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Positions of MonovalentLonePair virtual sites is incorrect (does not affect simulations) #939

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Yoshanuikabundi opened this issue Mar 20, 2024 · 1 comment
Open

Positions of MonovalentLonePair virtual sites is incorrect (does not affect simulations) #939

Yoshanuikabundi opened this issue Mar 20, 2024 · 1 comment

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@Yoshanuikabundi
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Description

In the Virtual Sites vignette, I noticed that the positions Interchange produces for monovalent lone pair virtual sites is incorrect. It looks like the angle is correctly defined, but distances are calculated from the wrong atom, though I haven't investigated this carefully.

Reproduction

vsites-bug-mwe.zip

Output
vsites_interchange_v_openmm

Software versions

  • Which operating system and version are you using? Arch Linux, all packages up to date
  • How did you install Interchange? Micromamba environment
  • What is the output of running conda list?
conda list
List of packages in environment: "/home/joshmitchell/Documents/openff/2024_workshops/.soap/test"

Name                           Version          Build                        Channel

────────────────────────────────────────────────────────────────────────────────────────────

_libgcc_mutex                  0.1              conda_forge                  conda-forge

_openmp_mutex                  4.5              2_gnu                        conda-forge

absl-py                        2.1.0            pyhd8ed1ab_0                 conda-forge

aiohttp                        3.9.3            py310h2372a71_0              conda-forge

aiosignal                      1.3.1            pyhd8ed1ab_0                 conda-forge

ambertools                     22.0             py310h206695f_3              conda-forge

annotated-types                0.6.0            pyhd8ed1ab_0                 conda-forge

anyio                          4.3.0            pyhd8ed1ab_0                 conda-forge

argcomplete                    3.2.3            pyhd8ed1ab_0                 conda-forge

argon2-cffi                    23.1.0           pyhd8ed1ab_0                 conda-forge

argon2-cffi-bindings           21.2.0           py310h2372a71_4              conda-forge

arpack                         3.7.0            hdefa2d7_2                   conda-forge

arrow                          1.3.0            pyhd8ed1ab_0                 conda-forge

arrow-cpp                      11.0.0           ha770c72_5_cpu               conda-forge

ase                            3.22.1           pyhd8ed1ab_1                 conda-forge

asttokens                      2.4.1            pyhd8ed1ab_0                 conda-forge

astunparse                     1.6.3            pyhd8ed1ab_0                 conda-forge

async-lru                      2.0.4            pyhd8ed1ab_0                 conda-forge

async-timeout                  4.0.3            pyhd8ed1ab_0                 conda-forge

attrs                          23.2.0           pyh71513ae_0                 conda-forge

aws-c-auth                     0.6.24           h84a1944_5                   conda-forge

aws-c-cal                      0.5.20           hc60faf5_6                   conda-forge

aws-c-common                   0.8.11           h0b41bf4_0                   conda-forge

aws-c-compression              0.2.16           h034cb4b_3                   conda-forge

aws-c-event-stream             0.2.18           h75388cd_6                   conda-forge

aws-c-http                     0.7.4            hf084cc8_2                   conda-forge

aws-c-io                       0.13.17          h10df833_2                   conda-forge

aws-c-mqtt                     0.8.6            hc41645a_6                   conda-forge

aws-c-s3                       0.2.4            h1b8f470_3                   conda-forge

aws-c-sdkutils                 0.1.7            h034cb4b_3                   conda-forge

aws-checksums                  0.1.14           h034cb4b_3                   conda-forge

aws-crt-cpp                    0.19.7           h0073717_7                   conda-forge

aws-sdk-cpp                    1.10.57          h4707e7a_4                   conda-forge

babel                          2.14.0           pyhd8ed1ab_0                 conda-forge

basis_set_exchange             0.9.1            pyhd8ed1ab_0                 conda-forge

beautifulsoup4                 4.12.3           pyha770c72_0                 conda-forge

binutils_impl_linux-64         2.40             hf600244_0                   conda-forge

binutils_linux-64              2.40             hbdbef99_2                   conda-forge

biopython                      1.83             py310h2372a71_0              conda-forge

black                          24.2.0           py310hff52083_0              conda-forge

bleach                         6.1.0            pyhd8ed1ab_0                 conda-forge

blinker                        1.7.0            pyhd8ed1ab_0                 conda-forge

blosc                          1.21.5           h0f2a231_0                   conda-forge

boost                          1.74.0           py310h7c3ba0c_5              conda-forge

boost-cpp                      1.74.0           h75c5d50_8                   conda-forge

brotli                         1.0.9            h166bdaf_9                   conda-forge

brotli-bin                     1.0.9            h166bdaf_9                   conda-forge

brotli-python                  1.0.9            py310hd8f1fbe_9              conda-forge

bson                           0.5.9            py_0                         conda-forge

bzip2                          1.0.8            hd590300_5                   conda-forge

c-ares                         1.27.0           hd590300_0                   conda-forge

ca-certificates                2024.2.2         hbcca054_0                   conda-forge

cached-property                1.5.2            hd8ed1ab_1                   conda-forge

cached_property                1.5.2            pyha770c72_1                 conda-forge

cachetools                     5.3.3            pyhd8ed1ab_0                 conda-forge

cairo                          1.16.0           ha61ee94_1014                conda-forge

cattrs                         23.2.3           pyhd8ed1ab_0                 conda-forge

certifi                        2024.2.2         pyhd8ed1ab_0                 conda-forge

cffi                           1.16.0           py310h2fee648_0              conda-forge

cftime                         1.6.3            py310h1f7b6fc_0              conda-forge

chardet                        5.2.0            py310hff52083_1              conda-forge

charset-normalizer             3.3.2            pyhd8ed1ab_0                 conda-forge

chemper                        1.0.1            pyhd8ed1ab_0                 conda-forge

click                          8.1.7            unix_pyh707e725_0            conda-forge

click-option-group             0.5.6            pyhd8ed1ab_0                 conda-forge

cloudpickle                    3.0.0            pyhd8ed1ab_0                 conda-forge

cmake                          3.28.3           hcfe8598_0                   conda-forge

colorama                       0.4.6            pyhd8ed1ab_0                 conda-forge

comm                           0.2.1            pyhd8ed1ab_0                 conda-forge

contourpy                      1.2.0            py310hd41b1e2_0              conda-forge

cryptography                   42.0.5           py310h75e40e8_0              conda-forge

cudatoolkit                    11.8.0           h4ba93d1_13                  conda-forge

curl                           8.5.0            hca28451_0                   conda-forge

cycler                         0.12.1           pyhd8ed1ab_0                 conda-forge

cython                         3.0.9            py310hc6cd4ac_0              conda-forge

cytoolz                        0.12.3           py310h2372a71_0              conda-forge

dask-core                      2024.2.1         pyhd8ed1ab_0                 conda-forge

dask-jobqueue                  0.8.5            pyhd8ed1ab_0                 conda-forge

debugpy                        1.8.1            py310hc6cd4ac_0              conda-forge

decorator                      5.1.1            pyhd8ed1ab_0                 conda-forge

defusedxml                     0.7.1            pyhd8ed1ab_0                 conda-forge

dgl                            1.1.2            py310hbc80768_2              conda-forge

distributed                    2024.2.1         pyhd8ed1ab_0                 conda-forge

dockstring                     0.3.2            pyhd8ed1ab_0                 conda-forge

docstring-to-markdown          0.15             pyhd8ed1ab_0                 conda-forge

entrypoints                    0.4              pyhd8ed1ab_0                 conda-forge

exceptiongroup                 1.2.0            pyhd8ed1ab_2                 conda-forge

executing                      2.0.1            pyhd8ed1ab_0                 conda-forge

expat                          2.6.1            h59595ed_0                   conda-forge

f90wrap                        0.2.13           py310h03ae0af_2              conda-forge

fasteners                      0.17.3           pyhd8ed1ab_0                 conda-forge

fftw                           3.3.10           nompi_hc118613_108           conda-forge

filelock                       3.13.1           pyhd8ed1ab_0                 conda-forge

flask                          3.0.2            pyhd8ed1ab_0                 conda-forge

flatbuffers                    22.12.06         hcb278e6_2                   conda-forge

font-ttf-dejavu-sans-mono      2.37             hab24e00_0                   conda-forge

font-ttf-inconsolata           3.000            h77eed37_0                   conda-forge

font-ttf-source-code-pro       2.038            h77eed37_0                   conda-forge

font-ttf-ubuntu                0.83             h77eed37_1                   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                      4.49.0           py310h2372a71_0              conda-forge

fqdn                           1.5.1            pyhd8ed1ab_0                 conda-forge

freetype                       2.12.1           h267a509_2                   conda-forge

freetype-py                    2.3.0            pyhd8ed1ab_0                 conda-forge

frozenlist                     1.4.1            py310h2372a71_0              conda-forge

fsspec                         2024.2.0         pyhca7485f_0                 conda-forge

gast                           0.4.0            pyh9f0ad1d_0                 conda-forge

gawk                           5.3.0            ha916aea_0                   conda-forge

gcc_impl_linux-64              11.4.0           h7aa1c59_5                   conda-forge

gcc_linux-64                   11.4.0           hfd045f2_2                   conda-forge

gettext                        0.21.1           h27087fc_0                   conda-forge

gflags                         2.2.2            he1b5a44_1004                conda-forge

gfortran_impl_linux-64         11.4.0           h86428dc_5                   conda-forge

gfortran_linux-64              11.4.0           h3047280_2                   conda-forge

giflib                         5.2.1            h0b41bf4_3                   conda-forge

gitdb                          4.0.11           pyhd8ed1ab_0                 conda-forge

gitpython                      3.1.42           pyhd8ed1ab_0                 conda-forge

glog                           0.6.0            h6f12383_0                   conda-forge

gmp                            6.3.0            h59595ed_0                   conda-forge

gmpy2                          2.1.2            py310h3ec546c_1              conda-forge

google-auth                    2.28.2           pyhca7485f_0                 conda-forge

google-auth-oauthlib           0.4.6            pyhd8ed1ab_0                 conda-forge

google-pasta                   0.2.0            pyh8c360ce_0                 conda-forge

greenlet                       3.0.3            py310hc6cd4ac_0              conda-forge

griddataformats                1.0.2            pyhd8ed1ab_0                 conda-forge

gromacs                        2023.1           nompi_h76c6bb2_102           conda-forge

grpcio                         1.51.1           py310h4a5735c_1              conda-forge

gsd                            3.2.1            py310h1f7b6fc_0              conda-forge

gsl                            2.7              he838d99_0                   conda-forge

gxx_impl_linux-64              11.4.0           h7aa1c59_5                   conda-forge

gxx_linux-64                   11.4.0           hfc1ae95_2                   conda-forge

h11                            0.14.0           pyhd8ed1ab_0                 conda-forge

h2                             4.1.0            pyhd8ed1ab_0                 conda-forge

h5py                           3.8.0            nompi_py310h0311031_100      conda-forge

hdf4                           4.2.15           h9772cbc_5                   conda-forge

hdf5                           1.12.2           nompi_h4df4325_101           conda-forge

hpack                          4.0.0            pyh9f0ad1d_0                 conda-forge

httpcore                       1.0.4            pyhd8ed1ab_0                 conda-forge

httpx                          0.27.0           pyhd8ed1ab_0                 conda-forge

hyperframe                     6.0.1            pyhd8ed1ab_0                 conda-forge

icu                            70.1             h27087fc_0                   conda-forge

idna                           3.6              pyhd8ed1ab_0                 conda-forge

importlib-metadata             7.0.2            pyha770c72_0                 conda-forge

importlib_metadata             7.0.2            hd8ed1ab_0                   conda-forge

importlib_resources            6.1.3            pyhd8ed1ab_0                 conda-forge

ipykernel                      6.29.3           pyhd33586a_0                 conda-forge

ipython                        8.22.2           pyh707e725_0                 conda-forge

ipywidgets                     8.1.2            pyhd8ed1ab_0                 conda-forge

isoduration                    20.11.0          pyhd8ed1ab_0                 conda-forge

isort                          5.13.2           pyhd8ed1ab_0                 conda-forge

itsdangerous                   2.1.2            pyhd8ed1ab_0                 conda-forge

jax                            0.4.4            pyhd8ed1ab_0                 conda-forge

jaxlib                         0.4.3            cpu_py310hdc47304_1          conda-forge

jedi                           0.19.1           pyhd8ed1ab_0                 conda-forge

jedi-language-server           0.41.3           pyhd8ed1ab_0                 conda-forge

jinja2                         3.1.3            pyhd8ed1ab_0                 conda-forge

joblib                         1.3.2            pyhd8ed1ab_0                 conda-forge

jpeg                           9e               h0b41bf4_3                   conda-forge

json5                          0.9.22           pyhd8ed1ab_0                 conda-forge

jsonpointer                    2.4              py310hff52083_3              conda-forge

jsonschema                     4.21.1           pyhd8ed1ab_0                 conda-forge

jsonschema-specifications      2023.12.1        pyhd8ed1ab_0                 conda-forge

jsonschema-with-format-nongpl  4.21.1           pyhd8ed1ab_0                 conda-forge

jupyter-lsp                    2.2.4            pyhd8ed1ab_0                 conda-forge

jupyter_client                 8.6.0            pyhd8ed1ab_0                 conda-forge

jupyter_core                   5.7.1            py310hff52083_0              conda-forge

jupyter_events                 0.9.0            pyhd8ed1ab_0                 conda-forge

jupyter_server                 2.13.0           pyhd8ed1ab_0                 conda-forge

jupyter_server_terminals       0.5.2            pyhd8ed1ab_0                 conda-forge

jupyterlab                     4.1.4            pyhd8ed1ab_0                 conda-forge

jupyterlab-lsp                 5.1.0            pyhd8ed1ab_1                 conda-forge

jupyterlab_code_formatter      2.2.1            pyhd8ed1ab_0                 conda-forge

jupyterlab_execute_time        3.1.2            pyhd8ed1ab_0                 conda-forge

jupyterlab_pygments            0.3.0            pyhd8ed1ab_1                 conda-forge

jupyterlab_server              2.25.3           pyhd8ed1ab_0                 conda-forge

jupyterlab_widgets             3.0.10           pyhd8ed1ab_0                 conda-forge

keras                          2.11.0           pyhd8ed1ab_0                 conda-forge

keras-preprocessing            1.1.2            pyhd8ed1ab_0                 conda-forge

kernel-headers_linux-64        2.6.32           he073ed8_17                  conda-forge

keyutils                       1.6.1            h166bdaf_0                   conda-forge

kim-api                        2.3.0            h097297d_1                   conda-forge

kiwisolver                     1.4.5            py310hd41b1e2_1              conda-forge

krb5                           1.21.2           h659d440_0                   conda-forge

lammps                         2022.06.23       py310hedc66b7_mpich_5        conda-forge

lcms2                          2.15             hfd0df8a_0                   conda-forge

ld_impl_linux-64               2.40             h41732ed_0                   conda-forge

lerc                           4.0.0            h27087fc_0                   conda-forge

libabseil                      20220623.0       cxx17_h05df665_6             conda-forge

libaec                         1.1.2            h59595ed_1                   conda-forge

libarrow                       11.0.0           h2ebd325_5_cpu               conda-forge

libblas                        3.9.0            21_linux64_openblas          conda-forge

libbrotlicommon                1.0.9            h166bdaf_9                   conda-forge

libbrotlidec                   1.0.9            h166bdaf_9                   conda-forge

libbrotlienc                   1.0.9            h166bdaf_9                   conda-forge

libcblas                       3.9.0            21_linux64_openblas          conda-forge

libcrc32c                      1.1.2            h9c3ff4c_0                   conda-forge

libcurl                        8.5.0            hca28451_0                   conda-forge

libdeflate                     1.17             h0b41bf4_0                   conda-forge

libedit                        3.1.20191231     he28a2e2_2                   conda-forge

libev                          4.33             hd590300_2                   conda-forge

libevent                       2.1.10           h28343ad_4                   conda-forge

libexpat                       2.6.1            h59595ed_0                   conda-forge

libffi                         3.4.2            h7f98852_5                   conda-forge

libgcc-devel_linux-64          11.4.0           h922705a_105                 conda-forge

libgcc-ng                      13.2.0           h807b86a_5                   conda-forge

libgfortran-ng                 13.2.0           h69a702a_5                   conda-forge

libgfortran5                   13.2.0           ha4646dd_5                   conda-forge

libglib                        2.78.4           hf2295e7_4                   conda-forge

libgomp                        13.2.0           h807b86a_5                   conda-forge

libgoogle-cloud                2.7.0            h21dfe5b_1                   conda-forge

libgrpc                        1.51.1           h4fad500_1                   conda-forge

libhwloc                       2.9.1            hd6dc26d_0                   conda-forge

libiconv                       1.17             hd590300_2                   conda-forge

libidn2                        2.3.7            hd590300_0                   conda-forge

liblapack                      3.9.0            21_linux64_openblas          conda-forge

liblapacke                     3.9.0            21_linux64_openblas          conda-forge

libllvm14                      14.0.6           hcd5def8_4                   conda-forge

libnetcdf                      4.8.1            nompi_h261ec11_106           conda-forge

libnghttp2                     1.58.0           h47da74e_1                   conda-forge

libnsl                         2.0.1            hd590300_0                   conda-forge

libopenblas                    0.3.26           pthreads_h413a1c8_0          conda-forge

libpng                         1.6.43           h2797004_0                   conda-forge

libprotobuf                    3.21.12          hfc55251_2                   conda-forge

libsanitizer                   11.4.0           h4dcbe23_5                   conda-forge

libsodium                      1.0.18           h36c2ea0_1                   conda-forge

libsqlite                      3.45.1           h2797004_0                   conda-forge

libssh2                        1.11.0           h0841786_0                   conda-forge

libstdcxx-devel_linux-64       11.4.0           h922705a_105                 conda-forge

libstdcxx-ng                   13.2.0           h7e041cc_5                   conda-forge

libthrift                      0.18.0           h5e4af38_0                   conda-forge

libtiff                        4.5.0            h6adf6a1_2                   conda-forge

libunistring                   0.9.10           h7f98852_0                   conda-forge

libutf8proc                    2.8.0            h166bdaf_0                   conda-forge

libuuid                        2.38.1           h0b41bf4_0                   conda-forge

libuv                          1.48.0           hd590300_0                   conda-forge

libwebp-base                   1.3.2            hd590300_0                   conda-forge

libxcb                         1.13             h7f98852_1004                conda-forge

libxcrypt                      4.4.36           hd590300_1                   conda-forge

libxml2                        2.10.3           hca2bb57_4                   conda-forge

libxslt                        1.1.37           h873f0b0_0                   conda-forge

libzip                         1.10.1           h2629f0a_3                   conda-forge

libzlib                        1.2.13           hd590300_5                   conda-forge

lightning-utilities            0.10.1           pyhd8ed1ab_0                 conda-forge

llvmlite                       0.42.0           py310h1b8f574_1              conda-forge

locket                         1.0.0            pyhd8ed1ab_0                 conda-forge

lsprotocol                     2023.0.1         pyhd8ed1ab_0                 conda-forge

lxml                           4.9.2            py310hbdc0903_0              conda-forge

lz4-c                          1.9.4            hcb278e6_0                   conda-forge

lzo                            2.10             h516909a_1000                conda-forge

make                           4.3              hd18ef5c_1                   conda-forge

markdown                       3.5.2            pyhd8ed1ab_0                 conda-forge

markdown-it-py                 3.0.0            pyhd8ed1ab_0                 conda-forge

markupsafe                     2.1.5            py310h2372a71_0              conda-forge

matplotlib-base                3.8.3            py310h62c0568_0              conda-forge

matplotlib-inline              0.1.6            pyhd8ed1ab_0                 conda-forge

mctc-lib                       0.3.1            h74f4db8_0                   conda-forge

mda-xdrlib                     0.2.0            pyhd8ed1ab_0                 conda-forge

mdanalysis                     2.7.0            py310hcc13569_1              conda-forge

mdtraj                         1.9.9            py310h523e8d7_1              conda-forge

mdurl                          0.1.2            pyhd8ed1ab_0                 conda-forge

metis                          5.1.1            h59595ed_2                   conda-forge

mistune                        3.0.2            pyhd8ed1ab_0                 conda-forge

mlip                           1.0              hd0d41c4_3                   conda-forge

mmcif_pdbx                     2.0.1            pyhd8ed1ab_0                 conda-forge

mmtf-python                    1.1.3            pyhd8ed1ab_0                 conda-forge

mpc                            1.3.1            hfe3b2da_0                   conda-forge

mpfr                           4.2.1            h9458935_0                   conda-forge

mpi                            1.0              mpich                        conda-forge

mpich                          4.2.0            h846660c_100                 conda-forge

mpiplus                        v0.0.2           pyhd8ed1ab_0                 conda-forge

mpmath                         1.3.0            pyhd8ed1ab_0                 conda-forge

mrcfile                        1.5.0            pyhd8ed1ab_0                 conda-forge

msgpack-python                 1.0.7            py310hd41b1e2_0              conda-forge

multidict                      6.0.5            py310h2372a71_0              conda-forge

munkres                        1.1.4            pyh9f0ad1d_0                 conda-forge

mypy_extensions                1.0.0            pyha770c72_0                 conda-forge

n2p2                           2.1.4            py310hbd49d13_2              conda-forge

nbclient                       0.8.0            pyhd8ed1ab_0                 conda-forge

nbconvert                      7.16.2           pyhd8ed1ab_0                 conda-forge

nbconvert-core                 7.16.2           pyhd8ed1ab_0                 conda-forge

nbconvert-pandoc               7.16.2           pyhd8ed1ab_0                 conda-forge

nbformat                       5.9.2            pyhd8ed1ab_0                 conda-forge

ncurses                        6.4              h59595ed_2                   conda-forge

nest-asyncio                   1.6.0            pyhd8ed1ab_0                 conda-forge

netcdf-fortran                 4.6.0            nompi_he1eeb6f_102           conda-forge

netcdf4                        1.6.2            nompi_py310h55e1e36_100      conda-forge

networkx                       3.2.1            pyhd8ed1ab_0                 conda-forge

nglview                        3.1.2            pyh15ce09e_0                 conda-forge

nomkl                          1.0              h5ca1d4c_0                   conda-forge

nose                           1.3.7            py_1006                      conda-forge

notebook                       7.1.1            pyhd8ed1ab_0                 conda-forge

notebook-shim                  0.2.4            pyhd8ed1ab_0                 conda-forge

numba                          0.59.0           py310h7dc5dd1_1              conda-forge

numexpr                        2.9.0            py310hc2d3c2e_100            conda-forge

numpy                          1.26.4           py310hb13e2d6_0              conda-forge

oauthlib                       3.2.2            pyhd8ed1ab_0                 conda-forge

ocl-icd                        2.3.2            hd590300_0                   conda-forge

ocl-icd-system                 1.0.0            1                            conda-forge

openbabel                      3.1.1            py310heaf86c6_5              conda-forge

openff-amber-ff-ports          0.0.4            pyhca7485f_0                 conda-forge

openff-forcefields             2024.03.0        pyhca7485f_0                 conda-forge

openff-interchange             0.3.23           pyhd8ed1ab_0                 conda-forge

openff-interchange-base        0.3.23           pyhd8ed1ab_0                 conda-forge

openff-models                  0.1.2            pyhca7485f_0                 conda-forge

openff-nagl                    0.3.4            pyhd8ed1ab_0                 conda-forge

openff-nagl-base               0.3.4            pyhd8ed1ab_0                 conda-forge

openff-nagl-models             0.1.2            pyhd8ed1ab_0                 conda-forge

openff-qcsubmit                0.50.2           pyhd8ed1ab_0                 conda-forge

openff-recharge                0.5.2            pyhd8ed1ab_0                 conda-forge

openff-toolkit                 0.15.2           pyhd8ed1ab_0                 conda-forge

openff-toolkit-base            0.15.2           pyhd8ed1ab_0                 conda-forge

openff-toolkit-examples        0.15.2           hd8ed1ab_0                   conda-forge

openff-units                   0.2.1            pyh1a96a4e_0                 conda-forge

openff-utilities               0.1.12           pyhd8ed1ab_0                 conda-forge

openjpeg                       2.5.0            hfec8fc6_2                   conda-forge

openmm                         8.1.1            py310h43b6314_1              conda-forge

openmmforcefields              0.12.0           pyhd8ed1ab_0                 conda-forge

openmmtools                    0.23.1           pyhd8ed1ab_0                 conda-forge

openssl                        3.2.1            hd590300_0                   conda-forge

opt_einsum                     3.3.0            pyhc1e730c_2                 conda-forge

orc                            1.8.2            hfdbbad2_2                   conda-forge

overrides                      7.7.0            pyhd8ed1ab_0                 conda-forge

packaging                      23.2             pyhd8ed1ab_0                 conda-forge

packmol                        20.010           h86c2bf4_0                   conda-forge

pandas                         2.2.1            py310hcc13569_0              conda-forge

pandoc                         3.1.12.2         ha770c72_0                   conda-forge

pandocfilters                  1.5.0            pyhd8ed1ab_0                 conda-forge

panedr                         0.8.0            pyhd8ed1ab_0                 conda-forge

parmed                         3.4.4            py310heca2aa9_0              conda-forge

parquet-cpp                    1.5.1            2                            conda-forge

parso                          0.8.3            pyhd8ed1ab_0                 conda-forge

partd                          1.4.1            pyhd8ed1ab_0                 conda-forge

pathspec                       0.12.1           pyhd8ed1ab_0                 conda-forge

patsy                          0.5.6            pyhd8ed1ab_0                 conda-forge

pcre2                          10.43            hcad00b1_0                   conda-forge

pdb2pqr                        3.6.1            pyhd8ed1ab_0                 conda-forge

pdbfixer                       1.9              pyh1a96a4e_0                 conda-forge

perl                           5.32.1           7_hd590300_perl5             conda-forge

pexpect                        4.9.0            pyhd8ed1ab_0                 conda-forge

pickleshare                    0.7.5            py_1003                      conda-forge

pillow                         9.4.0            py310h023d228_1              conda-forge

pint                           0.21             pyhd8ed1ab_0                 conda-forge

pip                            24.0             pyhd8ed1ab_0                 conda-forge

pixman                         0.43.2           h59595ed_0                   conda-forge

pkg-config                     0.29.2           h36c2ea0_1008                conda-forge

pkgutil-resolve-name           1.3.10           pyhd8ed1ab_1                 conda-forge

platformdirs                   4.2.0            pyhd8ed1ab_0                 conda-forge

plotly                         5.19.0           pyhd8ed1ab_0                 conda-forge

plumed                         2.9.0            nompi_h752ec8b_100           conda-forge

prometheus_client              0.20.0           pyhd8ed1ab_0                 conda-forge

prompt-toolkit                 3.0.42           pyha770c72_0                 conda-forge

propka                         3.5.1            pyhc1e730c_1                 conda-forge

protobuf                       4.21.12          py310heca2aa9_0              conda-forge

psutil                         5.9.8            py310h2372a71_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

pyarrow                        11.0.0           py310h633f555_5_cpu          conda-forge

pyasn1                         0.5.1            pyhd8ed1ab_0                 conda-forge

pyasn1-modules                 0.3.0            pyhd8ed1ab_0                 conda-forge

pycairo                        1.25.0           py310hda9f760_1              conda-forge

pycparser                      2.21             pyhd8ed1ab_0                 conda-forge

pydantic                       2.6.3            pyhd8ed1ab_0                 conda-forge

pydantic-core                  2.16.3           py310hcb5633a_0              conda-forge

pyedr                          0.8.0            pyhd8ed1ab_0                 conda-forge

pygls                          1.3.0            pyhd8ed1ab_0                 conda-forge

pygments                       2.17.2           pyhd8ed1ab_0                 conda-forge

pyjwt                          2.8.0            pyhd8ed1ab_1                 conda-forge

pymbar                         4.0.2            hff52083_0                   conda-forge

pymbar-core                    4.0.2            py310h278f3c1_0              conda-forge

pyopenssl                      24.0.0           pyhd8ed1ab_0                 conda-forge

pyparsing                      3.1.2            pyhd8ed1ab_0                 conda-forge

pysocks                        1.7.1            pyha2e5f31_6                 conda-forge

pytables                       3.7.0            py310hb60b9b2_3              conda-forge

python                         3.10.13          hd12c33a_1_cpython           conda-forge

python-constraint              1.4.0            py_0                         conda-forge

python-dateutil                2.9.0            pyhd8ed1ab_0                 conda-forge

python-fastjsonschema          2.19.1           pyhd8ed1ab_0                 conda-forge

python-flatbuffers             24.3.6           pyh59ac667_0                 conda-forge

python-json-logger             2.0.7            pyhd8ed1ab_0                 conda-forge

python-tzdata                  2024.1           pyhd8ed1ab_0                 conda-forge

python_abi                     3.10             4_cp310                      conda-forge

pytng                          0.3.1            py310h7d11597_1              conda-forge

pytorch                        2.0.0            cpu_generic_py310h7ffd2bf_1  conda-forge

pytorch-lightning              2.2.1            pyhd8ed1ab_0                 conda-forge

pytz                           2024.1           pyhd8ed1ab_0                 conda-forge

pyu2f                          0.1.5            pyhd8ed1ab_0                 conda-forge

pyyaml                         6.0.1            py310h2372a71_1              conda-forge

pyzmq                          25.1.2           py310h795f18f_0              conda-forge

qcelemental                    0.27.1           pyhd8ed1ab_0                 conda-forge

qcengine                       0.29.0           pyhd8ed1ab_0                 conda-forge

qcportal                       0.53             pyhd8ed1ab_0                 conda-forge

quippy                         0.0.1            py310hd2eb85d_4              conda-forge

rdkit                          2022.03.5        py310h1c297d8_0              conda-forge

re2                            2023.02.01       hcb278e6_0                   conda-forge

readline                       8.2              h8228510_1                   conda-forge

referencing                    0.33.0           pyhd8ed1ab_0                 conda-forge

regex                          2023.12.25       py310h2372a71_0              conda-forge

reportlab                      4.1.0            py310h2372a71_0              conda-forge

requests                       2.31.0           pyhd8ed1ab_0                 conda-forge

requests-oauthlib              1.3.1            pyhd8ed1ab_0                 conda-forge

rfc3339-validator              0.1.4            pyhd8ed1ab_0                 conda-forge

rfc3986-validator              0.1.1            pyh9f0ad1d_0                 conda-forge

rhash                          1.4.4            hd590300_0                   conda-forge

rich                           13.7.1           pyhd8ed1ab_0                 conda-forge

rlpycairo                      0.2.0            pyhd8ed1ab_0                 conda-forge

rpds-py                        0.18.0           py310hcb5633a_0              conda-forge

rsa                            4.9              pyhd8ed1ab_0                 conda-forge

s2n                            1.3.37           h3358134_0                   conda-forge

scikit-learn                   1.4.1.post1      py310h1fdf081_0              conda-forge

scipy                          1.12.0           py310hb13e2d6_2              conda-forge

seaborn                        0.13.2           hd8ed1ab_0                   conda-forge

seaborn-base                   0.13.2           pyhd8ed1ab_0                 conda-forge

send2trash                     1.8.2            pyh41d4057_0                 conda-forge

setuptools                     69.1.1           pyhd8ed1ab_0                 conda-forge

six                            1.16.0           pyh6c4a22f_0                 conda-forge

sleef                          3.5.1            h9b69904_2                   conda-forge

smirnoff99frosst               1.1.0            pyh44b312d_0                 conda-forge

smmap                          5.0.0            pyhd8ed1ab_0                 conda-forge

snappy                         1.1.10           h9fff704_0                   conda-forge

sniffio                        1.3.1            pyhd8ed1ab_0                 conda-forge

sortedcontainers               2.4.0            pyhd8ed1ab_0                 conda-forge

soupsieve                      2.5              pyhd8ed1ab_1                 conda-forge

sqlalchemy                     2.0.28           py310h2372a71_0              conda-forge

sqlite                         3.45.1           h2c6b66d_0                   conda-forge

stack_data                     0.6.2            pyhd8ed1ab_0                 conda-forge

statsmodels                    0.14.1           py310h1f7b6fc_0              conda-forge

sympy                          1.12             pypyh9d50eac_103             conda-forge

sysroot_linux-64               2.12             he073ed8_17                  conda-forge

tabulate                       0.9.0            pyhd8ed1ab_1                 conda-forge

tblib                          3.0.0            pyhd8ed1ab_0                 conda-forge

tenacity                       8.2.3            pyhd8ed1ab_0                 conda-forge

tensorboard                    2.11.2           pyhd8ed1ab_0                 conda-forge

tensorboard-data-server        0.6.1            py310h600f1e7_4              conda-forge

tensorboard-plugin-wit         1.8.1            pyhd8ed1ab_0                 conda-forge

tensorflow                     2.11.0           cpu_py310hd1aba9c_0          conda-forge

tensorflow-base                2.11.0           cpu_py310hc9b7e7f_0          conda-forge

tensorflow-estimator           2.11.0           cpu_py310hfed9998_0          conda-forge

termcolor                      2.4.0            pyhd8ed1ab_0                 conda-forge

terminado                      0.18.0           pyh0d859eb_0                 conda-forge

threadpoolctl                  3.3.0            pyhc1e730c_0                 conda-forge

tidynamics                     1.1.2            pyhd8ed1ab_0                 conda-forge

tinycss2                       1.2.1            pyhd8ed1ab_0                 conda-forge

tinydb                         4.8.0            pyhd8ed1ab_0                 conda-forge

tk                             8.6.13           noxft_h4845f30_101           conda-forge

tomli                          2.0.1            pyhd8ed1ab_0                 conda-forge

toolz                          0.12.1           pyhd8ed1ab_0                 conda-forge

torchmetrics                   1.3.1            pyhd8ed1ab_0                 conda-forge

tornado                        6.4              py310h2372a71_0              conda-forge

tqdm                           4.66.2           pyhd8ed1ab_0                 conda-forge

traitlets                      5.14.1           pyhd8ed1ab_0                 conda-forge

types-python-dateutil          2.8.19.20240106  pyhd8ed1ab_0                 conda-forge

typing-extensions              4.10.0           hd8ed1ab_0                   conda-forge

typing_extensions              4.10.0           pyha770c72_0                 conda-forge

typing_utils                   0.1.0            pyhd8ed1ab_0                 conda-forge

tzdata                         2024a            h0c530f3_0                   conda-forge

unicodedata2                   15.1.0           py310h2372a71_0              conda-forge

unidecode                      1.3.8            pyhd8ed1ab_0                 conda-forge

uri-template                   1.3.0            pyhd8ed1ab_0                 conda-forge

urllib3                        2.2.1            pyhd8ed1ab_0                 conda-forge

validators                     0.22.0           pyhd8ed1ab_0                 conda-forge

voro                           0.4.6            h00ab1b0_0                   conda-forge

wcwidth                        0.2.13           pyhd8ed1ab_0                 conda-forge

webcolors                      1.13             pyhd8ed1ab_0                 conda-forge

webencodings                   0.5.1            pyhd8ed1ab_2                 conda-forge

websocket-client               1.7.0            pyhd8ed1ab_0                 conda-forge

werkzeug                       3.0.1            pyhd8ed1ab_0                 conda-forge

wget                           1.20.3           ha35d2d1_1                   conda-forge

wheel                          0.42.0           pyhd8ed1ab_0                 conda-forge

widgetsnbextension             4.0.10           pyhd8ed1ab_0                 conda-forge

wrapt                          1.16.0           py310h2372a71_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                    1.8.4            h0b41bf4_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                             5.2.6            h166bdaf_0                   conda-forge

yaml                           0.2.5            h7f98852_2                   conda-forge

yarl                           1.9.4            py310h2372a71_0              conda-forge

zeromq                         4.3.5            h59595ed_1                   conda-forge

zict                           3.0.0            pyhd8ed1ab_0                 conda-forge

zipp                           3.17.0           pyhd8ed1ab_0                 conda-forge

zlib                           1.2.13           hd590300_5                   conda-forge

zstandard                      0.22.0           py310h1275a96_0              conda-forge

zstd                           1.5.5            hfc55251_0                   conda-forge

@mattwthompson
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This is one of my louder xfails:

openff-interchange/openff/interchange/_tests/unit_tests/interop/test_virtual_sites.py

Line 129 in 732079e

# TODO: Fix me!

The context, including links to the implementation it's copied from, is here: #832 (comment)

The other types of virtual sites seem to be fine, so those failures were super confusing.

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