forge
send2trash                1.8.2              pyh41d4057_0    conda-forge
setuptools                67.8.0          py310h06a4308_0  
six                       1.16.0             pyh6c4a22f_0    conda-forge
smirnoff99frosst          1.1.0              pyh44b312d_0    conda-forge
snappy                    1.1.10               h9fff704_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sqlalchemy                2.0.16          py310h2372a71_0    conda-forge
sqlite                    3.41.2               h5eee18b_0  
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h1ccaba5_0  
tornado                   6.3.2           py310h2372a71_0    conda-forge
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.6.3                hd8ed1ab_0    conda-forge
typing_extensions         4.6.3              pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2023c                h04d1e81_0  
unicodedata2              15.0.0          py310h5764c6d_0    conda-forge
urllib3                   2.0.3              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.3              pyhd8ed1ab_0    conda-forge
wheel                     0.38.4          py310h06a4308_0  
widgetsnbextension        3.6.4              pyhd8ed1ab_0    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_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               1.8.5                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.3.0                hd590300_0    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xtb                       6.5.1                h03160e7_1    conda-forge
xtb-python                22.1            py310h1fa729e_0    conda-forge
xz                        5.4.2                h5eee18b_0  
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zlib-ng                   2.0.7                h0b41bf4_0    conda-forge
zstd                      1.5.2                h3eb15da_6    conda-forge

Additional context