openff-interchange
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Published
20 hours ago •
openforcefield
openforcefield
JSON roundtrip doesn't work with `from_openmm` generated system
Description
Interchange.parse_raw() yields a KeyError: 'name' when passing a JSON generated from an Interchange object that was created from an OpenMM System & Topology (via Interchange.from_openmm).
Note: the openmm System & Topology were created using SystemGenerator.
Reproduction
from openmm import app, MonteCarloBarostat
from openmm import unit as omm_unit
from openmmforcefields.generators.system_generators import SystemGenerator
from openff.toolkit import Molecule
from openff.units import unit
from openff.units.openmm import to_openmm, from_openmm
from openff.interchange import Interchange
import os
os.environ['INTERCHANGE_EXPERIMENTAL'] = "1"
forcefield_kwargs = {
'constraints': app.HBonds,
'rigidWater': True,
'removeCMMotion': True,
'hydrogenMass': 4.0 * omm_unit.amu
}
periodic_kwargs = {
'nonbondedMethod': app.PME,
'nonbondedCutoff': to_openmm(9 * unit.angstrom)
}
non_periodic_kwargs = {
'nonbondedMethod': app.NoCutoff,
}
system_generator = SystemGenerator(
forcefields=['amber/ff14SB.xml', 'amber/tip3p_standard.xml'],
small_molecule_forcefield='openff-2.1.0',
forcefield_kwargs=forcefield_kwargs,
nonperiodic_forcefield_kwargs=non_periodic_kwargs,
periodic_forcefield_kwargs=periodic_kwargs,
cache=None,
barostat=None,
)
off = Molecule.from_smiles('C')
off.generate_conformers()
off.assign_partial_charges(partial_charge_method='am1bcc')
system_generator.create_system(off.to_topology().to_openmm(), molecules=[off])
model = app.Modeller(app.Topology(), [])
model.add(
off.to_topology().to_openmm(), to_openmm(off.conformers[0])
)
model.addSolvent(
system_generator.forcefield,
model='tip3p',
padding=to_openmm(12 * unit.angstrom),
positiveIon='Na+', negativeIon='Cl-',
ionicStrength=to_openmm(0.15 * unit.molar),
neutralize=True,
)
system = system_generator.create_system(
model.topology, molecules=[off],
)
inter = Interchange.from_openmm(system, model.topology, model.positions)
inter2 = Interchange.parse_raw(inter.json())
Output
Click me
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
Cell In[1], line 65
59 system = system_generator.create_system(
60 model.topology, molecules=[off],
61 )
63 inter = Interchange.from_openmm(system, model.topology, model.positions)
---> 65 inter2 = Interchange.parse_raw(inter.json())
File ~/software/mambaforge/install/envs/ofe_demo/lib/python3.11/site-packages/pydantic/v1/main.py:539, in BaseModel.parse_raw(cls, b, content_type, encoding, proto, allow_pickle)
528 @classmethod
529 def parse_raw(
530 cls: Type['Model'],
(...)
536 allow_pickle: bool = False,
537 ) -> 'Model':
538 try:
--> 539 obj = load_str_bytes(
540 b,
541 proto=proto,
542 content_type=content_type,
543 encoding=encoding,
544 allow_pickle=allow_pickle,
545 json_loads=cls.__config__.json_loads,
546 )
547 except (ValueError, TypeError, UnicodeDecodeError) as e:
548 raise ValidationError([ErrorWrapper(e, loc=ROOT_KEY)], cls)
File ~/software/mambaforge/install/envs/ofe_demo/lib/python3.11/site-packages/pydantic/v1/parse.py:37, in load_str_bytes(b, content_type, encoding, proto, allow_pickle, json_loads)
35 if isinstance(b, bytes):
36 b = b.decode(encoding)
---> 37 return json_loads(b)
38 elif proto == Protocol.pickle:
39 if not allow_pickle:
File ~/software/mambaforge/install/envs/ofe_demo/lib/python3.11/site-packages/openff/interchange/components/interchange.py:97, in interchange_loader(data)
95 tmp["box"] = Quantity(val["val"], unit.Unit(val["unit"]))
96 elif key == "topology":
---> 97 tmp["topology"] = Topology.from_json(val)
98 elif key == "collections":
99 from openff.interchange.smirnoff import (
100 SMIRNOFFAngleCollection,
101 SMIRNOFFBondCollection,
(...)
107 SMIRNOFFVirtualSiteCollection,
108 )
File ~/software/mambaforge/install/envs/ofe_demo/lib/python3.11/site-packages/openff/toolkit/utils/serialization.py:153, in Serializable.from_json(cls, serialized)
150 import json
152 d = json.loads(serialized)
--> 153 return cls.from_dict(d)
File ~/software/mambaforge/install/envs/ofe_demo/lib/python3.11/site-packages/openff/toolkit/topology/topology.py:1261, in Topology.from_dict(cls, topology_dict)
1246 """
1247 Create a new Topology from a dictionary representation
1248
(...)
1258
1259 """
1260 topology = cls()
-> 1261 topology._initialize_from_dict(topology_dict)
1262 return topology
File ~/software/mambaforge/install/envs/ofe_demo/lib/python3.11/site-packages/openff/toolkit/topology/topology.py:1285, in Topology._initialize_from_dict(self, topology_dict)
1282 self.box_vectors = Quantity(box_vectors_unitless, box_vectors_unit)
1284 for molecule_dict in topology_dict["molecules"]:
-> 1285 new_mol = Molecule.from_dict(molecule_dict)
1286 self._add_molecule_keep_cache(new_mol)
1287 self._invalidate_cached_properties()
File ~/software/mambaforge/install/envs/ofe_demo/lib/python3.11/site-packages/openff/toolkit/topology/molecule.py:1234, in FrozenMolecule.from_dict(cls, molecule_dict)
1232 # This implementation is a compromise to let this remain as a classmethod
1233 mol = cls()
-> 1234 mol._initialize_from_dict(molecule_dict)
1235 return mol
File ~/software/mambaforge/install/envs/ofe_demo/lib/python3.11/site-packages/openff/toolkit/topology/molecule.py:1249, in FrozenMolecule._initialize_from_dict(self, molecule_dict)
1246 # TODO: Provide useful exception messages if there are any failures
1248 self._initialize()
-> 1249 self.name = molecule_dict["name"]
1250 for atom_dict in molecule_dict["atoms"]:
1251 self._add_atom(**atom_dict, invalidate_cache=False)
KeyError: 'name'
Software versions
- Which operating system and version are you using? Ubuntu 20.04 LTS
- How did you install Interchange? conda-forge
- What is the output of running
conda list?
Click me
```
# packages in environment at /home/bioc1523/software/mambaforge/install/envs/ofe_demo:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
adjusttext 1.1.1 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.12 h4ab18f5_0 conda-forge
ambertools 23.6 nompi_py311he003265_102 conda-forge
amberutils 21.0 pypi_0 pypi
annotated-types 0.6.0 pyhd8ed1ab_0 conda-forge
anyio 4.3.0 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py311h459d7ec_4 conda-forge
arpack 3.8.0 nompi_h0baa96a_101 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
atk-1.0 2.38.0 h04ea711_2 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.tarfile 1.0.0 pyhd8ed1ab_1 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
biopython 1.83 py311h459d7ec_0 conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.5 hc2324a3_1 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py311hb755f60_1 conda-forge
bson 0.5.9 py_0 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.28.1 hd590300_0 conda-forge
c-blosc2 2.14.4 hb4ffafa_1 conda-forge
ca-certificates 2024.7.4 hbcca054_0 conda-forge
cachecontrol 0.14.0 pyhd8ed1ab_0 conda-forge
cachecontrol-with-filecache 0.14.0 pyhd8ed1ab_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
cachy 0.3.0 pyhd8ed1ab_1 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
certifi 2024.7.4 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py311hb3a22ac_0 conda-forge
cftime 1.6.3 py311h1f0f07a_0 conda-forge
chardet 5.2.0 py311h38be061_1 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
cinnabar 0.4.1 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
click-default-group 1.2.4 pyhd8ed1ab_0 conda-forge
clikit 0.6.2 pyhd8ed1ab_2 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
conda-lock 2.5.7 pyhd8ed1ab_0 conda-forge
contourpy 1.2.1 py311h9547e67_0 conda-forge
coverage 7.5.1 py311h331c9d8_0 conda-forge
crashtest 0.4.1 pyhd8ed1ab_0 conda-forge
cryptography 42.0.8 py311h4a61cc7_0 conda-forge
cudatoolkit 11.8.0 h4ba93d1_13 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.8.1 py311hb755f60_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dill 0.3.8 pyhd8ed1ab_0 conda-forge
distlib 0.3.8 pyhd8ed1ab_0 conda-forge
edgembar 0.2 pypi_0 pypi
ensureconda 1.4.4 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 2.6.2 h59595ed_0 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
fftw 3.3.10 nompi_hc118613_108 conda-forge
filelock 3.14.0 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 h77eed37_2 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 4.51.0 py311h459d7ec_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
fribidi 1.0.10 h36c2ea0_0 conda-forge
gdk-pixbuf 2.42.11 hb9ae30d_0 conda-forge
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
gitdb 4.0.11 pyhd8ed1ab_0 conda-forge
gitpython 3.1.43 pyhd8ed1ab_0 conda-forge
glew 2.1.0 h9c3ff4c_2 conda-forge
glib 2.80.2 hf974151_0 conda-forge
glib-tools 2.80.2 hb6ce0ca_0 conda-forge
glm 0.9.9.8 h00ab1b0_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
graphviz 9.0.0 h78e8752_1 conda-forge
greenlet 3.0.3 py311hb755f60_0 conda-forge
griddataformats 1.0.2 pyhd8ed1ab_0 conda-forge
gsd 3.2.1 py311h1f0f07a_0 conda-forge
gst-plugins-base 1.24.4 h9ad1361_0 conda-forge
gstreamer 1.24.4 haf2f30d_0 conda-forge
gtk2 2.24.33 h280cfa0_4 conda-forge
gts 0.7.6 h977cf35_4 conda-forge
gufe 1.0.0 pyhd8ed1ab_0 conda-forge
h5py 3.11.0 nompi_py311hebc2b07_100 conda-forge
harfbuzz 8.4.0 h3d44ed6_0 conda-forge
hdf4 4.2.15 h2a13503_7 conda-forge
hdf5 1.14.3 nompi_h4f84152_101 conda-forge
html5lib 1.1 pyh9f0ad1d_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.7 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 pyhd33586a_0 conda-forge
ipython 8.24.0 pyh707e725_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.6.0 pyhd3deb0d_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jaraco.classes 3.4.0 pyhd8ed1ab_1 conda-forge
jaraco.context 5.3.0 pyhd8ed1ab_1 conda-forge
jaraco.functools 4.0.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jeepney 0.8.0 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.4.2 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py311h38be061_3 conda-forge
jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.22.0 pyhd8ed1ab_0 conda-forge
jupyter_client 7.4.9 pyhd8ed1ab_0 conda-forge
jupyter_contrib_core 0.4.0 pyhd8ed1ab_0 conda-forge
jupyter_contrib_nbextensions 0.7.0 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 py311h38be061_0 conda-forge
jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge
jupyter_highlight_selected_word 0.2.0 pyhd8ed1ab_1006 conda-forge
jupyter_latex_envs 1.4.6 pyhd8ed1ab_1002 conda-forge
jupyter_nbextensions_configurator 0.6.1 pyhd8ed1ab_0 conda-forge
jupyter_server 2.14.0 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge
jupyterlab_widgets 3.0.10 pyhd8ed1ab_0 conda-forge
kartograf 1.0.1 pyhd8ed1ab_0 conda-forge
keyring 25.2.1 pyha804496_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py311h9547e67_1 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 h55db66e_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libblas 3.9.0 22_linux64_openblas conda-forge
libboost 1.84.0 h8013b2b_2 conda-forge
libboost-python 1.84.0 py311h92ebd52_2 conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 22_linux64_openblas conda-forge
libclang-cpp15 15.0.7 default_h127d8a8_5 conda-forge
libclang13 18.1.7 default_h087397f_0 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.7.1 hca28451_0 conda-forge
libdeflate 1.20 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-ng 13.2.0 h77fa898_7 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgd 2.3.3 h119a65a_9 conda-forge
libgettextpo 0.22.5 h59595ed_2 conda-forge
libgettextpo-devel 0.22.5 h59595ed_2 conda-forge
libgfortran-ng 13.2.0 h69a702a_7 conda-forge
libgfortran5 13.2.0 hca663fb_7 conda-forge
libglib 2.80.2 hf974151_0 conda-forge
libglu 9.0.0 hac7e632_1003 conda-forge
libgomp 13.2.0 h77fa898_7 conda-forge
libgpg-error 1.49 h4f305b6_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 22_linux64_openblas conda-forge
libllvm14 14.0.6 hcd5def8_4 conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
libllvm18 18.1.7 hb77312f_0 conda-forge
libnetcdf 4.9.2 nompi_h9612171_113 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libpq 16.3 ha72fbe1_0 conda-forge
librsvg 2.58.0 hadf69e7_1 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.45.3 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 hc0a3c3a_7 conda-forge
libsystemd0 255 h3516f8a_1 conda-forge
libtiff 4.6.0 h1dd3fc0_3 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp 1.4.0 h2c329e2_0 conda-forge
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libxcb 1.15 h0b41bf4_0 conda-forge
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libxml2 2.12.7 hc051c1a_0 conda-forge
libxslt 1.1.39 h76b75d6_0 conda-forge
libzip 1.10.1 h2629f0a_3 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
llvmlite 0.42.0 py311ha6695c7_1 conda-forge
lomap2 3.0.3 pyhd8ed1ab_0 conda-forge
lxml 5.2.2 py311hc0a218f_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 hd590300_1001 conda-forge
markupsafe 2.1.5 py311h459d7ec_0 conda-forge
matplotlib-base 3.8.4 py311h54ef318_0 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
mda-xdrlib 0.2.0 pyhd8ed1ab_0 conda-forge
mdanalysis 2.7.0 py311h320fe9a_1 conda-forge
mdtraj 1.9.9 py311h90fe790_1 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
mmtf-python 1.1.3 pyhd8ed1ab_0 conda-forge
more-itertools 10.3.0 pyhd8ed1ab_0 conda-forge
mpg123 1.32.6 h59595ed_0 conda-forge
mpiplus v0.0.2 pyhd8ed1ab_0 conda-forge
mrcfile 1.5.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.7 py311h9547e67_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.3.0 hf1915f5_4 conda-forge
mysql-libs 8.3.0 hca2cd23_4 conda-forge
nbclassic 1.0.0 pyhb4ecaf3_1 conda-forge
nbclient 0.10.0 pyhd8ed1ab_0 conda-forge
nbconvert 7.16.4 hd8ed1ab_0 conda-forge
nbconvert-core 7.16.4 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.16.4 hd8ed1ab_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
ncurses 6.5 h59595ed_0 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
netcdf-fortran 4.6.1 nompi_hacb5139_103 conda-forge
netcdf4 1.6.5 nompi_py311he8ad708_100 conda-forge
networkx 3.3 pyhd8ed1ab_1 conda-forge
nglview 3.0.3 pyh8a188c0_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook 6.5.6 pyha770c72_0 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.100 hca3bf56_0 conda-forge
numba 0.59.1 py311h96b013e_0 conda-forge
numexpr 2.9.0 py311h039bad6_100 conda-forge
numpy 1.26.4 py311h64a7726_0 conda-forge
ocl-icd 2.3.2 hd590300_1 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openfe 1.0.0 pyhd8ed1ab_1 conda-forge
openfe-analysis 0.2.0 pyhd8ed1ab_0 conda-forge
openff-amber-ff-ports 0.0.4 pyhca7485f_0 conda-forge
openff-forcefields 2024.04.0 pyhca7485f_0 conda-forge
openff-interchange 0.3.27 pyhd8ed1ab_0 conda-forge
openff-interchange-base 0.3.27 pyhd8ed1ab_0 conda-forge
openff-models 0.1.2 pyhca7485f_0 conda-forge
openff-toolkit 0.15.2 pyhd8ed1ab_0 conda-forge
openff-toolkit-base 0.15.2 pyhd8ed1ab_0 conda-forge
openff-units 0.2.2 pyhca7485f_0 conda-forge
openff-utilities 0.1.12 pyhd8ed1ab_0 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openmm 8.1.1 py311h6d2dbb8_1 conda-forge
openmmforcefields 0.13.0 pyhd8ed1ab_0 conda-forge
openmmtools 0.23.1 pyhd8ed1ab_0 conda-forge
openssl 3.3.1 h4ab18f5_1 conda-forge
overrides 7.7.0 pyhd8ed1ab_0 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
packmol-memgen 2024.2.9 pypi_0 pypi
pandas 2.2.2 py311h320fe9a_0 conda-forge
pandoc 3.2 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panedr 0.8.0 pyhd8ed1ab_0 conda-forge
pango 1.52.2 ha41ecd1_0 conda-forge
parmed 4.2.2 py311hb755f60_1 conda-forge
parso 0.8.4 pyhd8ed1ab_0 conda-forge
pastel 0.2.1 pyhd8ed1ab_0 conda-forge
patsy 0.5.6 pyhd8ed1ab_0 conda-forge
pcre2 10.43 hcad00b1_0 conda-forge
pdb4amber 22.0 pypi_0 pypi
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 10.3.0 py311h18e6fac_0 conda-forge
pint 0.23 pyhd8ed1ab_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
pkginfo 1.11.1 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.2.1 pyhd8ed1ab_0 conda-forge
plotly 5.22.0 pyhd8ed1ab_0 conda-forge
plugcli 0.2.0 pyhd8ed1ab_0 conda-forge
pluggy 1.5.0 pyhd8ed1ab_0 conda-forge
ply 3.11 pyhd8ed1ab_2 conda-forge
pmw 2.0.1 py311h38be061_1008 conda-forge
pooch 1.8.1 pyhd8ed1ab_0 conda-forge
prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.42 pyha770c72_0 conda-forge
psutil 5.9.8 py311h459d7ec_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio-client 17.0 hb77b528_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge
py3dmol 2.1.0 pyhd8ed1ab_0 conda-forge
pycairo 1.26.0 py311h8feb60e_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pydantic 2.7.1 pyhd8ed1ab_0 conda-forge
pydantic-core 2.18.2 py311h5ecf98a_0 conda-forge
pyedr 0.8.0 pyhd8ed1ab_0 conda-forge
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pygraphviz 1.12 py311hbf5cbc9_0 conda-forge
pylev 1.4.0 pyhd8ed1ab_0 conda-forge
pymbar 3.1.1 py311h7c22f60_3 conda-forge
pymol-open-source 3.0.0 py311hbd307dc_8 conda-forge
pymsmt 22.0 pypi_0 pypi
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py311hf0fb5b6_5 conda-forge
pyqt5-sip 12.12.2 py311hb755f60_5 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytables 3.9.2 py311h3e8b7c9_2 conda-forge
pytest 8.2.0 pyhd8ed1ab_0 conda-forge
python 3.11.9 hb806964_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-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.11 4_cp311 conda-forge
pytng 0.3.1 py311hb2be122_1 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py311h459d7ec_1 conda-forge
pyzmq 24.0.1 py311ha4b6469_1 conda-forge
qt-main 5.15.8 hc9dc06e_21 conda-forge
rdkit 2024.03.2 py311h1d78c4b_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.35.1 pyhd8ed1ab_0 conda-forge
reportlab 4.1.0 py311h459d7ec_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
rise 5.7.1 py311h38be061_2 conda-forge
rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.18.1 py311h5ecf98a_0 conda-forge
ruamel.yaml 0.18.6 py311h459d7ec_0 conda-forge
ruamel.yaml.clib 0.2.8 py311h459d7ec_0 conda-forge
sander 22.0 pypi_0 pypi
scikit-learn 1.4.2 py311hc009520_0 conda-forge
scipy 1.13.0 py311h517d4fd_1 conda-forge
seaborn 0.13.2 hd8ed1ab_2 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_2 conda-forge
secretstorage 3.3.3 py311h38be061_2 conda-forge
send2trash 1.8.3 pyh0d859eb_0 conda-forge
setuptools 69.5.1 pyhd8ed1ab_0 conda-forge
sip 6.7.12 py311hb755f60_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge
smmap 5.0.0 pyhd8ed1ab_0 conda-forge
snappy 1.2.0 hdb0a2a9_1 conda-forge
sniffio 1.3.1 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sqlalchemy 2.0.30 py311h331c9d8_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
statsmodels 0.14.1 py311h1f0f07a_0 conda-forge
tenacity 8.3.0 pyhd8ed1ab_0 conda-forge
terminado 0.18.1 pyh0d859eb_0 conda-forge
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tidynamics 1.1.2 pyhd8ed1ab_0 conda-forge
tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge
tinydb 4.8.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tomlkit 0.12.5 pyha770c72_0 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tornado 6.4 py311h459d7ec_0 conda-forge
tqdm 4.66.4 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge
typing-extensions 4.11.0 hd8ed1ab_0 conda-forge
typing_extensions 4.11.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 1.26.18 pyhd8ed1ab_0 conda-forge
validators 0.28.1 pyhd8ed1ab_0 conda-forge
virtualenv 20.26.2 pyhd8ed1ab_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 1.8.0 pyhd8ed1ab_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
widgetsnbextension 3.5.1 pyh9f0ad1d_3 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.42 h4ab18f5_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.9 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 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zeromq 4.3.5 h75354e8_4 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
```
Note: it's not isolated to SystemGenerator
from openff.interchange import Interchange
from openff.toolkit import Molecule, ForceField
from openff.units import unit
import numpy as np
import os
os.environ['INTERCHANGE_EXPERIMENTAL'] = "1"
mol = Molecule.from_smiles("CC")
mol.generate_conformers()
sage = ForceField("openff-2.0.0.offxml")
cubic_box = unit.Quantity(30 * np.eye(3), unit.angstrom)
interchange = Interchange.from_smirnoff(topology=[mol], force_field=sage, box=cubic_box)
interchange.positions = mol.conformers[0]
interchange2 = Interchange.from_openmm(interchange.to_openmm(), interchange.to_openmm_topology())
Interchange.parse_raw(interchange2.json())
This looks similar to https://github.com/openforcefield/openff-toolkit/issues/1783 ... which in that thread I insist was fixed in the version you're using ... hmm
The issue here is with the toolkit / how information is passed between Interchange and the toolkit since Topology didn't always play nicely with _SimpleMolecules that are necessary to use when importing from OpenMM
This is unlikely to land before 0.4.0 but I hope to take a closer look at this soon.
I assume the use case is simple on the surface (save state out to JSON, trust that it'll be loaded back and represent the same state) but I anticipate the work will mostly be in gathering up and testing various corner cases.
Probably won't make it in 0.4.1 but hoping to take a stab at this before the timeframe of a 0.4.2 release
With toolkit 0.16.6, I can get this snippet running locally without error: https://github.com/openforcefield/openff-interchange/issues/1003#issuecomment-2225655695
The linked PR includes a minimal test, even though the fix is ultimately upstream
This is done; the linked PR adds tests but the desired functionality is in place.
After running the original snippet:
In [2]: from openff.interchange.drivers.all import get_openmm_energies
In [3]: get_openmm_energies(inter), get_openmm_energies(inter2)
Out[3]:
(EnergyReport(energies={'Bond': <Quantity(0.0, 'kilojoule / mole')>, 'Angle': <Quantity(0.226034896, 'kilojoule / mole')>, 'Torsion': <Quantity(0.0, 'kilojoule / mole')>, 'Nonbonded': <Quantity(3125.7172, 'kilojoule / mole')>}),
EnergyReport(energies={'Bond': <Quantity(0.0, 'kilojoule / mole')>, 'Angle': <Quantity(0.226034896, 'kilojoule / mole')>, 'Torsion': <Quantity(0.0, 'kilojoule / mole')>, 'Nonbonded': <Quantity(3125.7172, 'kilojoule / mole')>}))
This is with the following versions installed, relevant ones being the toolkit and Interchange:
$ micromamba list openff 9:55:27 ☁ fcf43997 ☂
List of packages in environment: "/Users/mattthompson/micromamba/envs/openff-interchange-env"
Name Version Build Channel
─────────────────────────────────────────────────────────────────
openff-amber-ff-ports 0.0.4 pyhca7485f_0 conda-forge
openff-forcefields 2024.09.0 pyhff2d567_0 conda-forge
openff-interchange 0.4.0 pyhd8ed1ab_0 conda-forge
openff-interchange-base 0.4.0 pyhd8ed1ab_0 conda-forge
openff-nagl 0.5.0 pyhd8ed1ab_0 conda-forge
openff-nagl-base 0.5.0 pyhd8ed1ab_0 conda-forge
openff-nagl-models 0.3.0 pyhd8ed1ab_1 conda-forge
openff-recharge 0.5.2 pyhd8ed1ab_0 conda-forge
openff-toolkit 0.16.6 pyhd8ed1ab_0 conda-forge
openff-toolkit-base 0.16.6 pyhd8ed1ab_0 conda-forge
openff-units 0.2.2 pyhca7485f_0 conda-forge
openff-utilities 0.1.13 pyhd8ed1ab_0 conda-forge