openff-toolkit
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Published
20 hours ago •
openforcefield
openforcefield
ForceField round trip changes Angle parameterize field
trafficstars
Describe the bug
Parsing a ForceField and rewriting it a to file changes the parameterize field on some Angles from k to 1 * boltzmann_constant ** 1, upsetting ForceBalance.
To Reproduce I needed to remove the Constraints section of a ForceField for ForceBalance and got this suggestion from Lily:
from openff.toolkit import ForceField
ff = ForceField("input.offxml", allow_cosmetic_attributes=True)
ff.deregister_parameter_handler("Constraints")
ff.to_file("output.offxml")
But I can reproduce it even with the deregister_parameter_handler line commented out. The changes are clearly seen when running diff input.offxml output.xml or even just grepping for boltzmann in both files.
Output
--- input.offxml 2023-07-20 17:08:33.120707559 -0400
+++ output.offxml 2023-07-20 17:22:05.578948496 -0400
@@ -115,8 +115,8 @@
<Angle smirks="[*;r6:1]~;@[*;r5:2]~;@[*;r5;x2:3]" angle="126.74947883718123 * degree ** 1" k="165.02172217717344 * kilocalorie_per_mole ** 1 * radian ** -2" id="a13" parameterize="k, angle"></Angle>
<Angle smirks="[*:1]~;!@[*;X3;r5:2]~;@[*;r5:3]" angle="124.76218228987901 * degree ** 1" k="102.212672475332 * kilocalorie_per_mole ** 1 * radian ** -2" id="a14" parameterize="k, angle"></Angle>
<Angle smirks="[#8X1:1]~[#6X3:2]~[#8:3]" angle="123.69384605432525 * degree ** 1" k="126.52435713215367 * kilocalorie_per_mole ** 1 * radian ** -2" id="a15" parameterize="k, angle"></Angle>
- <Angle smirks="[*:1]~[#6X2:2]~[*:3]" angle="178.0651310592217 * degree ** 1" k="99.85352234417054 * kilocalorie_per_mole ** 1 * radian ** -2" id="a16" parameterize="k"></Angle>
- <Angle smirks="[*:1]~[#7X2:2]~[*:3]" angle="176.02345454674762 * degree ** 1" k="89.9604117556478 * kilocalorie_per_mole ** 1 * radian ** -2" id="a17" parameterize="k"></Angle>
+ <Angle smirks="[*:1]~[#6X2:2]~[*:3]" angle="178.0651310592217 * degree ** 1" k="99.85352234417054 * kilocalorie_per_mole ** 1 * radian ** -2" id="a16" parameterize="1 * boltzmann_constant ** 1"></Angle>
+ <Angle smirks="[*:1]~[#7X2:2]~[*:3]" angle="176.02345454674762 * degree ** 1" k="89.9604117556478 * kilocalorie_per_mole ** 1 * radian ** -2" id="a17" parameterize="1 * boltzmann_constant ** 1"></Angle>
<Angle smirks="[*:1]~[#7X4,#7X3,#7X2-1:2]~[*:3]" angle="113.18673214011471 * degree ** 1" k="249.16533568188814 * kilocalorie_per_mole ** 1 * radian ** -2" id="a18" parameterize="k, angle"></Angle>
<Angle smirks="[*:1]@-[r!r6;#7X4,#7X3,#7X2-1:2]@-[*:3]" angle="98.4609417604599 * degree ** 1" k="215.46610831911238 * kilocalorie_per_mole ** 1 * radian ** -2" id="a18a" parameterize="k, angle"></Angle>
<Angle smirks="[#1:1]-[#7X4,#7X3,#7X2-1:2]-[*:3]" angle="109.26647374981178 * degree ** 1" k="107.59800871001211 * kilocalorie_per_mole ** 1 * radian ** -2" id="a19" parameterize="k, angle"></Angle>
@@ -128,7 +128,7 @@
<Angle smirks="[#1:1]-[#7X2+0:2]~[*:3]" angle="111.61555367908721 * degree ** 1" k="104.67457969782329 * kilocalorie_per_mole ** 1 * radian ** -2" id="a24" parameterize="k, angle"></Angle>
<Angle smirks="[#6,#7,#8:1]-[#7X3:2](~[#8X1])~[#8X1:3]" angle="117.56973608432911 * degree ** 1" k="145.03189317662233 * kilocalorie_per_mole ** 1 * radian ** -2" id="a25" parameterize="k, angle"></Angle>
<Angle smirks="[#8X1:1]~[#7X3:2]~[#8X1:3]" angle="124.45512289998524 * degree ** 1" k="140.35006169568325 * kilocalorie_per_mole ** 1 * radian ** -2" id="a26" parameterize="k, angle"></Angle>
- <Angle smirks="[*:1]~[#7X2:2]~[#7X1:3]" angle="175.2204655094496 * degree ** 1" k="117.562291770754 * kilocalorie_per_mole ** 1 * radian ** -2" id="a27" parameterize="k"></Angle>
+ <Angle smirks="[*:1]~[#7X2:2]~[#7X1:3]" angle="175.2204655094496 * degree ** 1" k="117.562291770754 * kilocalorie_per_mole ** 1 * radian ** -2" id="a27" parameterize="1 * boltzmann_constant ** 1"></Angle>
<Angle smirks="[*:1]-[#8:2]-[*:3]" angle="111.96993713031328 * degree ** 1" k="249.99419564046633 * kilocalorie_per_mole ** 1 * radian ** -2" id="a28" parameterize="k, angle"></Angle>
<Angle smirks="[#6X3,#7:1]~;@[#8;r:2]~;@[#6X3,#7:3]" angle="109.19365977372304 * degree ** 1" k="337.3883162802198 * kilocalorie_per_mole ** 1 * radian ** -2" id="a29" parameterize="k, angle"></Angle>
<Angle smirks="[*:1]-[#8X2+1:2]=[*:3]" angle="122.99067282760342 * degree ** 1" k="324.48394466290887 * kilocalorie_per_mole ** 1 * radian ** -2" id="a30"></Angle>
Computing environment (please complete the following information):
- Arch Linux
- ForceField files (renamed for GitHub): output.txt input.txt
conda list(important part is openff-toolkit 0.14.0, but I reproduced on 0.13.2 too):
# packages in environment at /home/brent/mambaforge/envs/temp-valence-fitting-repro:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.8 h166bdaf_0 conda-forge
amberlite 22.0 pypi_0 pypi
ambertools 22.5 py310hd182041_0 conda-forge
amberutils 21.0 pypi_0 pypi
amqp 5.1.1 pyhd8ed1ab_0 conda-forge
anyio 3.7.1 pyhd8ed1ab_0 conda-forge
argcomplete 3.1.1 pyhd8ed1ab_0 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
async-lru 2.0.3 pyhd8ed1ab_0 conda-forge
async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
aws-c-auth 0.7.0 hf8751d9_2 conda-forge
aws-c-cal 0.6.0 h93469e0_0 conda-forge
aws-c-common 0.8.23 hd590300_0 conda-forge
aws-c-compression 0.2.17 h862ab75_1 conda-forge
aws-c-event-stream 0.3.1 h9599702_1 conda-forge
aws-c-http 0.7.11 hbe98c3e_0 conda-forge
aws-c-io 0.13.28 h3870b5a_0 conda-forge
aws-c-mqtt 0.8.14 h2e270ba_2 conda-forge
aws-c-s3 0.3.13 heb0bb06_2 conda-forge
aws-c-sdkutils 0.1.11 h862ab75_1 conda-forge
aws-checksums 0.1.16 h862ab75_1 conda-forge
aws-crt-cpp 0.20.3 he9c0e7f_4 conda-forge
aws-sdk-cpp 1.10.57 hbc2ea52_17 conda-forge
babel 2.12.1 pyhd8ed1ab_1 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge
backports.zoneinfo 0.2.1 py310hff52083_7 conda-forge
basis_set_exchange 0.9.1 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
billiard 4.1.0 py310h2372a71_0 conda-forge
black 23.7.0 py310hff52083_1 conda-forge
bleach 6.0.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.4 h0f2a231_0 conda-forge
boltons 23.0.0 pyhd8ed1ab_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_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 h7f98852_4 conda-forge
c-ares 1.19.1 hd590300_0 conda-forge
c-blosc2 2.10.0 hb4ffafa_0 conda-forge
ca-certificates 2023.5.7 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.1 pyhd8ed1ab_0 conda-forge
cairo 1.16.0 hbbf8b49_1016 conda-forge
celery 5.3.1 pyhd8ed1ab_0 conda-forge
certifi 2023.5.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py310h255011f_3 conda-forge
charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge
chemper 1.0.1 pyhd8ed1ab_0 conda-forge
click 8.1.6 unix_pyh707e725_0 conda-forge
click-didyoumean 0.3.0 pyhd8ed1ab_0 conda-forge
click-option-group 0.5.6 pyhd8ed1ab_0 conda-forge
click-plugins 1.1.1 py_0 conda-forge
click-repl 0.2.0 pyhd8ed1ab_0 conda-forge
cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge
cmiles 0.1.6 ha770c72_2 conda-forge
cmiles-base 0.1.6 pyhd8ed1ab_2 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.1.3 pyhd8ed1ab_0 conda-forge
conda 23.5.2 py310hff52083_0 conda-forge
conda-pack 0.7.0 pyh6c4a22f_0 conda-forge
conda-package-handling 2.0.2 pyh38be061_0 conda-forge
conda-package-streaming 0.8.0 pyhd8ed1ab_0 conda-forge
contourpy 1.1.0 py310hd41b1e2_0 conda-forge
cryptography 41.0.2 py310h75e40e8_0 conda-forge
cudatoolkit 11.8.0 h37601d7_11 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 3.0.0 py310hc6cd4ac_0 conda-forge
dbus 1.13.6 h5008d03_3 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
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.1.2 pyhd8ed1ab_0 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fastapi 0.86.0 pyhd8ed1ab_0 conda-forge
fftw 3.3.10 nompi_hc118613_108 conda-forge
flake8 6.0.0 pyhd8ed1ab_0 conda-forge
flit-core 3.9.0 pyhd8ed1ab_0 conda-forge
fmt 9.1.0 h924138e_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 4.41.0 py310h2372a71_0 conda-forge
forcebalance 1.9.5 py310h5a539fb_0 conda-forge
freetype 2.12.1 hca18f0e_1 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
future 0.18.3 pyhd8ed1ab_0 conda-forge
geometric 1.0 pyhd8ed1ab_1 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
glib 2.76.4 hfc55251_0 conda-forge
glib-tools 2.76.4 hfc55251_0 conda-forge
glog 0.6.0 h6f12383_0 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
greenlet 2.0.2 py310hc6cd4ac_1 conda-forge
gst-plugins-base 1.22.3 h938bd60_1 conda-forge
gstreamer 1.22.3 h977cf35_1 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
h5py 3.9.0 nompi_py310hcca72df_101 conda-forge
harfbuzz 7.3.0 hdb3a94d_0 conda-forge
hdf4 4.2.15 h501b40f_6 conda-forge
hdf5 1.14.1 nompi_h4f84152_100 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 0.17.3 pyhd8ed1ab_0 conda-forge
httpx 0.24.1 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 72.1 hcb278e6_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
importlib-metadata 6.8.0 pyha770c72_0 conda-forge
importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge
importlib_resources 6.0.0 pyhd8ed1ab_1 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.24.0 pyh71e2992_0 conda-forge
ipython 8.14.0 pyh41d4057_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 8.0.7 pyhd8ed1ab_0 conda-forge
isort 5.12.0 pyhd8ed1ab_1 conda-forge
jedi 0.18.2 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
json5 0.9.14 pyhd8ed1ab_0 conda-forge
jsonpatch 1.32 pyhd8ed1ab_0 conda-forge
jsonpointer 2.0 py_0 conda-forge
jsonschema 4.18.4 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge
jupyter 1.0.0 py310hff52083_8 conda-forge
jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge
jupyter_client 8.3.0 pyhd8ed1ab_0 conda-forge
jupyter_console 6.6.3 pyhd8ed1ab_0 conda-forge
jupyter_core 5.3.1 py310hff52083_0 conda-forge
jupyter_events 0.6.3 pyhd8ed1ab_0 conda-forge
jupyter_server 2.7.0 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge
jupyterlab 4.0.3 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.23.0 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.8 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py310hbf28c38_1 conda-forge
kombu 5.3.1 py310hff52083_0 conda-forge
krb5 1.20.1 h81ceb04_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.15 haa2dc70_1 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20230125.3 cxx17_h59595ed_0 conda-forge
libaec 1.0.6 hcb278e6_1 conda-forge
libarchive 3.6.2 h039dbb9_1 conda-forge
libarrow 12.0.1 h657c46f_5_cpu conda-forge
libblas 3.9.0 17_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
libcap 2.67 he9d0100_0 conda-forge
libcblas 3.9.0 17_linux64_openblas conda-forge
libclang 15.0.7 default_h7634d5b_2 conda-forge
libclang13 15.0.7 default_h9986a30_2 conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcups 2.3.3 h36d4200_3 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
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-ng 13.1.0 he5830b7_0 conda-forge
libgcrypt 1.10.1 h166bdaf_0 conda-forge
libgfortran-ng 13.1.0 h69a702a_0 conda-forge
libgfortran5 13.1.0 h15d22d2_0 conda-forge
libglib 2.76.4 hebfc3b9_0 conda-forge
libgomp 13.1.0 he5830b7_0 conda-forge
libgoogle-cloud 2.12.0 h840a212_1 conda-forge
libgpg-error 1.47 h71f35ed_0 conda-forge
libgrpc 1.56.2 h3905398_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
libllvm15 15.0.7 h5cf9203_2 conda-forge
libmamba 1.4.9 h658169a_0 conda-forge
libmambapy 1.4.9 py310h8aae740_0 conda-forge
libnetcdf 4.9.2 nompi_h7e745eb_109 conda-forge
libnghttp2 1.52.0 h61bc06f_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libnuma 2.0.16 h0b41bf4_1 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.23 pthreads_h80387f5_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libpq 15.3 hbcd7760_1 conda-forge
libprotobuf 4.23.3 hd1fb520_0 conda-forge
libsndfile 1.2.0 hb75c966_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsolv 0.7.24 hfc55251_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
libsystemd0 253 h8c4010b_1 conda-forge
libthrift 0.18.1 h8fd135c_2 conda-forge
libtiff 4.5.1 h8b53f26_0 conda-forge
libutf8proc 2.8.0 h166bdaf_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.3.1 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxkbcommon 1.5.0 h5d7e998_3 conda-forge
libxml2 2.11.4 h0d562d8_0 conda-forge
libxslt 1.1.37 h0054252_1 conda-forge
libzip 1.9.2 hc929e4a_1 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lxml 4.9.3 py310h9b7343a_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h516909a_1000 conda-forge
mamba 1.4.9 py310h51d5547_0 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.3 py310h2372a71_0 conda-forge
matplotlib-base 3.7.2 py310hf38f957_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mccabe 0.7.0 pyhd8ed1ab_0 conda-forge
mctc-lib 0.3.1 h74f4db8_0 conda-forge
mdtraj 1.9.8 py310h8e08b51_2 conda-forge
mdurl 0.1.0 pyhd8ed1ab_0 conda-forge
mistune 3.0.0 pyhd8ed1ab_0 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
mpg123 1.31.3 hcb278e6_0 conda-forge
msgpack-python 1.0.5 py310hdf3cbec_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mypy_extensions 1.0.0 pyha770c72_0 conda-forge
mysql-common 8.0.33 hf1915f5_2 conda-forge
mysql-libs 8.0.33 hca2cd23_2 conda-forge
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert 7.7.1 pyhd8ed1ab_1 conda-forge
nbconvert-core 7.7.1 pyhd8ed1ab_1 conda-forge
nbconvert-pandoc 7.7.1 pyhd8ed1ab_1 conda-forge
nbformat 5.9.1 pyhd8ed1ab_0 conda-forge
ncurses 6.4 hcb278e6_0 conda-forge
ndcctools 7.6.0 py310he2ed3e8_0 conda-forge
nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
netcdf-fortran 4.6.1 nompi_hec59055_101 conda-forge
networkx 3.1 pyhd8ed1ab_0 conda-forge
nglview 3.0.6 pyhba93850_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
notebook 7.0.0 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.89 he45b914_0 conda-forge
numexpr 2.8.4 py310h690d005_100 conda-forge
numpy 1.25.1 py310ha4c1d20_0 conda-forge
ocl-icd 2.3.1 h7f98852_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openeye-toolkits 2023.1.0 py310_0 openeye
openff-amber-ff-ports 0.0.3 pyh6c4a22f_0 conda-forge
openff-bespokefit 0.2.2 pyhd8ed1ab_0 conda-forge
openff-forcefields 2023.06.0 pyh1a96a4e_0 conda-forge
openff-fragmenter-base 0.2.0 pyhd8ed1ab_0 conda-forge
openff-interchange 0.3.8 pyhd8ed1ab_0 conda-forge
openff-interchange-base 0.3.8 pyhd8ed1ab_0 conda-forge
openff-models 0.0.5 pyh1a96a4e_1 conda-forge
openff-qcsubmit 0.4.1 pyhd8ed1ab_0 conda-forge
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I don't recall if cosmetic attributes are meant to be serialized out - the docstring of ForceField.to_file implies they are by default.
Is this an issue with just AngleHandler and/or parameterize? Does the same thing happen with other cosmetic attributes?
I don't recall if cosmetic attributes are meant to be serialized out - the docstring of ForceField.to_file implies they are by default.
Yes, having discard_cosmetic_attributes=False by default implies to me that they should be written out as faithfully as possible.
Does the same thing happen with other cosmetic attributes?
This feels like more of #1633 and #1493, where I think the current fix so far only safeguards specific ParameterAttributes so everything else, including cosmetics, is fair game.
>>> from openff.toolkit import ForceField
>>> ff = ForceField("/Users/lily/Downloads/input.offxml", allow_cosmetic_attributes=True)
>>> handler = ff.get_parameter_handler("Angles")
>>> handler.parameters[15]._parameterize
1 boltzmann_constant
>>> handler.parameters[14]._parameterize
'k, angle'
This only happens with parameters where parameterize="k", as the toolkit correctly interprets parameterize="k, length" as a string.
Agreed - The right resolution for this would be to not convert cosmetics - There's no safe way to encode that those should be quantities vs. strings, so we should always treat them as strings. I'll accept a PR that changes this, or will get to it myself after my current backlog!
