`Topology.set_positions` chokes when setting positions on `_SimpleMolecule`s which lacked conformers
mattwthompson opened this issue · 0 comments
mattwthompson commented
Describe the bug
To Reproduce
In [1]: import numpy
In [2]: from openff.toolkit import Molecule, Topology, Quantity
In [3]: from openff.toolkit.topology._mm_molecule import _SimpleMolecule
In [4]: simple = _SimpleMolecule.from_molecule(Molecule.from_smiles("CCO"))
In [5]: topology = Topology.from_molecules([simple, simple])
In [6]: topology.set_positions(Quantity(numpy.zeros((topology.n_atoms, 3)), "nanometer"))
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[6], line 1
----> 1 topology.set_positions(Quantity(numpy.zeros((topology.n_atoms, 3)), "nanometer"))
File ~/software/openff-toolkit/openff/toolkit/topology/topology.py:2175, in Topology.set_positions(self, array)
2173 molecule._conformers = [array[start:stop]]
2174 else:
-> 2175 molecule.conformers = [array[start:stop]] # type: ignore[misc]
2176 else:
2177 molecule.conformers[0:1] = [array[start:stop]]
AttributeError: property 'conformers' of '_SimpleMolecule' object has no setterOutput
Computing environment (please complete the following information):
- Operating system
- Output of running
conda list
$ zsh ~/software/status/devtools/support/debug.sh 8:18:34 ☁ 0.16.0 ☂
=====================================HEADER=====================================
Run this script with your conda/mamba environment activated
Invoke the script like this:
source debug.sh | tee -a debug.log
Then copy/upload/send us debug.log
If pasting to a GitHub issue, it might be useful to put into an expandable block
<details>
<summary>Debug log (click me!)</summary>
Copy the debug log here!
</details>
https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/organizing-information-with-collapsed-sections
=====================================SYSTEM=====================================
Fri Apr 26 08:18:38 CDT 2024
darwin23.0
arm64
/Users/mattthompson/software/status/devtools/support/debug.sh:31: command not found: nvidia-smi
no nvidia-smi, system either does not have an nvidia card or cuda is not properly configured
=====================================CONDA======================================
/Users/mattthompson/micromamba/envs/openff-toolkit-test/bin/python
/Users/mattthompson/software/status/devtools/support/debug.sh:36: command not found: conda
no conda
/Users/mattthompson/software/status/devtools/support/debug.sh:37: command not found: mamba
no mamba
libmamba version : 1.5.8
micromamba version : 1.5.8
curl version : libcurl/8.4.0 (SecureTransport) LibreSSL/3.3.6 zlib/1.2.12 nghttp2/1.58.0
libarchive version : libarchive 3.5.3 zlib/1.2.12 liblzma/5.4.3 bz2lib/1.0.8
envs directories : /Users/mattthompson/micromamba/envs
package cache : /Users/mattthompson/micromamba/pkgs
/Users/mattthompson/.mamba/pkgs
environment : openff-toolkit-test (active)
env location : /Users/mattthompson/micromamba/envs/openff-toolkit-test
user config files : /Users/mattthompson/.mambarc
populated config files : /Users/mattthompson/.mambarc
virtual packages : __unix=0=0
__osx=14.4=0
__archspec=1=arm64
channels :
base environment : /Users/mattthompson/micromamba
platform : osx-arm64
/Users/mattthompson/software/status/devtools/support/debug.sh:40: command not found: conda
no conda
/Users/mattthompson/software/status/devtools/support/debug.sh:41: command not found: mamba
no mamba
List of packages in environment: "/Users/mattthompson/micromamba/envs/openff-toolkit-test"
Name Version Build Channel
─────────────────────────────────────────────────────────────────────────────────────
ambertools 23.3 py311hd5bda53_6 conda-forge
appnope 0.1.4 pyhd8ed1ab_0 conda-forge
arpack 3.8.0 nompi_ha3438d0_101 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
aws-c-auth 0.7.16 h51b92d1_6 conda-forge
aws-c-cal 0.6.10 hf888d4c_1 conda-forge
aws-c-common 0.9.13 h93a5062_0 conda-forge
aws-c-compression 0.2.18 hf888d4c_1 conda-forge
aws-c-event-stream 0.4.2 h1b95c93_4 conda-forge
aws-c-http 0.8.1 heb97226_5 conda-forge
aws-c-io 0.14.5 hb51f26e_1 conda-forge
aws-c-mqtt 0.10.2 hd37591b_4 conda-forge
aws-c-s3 0.5.2 h09f5dbc_0 conda-forge
aws-c-sdkutils 0.1.15 hf888d4c_1 conda-forge
aws-checksums 0.1.18 hf888d4c_1 conda-forge
aws-crt-cpp 0.26.2 h06549c9_7 conda-forge
aws-sdk-cpp 1.11.267 h73c0887_1 conda-forge
blosc 1.21.5 hc338f07_0 conda-forge
brotli 1.1.0 hb547adb_1 conda-forge
brotli-bin 1.1.0 hb547adb_1 conda-forge
brotli-python 1.1.0 py311ha891d26_1 conda-forge
bson 0.5.9 py_0 conda-forge
bzip2 1.0.8 h93a5062_5 conda-forge
c-ares 1.28.1 h93a5062_0 conda-forge
c-blosc2 2.14.4 ha57e6be_1 conda-forge
ca-certificates 2024.2.2 hf0a4a13_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 1.18.0 hd1e100b_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py311h4a08483_0 conda-forge
chardet 5.2.0 py311h267d04e_1 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
click-option-group 0.5.6 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
contourpy 1.2.1 py311hcc98501_0 conda-forge
coverage 7.4.4 py311h05b510d_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
debugpy 1.8.1 py311h92babd0_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge
execnet 2.1.1 pyhd8ed1ab_0 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.6.2 hebf3989_0 conda-forge
fftw 3.3.10 nompi_h3046061_108 conda-forge
filelock 3.13.4 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 h77eed37_1 conda-forge
fontconfig 2.14.2 h82840c6_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.51.0 py311h05b510d_0 conda-forge
freetype 2.12.1 hadb7bae_2 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
fsspec 2024.3.1 pyhca7485f_0 conda-forge
gflags 2.2.2 hc88da5d_1004 conda-forge
glog 0.7.0 hc6770e3_0 conda-forge
gmp 6.3.0 hebf3989_1 conda-forge
gmpy2 2.1.2 py311h2ba9262_1 conda-forge
greenlet 3.0.3 py311h92babd0_0 conda-forge
hdf4 4.2.15 h2ee6834_7 conda-forge
hdf5 1.14.3 nompi_h5bb55e9_100 conda-forge
icu 73.2 hc8870d7_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.1.0 pyha770c72_0 conda-forge
importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.3 pyh3cd1d5f_0 conda-forge
ipython 8.22.2 pyh707e725_0 conda-forge
ipywidgets 8.1.2 pyhd8ed1ab_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.3 pyhd8ed1ab_0 conda-forge
joblib 1.4.0 pyhd8ed1ab_0 conda-forge
jsonschema 4.21.1 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.1 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 py311h267d04e_0 conda-forge
jupyterlab_widgets 3.0.10 pyhd8ed1ab_0 conda-forge
khronos-opencl-icd-loader 2023.04.17 h1a8c8d9_0 conda-forge
kiwisolver 1.4.5 py311he4fd1f5_1 conda-forge
krb5 1.21.2 h92f50d5_0 conda-forge
lcms2 2.16 ha0e7c42_0 conda-forge
lerc 4.0.0 h9a09cb3_0 conda-forge
libabseil 20230802.1 cxx17_h13dd4ca_0 conda-forge
libaec 1.1.3 hebf3989_0 conda-forge
libarrow 15.0.0 h4f70cd7_6_cpu conda-forge
libarrow-acero 15.0.0 hebf3989_6_cpu conda-forge
libarrow-dataset 15.0.0 hebf3989_6_cpu conda-forge
libarrow-flight 15.0.0 hef2a8c6_6_cpu conda-forge
libarrow-flight-sql 15.0.0 h611cb26_6_cpu conda-forge
libarrow-gandiva 15.0.0 h5211482_6_cpu conda-forge
libarrow-substrait 15.0.0 h2e851bb_6_cpu conda-forge
libblas 3.9.0 22_osxarm64_openblas conda-forge
libboost 1.82.0 h489e689_6 conda-forge
libboost-python 1.82.0 py311hddbb800_6 conda-forge
libbrotlicommon 1.1.0 hb547adb_1 conda-forge
libbrotlidec 1.1.0 hb547adb_1 conda-forge
libbrotlienc 1.1.0 hb547adb_1 conda-forge
libcblas 3.9.0 22_osxarm64_openblas conda-forge
libcrc32c 1.1.2 hbdafb3b_0 conda-forge
libcurl 8.7.1 h2d989ff_0 conda-forge
libcxx 16.0.6 h4653b0c_0 conda-forge
libdeflate 1.20 h93a5062_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h93a5062_2 conda-forge
libevent 2.1.12 h2757513_1 conda-forge
libexpat 2.6.2 hebf3989_0 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgfortran 5.0.0 13_2_0_hd922786_3 conda-forge
libgfortran5 13.2.0 hf226fd6_3 conda-forge
libglib 2.80.0 hfc324ee_4 conda-forge
libgoogle-cloud 2.17.0 hfb9b341_2 conda-forge
libgoogle-cloud-storage 2.17.0 h8a76758_2 conda-forge
libgrpc 1.60.1 hfc68871_0 conda-forge
libiconv 1.17 h0d3ecfb_2 conda-forge
libintl 0.22.5 h8fbad5d_2 conda-forge
libjpeg-turbo 3.0.0 hb547adb_1 conda-forge
liblapack 3.9.0 22_osxarm64_openblas conda-forge
libllvm16 16.0.6 haab561b_3 conda-forge
libnetcdf 4.9.2 nompi_h291a7c2_113 conda-forge
libnghttp2 1.58.0 ha4dd798_1 conda-forge
libopenblas 0.3.27 openmp_h6c19121_0 conda-forge
libparquet 15.0.0 h278d484_6_cpu conda-forge
libpng 1.6.43 h091b4b1_0 conda-forge
libprotobuf 4.25.1 h810fc01_2 conda-forge
libre2-11 2023.09.01 h741fcf5_1 conda-forge
libsodium 1.0.18 h27ca646_1 conda-forge
libsqlite 3.45.2 h091b4b1_0 conda-forge
libssh2 1.11.0 h7a5bd25_0 conda-forge
libthrift 0.19.0 h026a170_1 conda-forge
libtiff 4.6.0 h07db509_3 conda-forge
libtorch 2.1.2 cpu_generic_hda0de89_3 conda-forge
libutf8proc 2.8.0 h1a8c8d9_0 conda-forge
libuv 1.48.0 h93a5062_0 conda-forge
libwebp-base 1.3.2 h93a5062_1 conda-forge
libxcb 1.15 hf346824_0 conda-forge
libxml2 2.12.6 h0d0cfa8_1 conda-forge
libzip 1.10.1 ha0bc3c6_3 conda-forge
libzlib 1.2.13 h53f4e23_5 conda-forge
lightning-utilities 0.11.2 pyhd8ed1ab_0 conda-forge
llvm-openmp 18.1.3 hcd81f8e_0 conda-forge
lz4-c 1.9.4 hb7217d7_0 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py311h05b510d_0 conda-forge
matplotlib-base 3.8.4 py311hb58f1d1_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdtraj 1.9.9 py311h06bfd7f_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
mpc 1.3.1 h91ba8db_0 conda-forge
mpfr 4.2.1 h41d338b_1 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.7 py311hd03642b_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mypy 1.8.0 py311h05b510d_0 conda-forge
mypy_extensions 1.0.0 pyha770c72_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
nbval 0.11.0 pyhd8ed1ab_0 conda-forge
ncurses 6.4.20240210 h078ce10_0 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
netcdf-fortran 4.6.1 nompi_he6a98ad_103 conda-forge
networkx 3.3 pyhd8ed1ab_1 conda-forge
nglview 3.1.2 pyh15ce09e_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
numexpr 2.9.0 py311hfbe21a1_0 conda-forge
numpy 1.26.4 py311h7125741_0 conda-forge
ocl_icd_wrapper_apple 1.0.0 h27ca646_0 conda-forge
openeye-toolkits 2023.2.3 py311_0 openeye
openff-amber-ff-ports 0.0.4 pyhca7485f_0 conda-forge
openff-forcefields 2024.03.0 pyhca7485f_0 conda-forge
openff-interchange-base 0.3.25 pyhd8ed1ab_1 conda-forge
openff-models 0.1.2 pyhca7485f_0 conda-forge
openff-nagl-base 0.3.0 pyhd8ed1ab_0 conda-forge
openff-nagl-models 0.1.0 pyhd8ed1ab_0 conda-forge
openff-toolkit-base 0.15.2 pyhd8ed1ab_0 conda-forge
openff-units 0.2.0 pyh1a96a4e_2 conda-forge
openff-utilities 0.1.12 pyhd8ed1ab_0 conda-forge
openjpeg 2.5.2 h9f1df11_0 conda-forge
openmm 8.1.1 py311h8ced375_1_khronos conda-forge
openssl 3.2.1 h0d3ecfb_1 conda-forge
orc 1.9.2 hb41d57e_1 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
packmol 20.2.2 h9318095_1 conda-forge
pandas 2.2.2 py311hfbe21a1_0 conda-forge
parmed 4.2.2 py311h92babd0_1 conda-forge
parso 0.8.4 pyhd8ed1ab_0 conda-forge
pcre2 10.43 h26f9a81_0 conda-forge
perl 5.32.1 7_h4614cfb_perl5 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.3.0 py311h0b5d0a1_0 conda-forge
pint 0.21 pyhd8ed1ab_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.4 hebf3989_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.2.0 pyhd8ed1ab_0 conda-forge
pluggy 1.4.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.42 pyha770c72_0 conda-forge
psutil 5.9.8 py311h05b510d_0 conda-forge
pthread-stubs 0.4 h27ca646_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 15.0.0 py311hce53c6f_6_cpu conda-forge
pycairo 1.26.0 py311hb98ac6d_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pydantic 1.10.14 py311h05b510d_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyjwt 2.8.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytables 3.9.2 py311hf4904c8_2 conda-forge
pytest 8.1.1 pyhd8ed1ab_0 conda-forge
pytest-cov 5.0.0 pyhd8ed1ab_0 conda-forge
pytest-rerunfailures 14.0 pyhd8ed1ab_0 conda-forge
pytest-xdist 3.5.0 pyhd8ed1ab_0 conda-forge
python 3.11.8 hdf0ec26_0_cpython conda-forge
python-constraint 1.4.0 py_0 conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.19.1 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.11 4_cp311 conda-forge
pytorch 2.1.2 cpu_generic_py311h38827da_3 conda-forge
pytorch-lightning 2.2.1 pyhd8ed1ab_0 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py311heffc1b2_1 conda-forge
pyzmq 25.1.2 py311h6727e71_0 conda-forge
qcelemental 0.27.1 pyhd8ed1ab_0 conda-forge
qcengine 0.29.0 pyhd8ed1ab_0 conda-forge
qcportal 0.54 pyhd8ed1ab_0 conda-forge
rdkit 2023.09.5 py311h38ec0cb_0 conda-forge
re2 2023.09.01 h4cba328_1 conda-forge
readline 8.2 h92ec313_1 conda-forge
referencing 0.34.0 pyhd8ed1ab_0 conda-forge
reportlab 4.1.0 py311h05b510d_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rich 13.7.1 pyhd8ed1ab_0 conda-forge
rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.18.0 py311ha958965_0 conda-forge
scipy 1.13.0 py311h4f9446f_0 conda-forge
setuptools 69.2.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sleef 3.5.1 he9cb808_2 conda-forge
smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge
snappy 1.1.10 hd04f947_1 conda-forge
sqlalchemy 2.0.29 py311h05b510d_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
sympy 1.12 pypyh9d50eac_103 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
tk 8.6.13 h5083fa2_1 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
torchmetrics 1.3.2 pyhd8ed1ab_0 conda-forge
tornado 6.4 py311h05b510d_0 conda-forge
tqdm 4.66.2 pyhd8ed1ab_0 conda-forge
traitlets 5.14.2 pyhd8ed1ab_0 conda-forge
typing-extensions 4.11.0 hd8ed1ab_0 conda-forge
typing_extensions 4.11.0 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.10 pyhd8ed1ab_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h27ca646_1002 conda-forge
xorg-libice 1.1.1 hb547adb_0 conda-forge
xorg-libsm 1.2.4 hb547adb_0 conda-forge
xorg-libx11 1.8.9 h570a39f_0 conda-forge
xorg-libxau 1.0.11 hb547adb_0 conda-forge
xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge
xorg-libxext 1.3.4 h1a8c8d9_2 conda-forge
xorg-libxt 1.3.0 hb547adb_1 conda-forge
xorg-xextproto 7.3.0 h1a8c8d9_1003 conda-forge
xorg-xproto 7.0.31 h27ca646_1007 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
zeromq 4.3.5 hebf3989_1 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h53f4e23_5 conda-forge
zlib-ng 2.0.7 h1a8c8d9_0 conda-forge
zstandard 0.22.0 py311h67b91a1_0 conda-forge
zstd 1.5.5 h4f39d0f_0 conda-forge
====================================TOOLKITS====================================
("GLOBAL_TOOLKIT_REGISTRY.registered_toolkit_versions={'OpenEye Toolkit': "
"'2023.2.3', 'The RDKit': '2023.09.5', 'AmberTools': '22.0', 'Built-in "
"Toolkit': None}")
'OpenEyeToolkitWrapper.is_available()=True'
==============================FORCEFIELDS/PLUGINS===============================
'FORCE FIELD PATHS:'
("_get_installed_offxml_dir_paths()=['/Users/mattthompson/micromamba/envs/openff-toolkit-test/lib/python3.11/site-packages/smirnoff99frosst/offxml', "
"'/Users/mattthompson/micromamba/envs/openff-toolkit-test/lib/python3.11/site-packages/openff/amber_ff_ports/offxml', "
"'/Users/mattthompson/micromamba/envs/openff-toolkit-test/lib/python3.11/site-packages/openforcefields/offxml']")
'FORCE FIELD FILES IN PATHS:'
[['smirnoff99Frosst-1.0.2.offxml',
'smirnoff99Frosst-1.0.0.offxml',
'smirnoff99Frosst-1.1.0.offxml',
'smirnoff99Frosst-1.0.4.offxml',
'smirnoff99Frosst-1.0.8.offxml',
'smirnoff99Frosst-1.0.6.offxml',
'README.md',
'smirnoff99Frosst-1.0.3.offxml',
'smirnoff99Frosst-1.0.1.offxml',
'smirnoff99Frosst-1.0.5.offxml',
'smirnoff99Frosst-1.0.9.offxml',
'smirnoff99Frosst-1.0.7.offxml'],
['ff14sb_off_impropers_0.0.2.offxml',
'ff14sb_0.0.1.offxml',
'ff14sb_off_impropers_0.0.4.offxml',
'ff14sb_0.0.3.offxml',
'ff14sb_off_impropers_0.0.1.offxml',
'ff14sb_off_impropers_0.0.3.offxml',
'ff14sb_0.0.4.offxml',
'ff14sb_0.0.2.offxml'],
['tip3p_fb-1.1.0.offxml',
'tip3p_fb-1.0.0.offxml',
'openff-1.0.1.offxml',
'openff-1.1.1.offxml',
'spce-1.0.0.offxml',
'openff-1.0.0-RC1.offxml',
'opc3.offxml',
'opc3-1.0.0.offxml',
'openff_unconstrained-2.1.1.offxml',
'openff-2.1.0-rc.1.offxml',
'openff-1.2.0.offxml',
'openff-1.3.0.offxml',
'tip3p-1.0.0.offxml',
'openff_unconstrained-2.0.0-rc.1.offxml',
'openff_unconstrained-1.3.1.offxml',
'openff_unconstrained-1.2.1.offxml',
'opc-1.0.2.offxml',
'openff-2.0.0-rc.2.offxml',
'opc-1.0.0.offxml',
'openff_unconstrained-2.2.0-rc1.offxml',
'openff_unconstrained-1.0.0-RC2.offxml',
'openff_unconstrained-1.1.0.offxml',
'openff_unconstrained-1.0.0.offxml',
'openff-2.1.0.offxml',
'openff-2.0.0.offxml',
'tip4p_fb-1.0.1.offxml',
'tip3p.offxml',
'tip4p_ew.offxml',
'opc3-1.0.1.offxml',
'opc.offxml',
'README.md',
'openff_unconstrained-2.1.0.offxml',
'openff_unconstrained-2.0.0.offxml',
'openff_unconstrained-2.0.0-rc.2.offxml',
'tip3p_fb-1.1.1.offxml',
'openff-1.1.0.offxml',
'openff-1.0.0.offxml',
'openff-1.0.0-RC2.offxml',
'openff-2.2.0-rc1.offxml',
'tip3p-1.0.1.offxml',
'openff-1.3.1.offxml',
'openff-1.2.1.offxml',
'tip4p_ew-1.0.0.offxml',
'openff-1.3.1-alpha.1.offxml',
'tip4p_fb.offxml',
'tip3p_fb.offxml',
'openff_unconstrained-1.0.0-RC1.offxml',
'spce.offxml',
'openff_unconstrained-2.1.0-rc.1.offxml',
'tip5p.offxml',
'openff_unconstrained-1.2.0.offxml',
'openff_unconstrained-1.3.0.offxml',
'tip4p_fb-1.0.0.offxml',
'openff-2.1.1.offxml',
'openff-2.0.0-rc.1.offxml',
'openff_unconstrained-1.0.1.offxml',
'openff_unconstrained-1.1.1.offxml',
'openff_unconstrained-1.3.1-alpha.1.offxml',
'tip5p-1.0.0.offxml',
'opc-1.0.1.offxml']]
'HANDLER PLUGINS:'
('load_handler_plugins()=[<class '
"'custom_plugins.handler_plugins.CustomHandler'>]")
'COLLECTION PLUGINS:'
'load_smirnoff_plugins()=[]'
=====================================OPENMM=====================================
test openmm
OpenMM Version: 8.1.1
Git Revision: ec797acabe5de4ce9f56c92d349baa889f4b0821
There are 3 Platforms available:
1 Reference - Successfully computed forces
2 CPU - Successfully computed forces
3 OpenCL - Successfully computed forces
Median difference in forces between platforms:
Reference vs. CPU: 6.30441e-06
Reference vs. OpenCL: 6.7451e-06
CPU vs. OpenCL: 7.36143e-07
All differences are within tolerance.
checking plugin load failures
()
checking which platforms support mixed precision
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'openmmtools'
possible openmm errors
Additional context