openforcefield/openff-toolkit-0.16.7.zip
openforcefield-openff-toolkit-a75ffe6
.git-blame-ignore-revs
272 Bytes
.github
ISSUE_TEMPLATE
bug_report.md
702 Bytes
feature_request.md
631 Bytes
dependabot.yml
118 Bytes
pull_request_template.md
468 Bytes
workflows
CI.yml
7.0 kB
beta_rc.yaml
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conda.yml
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examples.yml
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installer.yml
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release.yml
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.gitignore
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.pre-commit-config.yaml
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.readthedocs.yaml
252 Bytes
FAQ.md
40 Bytes
LICENSE
1.1 kB
MANIFEST.in
92 Bytes
README.md
9.6 kB
The-SMIRNOFF-force-field-format.md
208 Bytes
codecov.yml
230 Bytes
devtools
conda-envs
conda.yaml
251 Bytes
conda_oe.yaml
286 Bytes
installer.yaml
137 Bytes
openeye-examples.yaml
840 Bytes
openeye.yaml
985 Bytes
rdkit-examples.yaml
1.1 kB
rdkit.yaml
893 Bytes
release-build.yaml
116 Bytes
test_env.yaml
1.4 kB
scripts
build_cookiecutter_json.py
433 Bytes
docs
Makefile
583 Bytes
_static
images
favicon.svg
8.6 kB
logos
openff_toolkit_v1_white.png
56.3 kB
openforcefield.png
10.5 kB
_templates
autosummary
base.rst
612 Bytes
class.rst
564 Bytes
module.rst
1.1 kB
api
toolkits.md
3.9 kB
conf.py
9.4 kB
conftest.py
806 Bytes
environment.yml
890 Bytes
examples.md
52 Bytes
index.md
734 Bytes
installation.md
4.8 kB
make.bat
812 Bytes
releasehistory.md
182.7 kB
topology.md
1.2 kB
typing.rst
3.1 kB
users
concepts.md
2.0 kB
developing.md
33.9 kB
figures
vsite_examples.svg
84.3 kB
vsite_matches.svg
202.7 kB
vsite_matches_name.svg
240.6 kB
vsite_smirks_to_particle.svg
94.9 kB
molecule_conversion.md
8.3 kB
molecule_cookbook.ipynb
207.9 kB
pdb_cookbook
6hvi_prepared.pdb
655.2 kB
RAMP1_solv_box_ions.pdb
1.3 MB
gromacs_solv_complex.pdb
3.8 MB
index.ipynb
11.1 MB
smirnoff.md
4.9 kB
virtualsites.md
7.7 kB
zw_l_alanine.pdb
1.2 kB
zw_l_alanine.sdf
1.2 kB
utils.rst
1.0 kB
examples
QCArchive_interface
QCarchive_interface.ipynb
63.1 kB
README.md
3.4 kB
SMIRNOFF_simulation
.gitignore
24 Bytes
README.md
260 Bytes
run_simulation.ipynb
12.7 kB
conformer_energies
.gitignore
47 Bytes
README.md
641 Bytes
conformer_energies.ipynb
133.0 kB
conformer_energies.py
6.0 kB
ruxolitinib_conformers.sdf
35.3 kB
thumbnail.png
134.2 kB
deprecated
SMIRNOFF_comparison
README.md
1.3 kB
compare_molecule_energies.py
1.8 kB
compare_set_energies.py
2.4 kB
check_dataset_parameter_coverage
.gitignore
10 Bytes
README.md
204 Bytes
check_parameter_coverage.ipynb
670.7 kB
example_molecules.mol2
16.4 kB
example_molecules.sdf
15.5 kB
example_molecules.smi
230 Bytes
problem_smiles.smi
49.0 kB
chemicalEnvironments
AlkEthOH_dvrs1.oeb
792 Bytes
README.md
9.2 kB
create_move_types_and_weights.ipynb
16.9 kB
moveTrees.uniq.Angle.txt
2.0 kB
moveTrees.uniq.Bond.txt
1.5 kB
moveTrees.uniq.Improper.txt
2.6 kB
moveTrees.uniq.Torsion.txt
2.6 kB
moveTrees.uniq.VdW.txt
898 Bytes
moves_using_environments.ipynb
64.4 kB
using_environments.ipynb
27.1 kB
host_guest_simulation
OA.mol2
20.2 kB
README.md
1.3 kB
hbonds.ffxml
475 Bytes
smirnoff_host_guest.ipynb
25.4 kB
liquid_box
ETH-box.pdb
259.0 kB
ETH.mol2
954 Bytes
create_mol2_pdb
README.md
649 Bytes
create_mol2_pdb.py
7.1 kB
input.smi
4 Bytes
openff_simulation.py
2.7 kB
mixedFF_structure
README.md
2.2 kB
generate_mixedFF_complex.py
2.2 kB
partial_bondorder
Frosst_AlkEthOH_extracarbons.ffxml
10.3 kB
README.md
1.4 kB
test_partialbondorder.ipynb
7.4 kB
rdkit_openeye_comparison
compare_rdk_oe_mol_loading.ipynb
58.9 kB
testing
OE_bondorder_testing.ipynb
6.7 kB
README.md
998 Bytes
test_impropers
1,2-ditert-butylbenzene.crd
1.3 kB
1,2-ditert-butylbenzene.mol2
3.7 kB
1,2-ditert-butylbenzene.prmtop
21.2 kB
README.md
933 Bytes
benzene.crd
451 Bytes
benzene.mol2
1.3 kB
benzene.prmtop
11.6 kB
o-xylene.crd
670 Bytes
o-xylene.mol2
1.9 kB
o-xylene.prmtop
14.1 kB
parm_Frosst.frcmod
154.2 kB
smirnoff99Frosst_modified.ffxml
35.8 kB
test_impropers.ipynb
14.0 kB
tleap_tools.py
4.8 kB
test_system_conversion
README.md
512 Bytes
amber_system.xml
2.9 MB
convert_to_amber.ipynb
6.7 MB
cyclohexane.frcmod
67 Bytes
cyclohexane.inpcrd
668 Bytes
cyclohexane.mol2
2.2 kB
cyclohexane.prmtop
15.2 kB
cyclohexane.sdf
2.2 kB
cyclohexane_ethanol_0.4_0.6.pdb
315.7 kB
ethanol.frcmod
67 Bytes
ethanol.inpcrd
340 Bytes
ethanol.mol2
1.2 kB
ethanol.prmtop
11.3 kB
ethanol.sdf
1.2 kB
openforcefield_system.xml
3.0 MB
smarty_system.xml
3.0 MB
using_smirnoff_with_amber_protein_forcefield
toluene_in_T4_lysozyme.ipynb
5.2 kB
examples_helper.py
1.7 kB
external
README.md
504 Bytes
swap_amber_parameters
.gitignore
53 Bytes
README.md
1.1 kB
swap_existing_ligand_parameters.ipynb
25.9 kB
thumbnail.png
114.5 kB
swap_existing_ligand_parameters_with_openmmforcefields
.gitignore
53 Bytes
README.md
996 Bytes
swap_existing_ligand_parameters_with_openmmforcefields.ipynb
14.8 kB
thumbnail.png
97.4 kB
using_smirnoff_with_amber_protein_forcefield
.gitignore
29 Bytes
BRD4_inhibitor_benchmark.ipynb
11.5 kB
README.md
522 Bytes
forcefield_modification
.gitignore
16 Bytes
README.md
412 Bytes
forcefield_modification.ipynb
265.5 kB
thumbnail.png
95.4 kB
inspect_assigned_parameters
README.md
221 Bytes
inspect_assigned_parameters.ipynb
28.5 kB
toolkit_showcase
.gitignore
168 Bytes
5tbm_prepared.pdb
143.9 kB
PT2385.sdf
2.9 kB
README.md
491 Bytes
minim.mdp
2.2 kB
sim.mdp
3.5 kB
toolkit_showcase.ipynb
52.4 kB
using_smirnoff_in_amber_or_gromacs
.gitignore
35 Bytes
1_cyclohexane_1_ethanol.pdb
3.0 kB
README.md
594 Bytes
export_with_interchange.ipynb
17.4 kB
using_smirnoff_with_amber_protein_forcefield
.gitignore
42 Bytes
BRD4_inhibitor_benchmark.ipynb
5.9 kB
README.md
364 Bytes
virtual_sites
.gitignore
24 Bytes
thumbnail.png
142.2 kB
vsite_showcase.ipynb
56.5 kB
visualization
README.md
1.0 kB
visualization.ipynb
75.5 kB
openff
toolkit
__init__.py
3.1 kB
_tests
__init__.py
0 Bytes
_stale_tests.py
7.4 kB
conftest.py
4.1 kB
create_molecules.py
17.5 kB
mocking.py
5.1 kB
molecule
__init__.py
33 Bytes
test_state_enumeration.py
12.2 kB
test_energies.py
4.4 kB
test_examples.py
3.4 kB
test_forcefield.py
176.8 kB
test_interchange.py
641 Bytes
test_io.py
519 Bytes
test_links.py
2.3 kB
test_mm_molecule.py
13.5 kB
test_molecule.py
185.2 kB
test_nagl.py
5.2 kB
test_parameter_plugins.py
2.9 kB
test_parameters.py
106.5 kB
test_toolkit_io.py
34.7 kB
test_toolkits.py
197.3 kB
test_topology.py
100.9 kB
test_utils.py
2.8 kB
test_utils_callback.py
7.0 kB
test_utils_collections.py
8.9 kB
test_utils_serialization.py
5.8 kB
utils.py
67.1 kB
data
README.md
418 Bytes
molecules
AlkEthOH_test_filt1_ff.mol2
85.1 kB
AlkEthOH_test_filt1_tripos.mol2
85.1 kB
AlkEthOH_tripos.tar.gz
5.0 MB
CID20742535_anion.sdf
2.0 kB
CID20742535_neutral.sdf
2.1 kB
FreeSolv.tar.gz
1.5 MB
MiniDrugBank.sdf
1.5 MB
MiniDrugBank_tripos.mol2
1.6 MB
PT2385.sdf
2.9 kB
QL8.sdf
16.8 kB
README.md
1.5 kB
benzene.crd
451 Bytes
benzene.mol2
1.3 kB
benzene.top
11.6 kB
butane_multi.sdf
9.4 kB
cyclohexane.mol2
1.8 kB
ethanol.mol2
954 Bytes
ethanol.sdf
888 Bytes
ethanol_partial_charges.sdf
1.1 kB
ethanol_reordered.mol2
954 Bytes
ethanol_reordered.sdf
888 Bytes
ethene_rdkit.sdf
562 Bytes
laromustine_ff.mol2
3.2 kB
laromustine_tripos.mol2
3.2 kB
methane_multiconformer.sdf
1.0 kB
methane_multiconformer_properties.sdf
1.3 kB
po4_phenylphosphate.pdb
2.3 kB
ruxolitinib_conformers.sdf
35.3 kB
toluene.mol2
1.6 kB
toluene.mol2.gz
440 Bytes
toluene.pdb
1.5 kB
toluene.sdf
1.5 kB
toluene_charged.mol2
1.6 kB
z_3_hydroxy_propenal.sdf
882 Bytes
proteins
5tbm_complex_solv.pdb
150.9 kB
5tbm_complex_solv_box.pdb
1.3 MB
CTerminal_ALA.pdb
1.5 kB
CTerminal_ALA.sdf
1.8 kB
CTerminal_ALA_ALA.pdb
2.3 kB
CTerminal_ALA_ALA_misnamedH.pdb
2.3 kB
CTerminal_ARG.pdb
2.6 kB
CTerminal_TRP.pdb
2.6 kB
MainChain_ALA.pdb
1.9 kB
MainChain_ALA.sdf
2.3 kB
MainChain_ALA_ALA.pdb
2.7 kB
MainChain_ALA_ALA.sdf
3.0 kB
MainChain_ALA_ALA_icodes.pdb
2.7 kB
MainChain_ALA_ALA_no_hydrogens.pdb
1.3 kB
MainChain_ARG.pdb
3.0 kB
MainChain_ARG.sdf
3.8 kB
MainChain_CYM.pdb
1.8 kB
MainChain_CYS.pdb
2.0 kB
MainChain_CYX.pdb
3.7 kB
MainChain_CYX.sdf
4.6 kB
MainChain_GLH.sdf
2.9 kB
MainChain_GLU.sdf
2.9 kB
MainChain_HID.pdb
2.5 kB
MainChain_HIE.pdb
2.5 kB
MainChain_HIE.sdf
3.1 kB
MainChain_HIP.pdb
2.5 kB
MainChain_HIP.sdf
3.2 kB
MainChain_PRO.pdb
2.2 kB
MainChain_TRP.pdb
3.0 kB
NTerminal_ALA.pdb
1.6 kB
NTerminal_ALA.sdf
1.9 kB
NTerminal_ALA_ALA.pdb
2.4 kB
NTerminal_ARG.pdb
2.7 kB
NTerminal_TRP.pdb
2.7 kB
T4-protein-unprocessed-4w51.pdb
153.3 kB
T4-protein.mol2
263.0 kB
T4-protein.pdb
213.5 kB
T4-protein.sdf
207.6 kB
T4_protein_waters.pdb
240.0 kB
TwoMol_SER_CYS.pdb
3.7 kB
aa_residues_substructures_explicit_bond_orders_with_caps.json
152.5 kB
aa_residues_substructures_explicit_bond_orders_with_caps_explicit_connectivity.json
191.6 kB
aa_residues_substructures_with_caps.json
149.2 kB
ace-ZZZ-gly-nme.pdb
4.4 kB
ace-ZZZ-gly-nme.sdf
3.9 kB
ace-a10-nme.sdf
9.4 kB
ace-ala-nh2.pdb
1.3 kB
fluoresceine_dyed_helix_capped.pdb
17.2 kB
neutral_arginine.pdb
2.4 kB
reference_energies
README.md
846 Bytes
reference_0.8.0.json
338 Bytes
reference_0.8.0.json.txt
13.0 kB
reference_after_1007.json
334 Bytes
reference_after_1007.json.txt
11.0 kB
reference_after_802.json
339 Bytes
reference_after_802.json.txt
21.1 kB
systems
README.md
596 Bytes
amber
cyclohexane_ethanol_0.4_0.6.inpcrd
110.1 kB
cyclohexane_ethanol_0.4_0.6.prmtop
1.1 MB
monomers
butanol.mol2
1.9 kB
butanol.sdf
1.8 kB
cyclohexane.mol2
2.2 kB
cyclohexane.sdf
2.2 kB
ethanol.mol2
1.2 kB
ethanol.sdf
1.2 kB
methane.mol2
709 Bytes
methane.sdf
698 Bytes
propane.mol2
1.4 kB
propane.sdf
1.4 kB
tip3p_water.mol2
441 Bytes
water.mol2
477 Bytes
water.sdf
478 Bytes
packmol_boxes
cyclohexane_ethanol_0.4_0.6.pdb
315.7 kB
cyclohexane_water.pdb
372.2 kB
ethanol_water.pdb
348.8 kB
propane_methane_butanol_0.2_0.3_0.5.pdb
398.1 kB
test_systems
1_cyclohexane_1_ethanol.pdb
3.0 kB
1_ethanol.pdb
1.1 kB
1_ethanol_no_conect.pdb
903 Bytes
1_ethanol_reordered.pdb
1.1 kB
PE.pdb
4.5 kB
README.md
208 Bytes
T4_lysozyme_water_ions.pdb
2.4 MB
test_forcefields
Frosst_AlkEthOH.offxml
8.4 kB
Frosst_AlkEthOH_GBSA.offxml
9.5 kB
Frosst_AlkEthOH_MDL.offxml
8.4 kB
Frosst_AlkEthOH_parmAtFrosst.offxml
9.4 kB
GBSA_HCT-1.0.offxml
1.5 kB
GBSA_OBC1-1.0.offxml
1.3 kB
GBSA_OBC2-1.0.offxml
1.3 kB
README.md
3.6 kB
ammonia_minimal.offxml
2.2 kB
benzene_minimal.offxml
2.4 kB
chargeincrement-test.offxml
1.1 kB
frcmod.Frosst_AlkEthOH_withIDs
5.2 kB
ion_charges.offxml
1.2 kB
mangled.offxml
772 Bytes
old
README.md
948 Bytes
hbonds.offxml
510 Bytes
test_ff_0_0_2_spec_0_1.offxml
38.5 kB
test_ff_0_0_2_spec_0_2.offxml
39.2 kB
test_ff_0_0_2_spec_0_3.offxml
55.7 kB
test_ff_0_0_4_fixed_spec_0_1.offxml
39.4 kB
test_ff_0_0_4_fixed_spec_0_2.offxml
40.1 kB
test_ff_0_0_4_fixed_spec_0_3.offxml
56.7 kB
test_ff_0_0_4_spec_0_1.offxml
39.1 kB
test_ff_0_0_4_spec_0_2.offxml
39.8 kB
test_ff_0_0_4_spec_0_3.offxml
56.7 kB
smirff99Frosst_reference_0_1_spec.offxml
40.0 kB
smirnoff99Frosst_experimental.offxml
57.3 kB
smirnoff99Frosst_reference_0_1_spec.offxml
40.1 kB
smirnoff99Frosst_reference_0_2_spec.offxml
40.5 kB
test_forcefield.offxml
57.8 kB
tip3p.offxml
1.9 kB
unsupported_smirnoff_version.offxml
756 Bytes
topology
__init__.py
863 Bytes
_mm_molecule.py
21.7 kB
molecule.py
226.0 kB
topology.py
101.7 kB
typing
__init__.py
32 Bytes
engines
__init__.py
33 Bytes
smirnoff
__init__.py
784 Bytes
forcefield.py
60.6 kB
io.py
6.8 kB
parameters.py
147.4 kB
plugins.py
3.3 kB
utils
__init__.py
1.6 kB
_viz.py
3.3 kB
ambertools_wrapper.py
20.0 kB
base_wrapper.py
9.2 kB
builtin_wrapper.py
5.3 kB
callback.py
6.5 kB
collections.py
8.2 kB
constants.py
547 Bytes
exceptions.py
27.9 kB
nagl_wrapper.py
5.5 kB
openeye_wrapper.py
109.7 kB
rdkit_wrapper.py
137.4 kB
serialization.py
12.4 kB
toolkit_registry.py
20.0 kB
toolkits.py
7.4 kB
utils.py
27.1 kB
pyproject.toml
2.6 kB
utilities
README.md
788 Bytes
deprecated
convert_frosst
README.md
4.1 kB
check_different_smirnoffs.ipynb
16.8 kB
convert_frcmod_0.1.py
10.1 kB
convert_frcmod_0.2.py
10.3 kB
convert_frcmod_0.3.py
10.5 kB
example.frcmod
1.4 kB
example.offxml
2.3 kB
example_plusgeneric.offxml
2.7 kB
frcmod.parm_Frosst
151.6 kB
generics.offxml
1.9 kB
parameter_usage.ipynb
97.3 kB
parm99.dat
42.4 kB
smirnoff99Frosst.offxml
39.1 kB
smirnoff99Frosst_AlkEthOH.offxml
37.7 kB
smirnoffishFrcmod.parm99Frosst.txt
43.4 kB
smirnoffishFrcmod.parm99Frosst_AlkEthOH.txt
40.9 kB
template_0.1.offxml
1.5 kB
template_0.2.offxml
1.9 kB
template_0.3.offxml
1.6 kB
make_substructure_dict
_cif_to_substructure_dict.py
41.5 kB
_make_chemical_substructures.py
1.5 kB
_make_metadata_assignment_substructures.py
1.1 kB
test_plugins
custom_plugins
handler_plugins.py
1.2 kB
setup.py
589 Bytes