├── .git-blame-ignore-revs ├── .github ├── CODEOWNERS ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── BUG_REPORT.md │ ├── FEATURE_REQUEST.md │ └── USER_SUPPORT.md ├── PULL_REQUEST_TEMPLATE.md ├── dependabot.yml └── workflows │ ├── beta.yaml │ ├── ci.yaml │ └── examples.yaml ├── .gitignore ├── .markdownlint.yaml ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── CITATION.cff ├── LICENSE ├── LICENSE-3RD-PARTY ├── MANIFEST.in ├── README.md ├── benchmarks ├── 0.4.8 │ ├── large_peg.csv │ ├── ligand_in_water.csv │ ├── mixed_solvent.csv │ └── protein_in_water.csv ├── README.md ├── large-peg.py ├── ligand-in-water.py ├── mixed-solvent.py ├── protein-in-water.py ├── run.sh └── summarize.py ├── devtools ├── conda-envs │ ├── dev_env.yaml │ ├── docs_env.yaml │ ├── examples_env.yaml │ ├── test_env.yaml │ └── test_not_py313.yaml └── scripts │ └── molecule-regressions.py ├── docs ├── Makefile ├── README.md ├── _static │ └── README.md ├── _templates │ ├── README.md │ └── autosummary │ │ ├── base.rst │ │ ├── class.rst │ │ └── module.rst ├── annotations.md ├── conf.py ├── developing.md ├── docutils.conf ├── index.md ├── installation.md ├── make.bat ├── releasehistory.md └── using │ ├── advanced.md │ ├── collections.md │ ├── construction.md │ ├── edges.md │ ├── experimental.md │ ├── intro.md │ ├── migrating.md │ ├── output.md │ ├── plugins.md │ ├── serialization.md │ └── status.md ├── examples ├── README.md ├── amber │ ├── .gitignore │ └── amber.ipynb ├── conformer_energies │ ├── README.md │ └── conformer_energies.ipynb ├── experimental │ ├── openmmforcefields │ │ ├── gaff.ipynb │ │ └── smirnoff.ipynb │ └── solvate │ │ ├── .gitignore │ │ ├── README.md │ │ ├── ace-a5ca5-nme.pdb │ │ └── solvate.ipynb ├── host-guest │ ├── .gitignore │ ├── README.md │ ├── guest.sdf │ ├── host.sdf │ └── host_guest.ipynb ├── lammps │ ├── .gitignore │ ├── README.md │ └── lammps.ipynb ├── ligand_in_water │ ├── .gitignore │ ├── README.md │ ├── ligand_in_water.ipynb │ ├── run.mdp │ └── tip5p.offxml ├── load-SAMPL6 │ ├── README.md │ └── load-SAMPL6.ipynb ├── openmm-import │ ├── .gitignore │ ├── README.md │ └── protein-ligand.ipynb ├── openmm │ ├── .gitignore │ ├── README.md │ └── openmm.ipynb ├── packed_box │ ├── .gitignore │ ├── README.md │ └── packed_box.ipynb ├── protein_ligand │ ├── .gitignore │ ├── README.md │ └── protein_ligand.ipynb ├── vectorized_representations │ ├── README.md │ └── vectorized_representations.ipynb └── virtual_sites │ ├── .gitignore │ ├── 4_site_water.xml │ ├── 5_site_water.xml │ ├── README.md │ ├── example-vsites-parameters-forcefield.offxml │ ├── ligand.xml │ ├── planar_carbonyl.xml │ ├── sigma_hole.xml │ ├── tip5p.offxml │ ├── trivalent_nitrogen.xml │ └── virtual_sites.ipynb ├── openff └── interchange │ ├── __init__.py │ ├── _annotations.py │ ├── _experimental.py │ ├── _tests │ ├── __init__.py │ ├── _gromacs.py │ ├── _openmm.py │ ├── conftest.py │ ├── data │ │ ├── 10-argons.pdb │ │ ├── ALA_GLY │ │ │ ├── ALA_GLY.gro │ │ │ ├── ALA_GLY.pdb │ │ │ ├── ALA_GLY.sdf │ │ │ └── ALA_GLY.top │ │ ├── CB8.sdf │ │ ├── MiniDrugBankTrimmed.sdf │ │ ├── README.md │ │ ├── SAMPL6 │ │ │ ├── README.md │ │ │ ├── complex.gro │ │ │ ├── complex.pdb │ │ │ ├── complex.prmtop │ │ │ ├── complex.top │ │ │ └── complex.xml │ │ ├── ammonia.offxml │ │ ├── asterisk.gro │ │ ├── asterisk.top │ │ ├── benzene.sdf │ │ ├── buckingham.offxml │ │ ├── buckingham_virtual_sites.offxml │ │ ├── chosen.smi │ │ ├── complex.gro │ │ ├── complex.top │ │ ├── copied_reordered_water.pdb │ │ ├── cube.pdb │ │ ├── de-force-1.0.1.offxml │ │ ├── dodecahedron.pdb │ │ ├── ethanol_param_angles.npy │ │ ├── ethanol_param_bonds.npy │ │ ├── ethanol_param_vdw.npy │ │ ├── ethanol_rb_torsions.gro │ │ ├── ethanol_rb_torsions.top │ │ ├── example-sigma-hole-bromine.offxml │ │ ├── foyer_test_molecules │ │ │ ├── acetate.sdf │ │ │ ├── adamantane.sdf │ │ │ ├── benzene.sdf │ │ │ ├── cyclohexane.sdf │ │ │ ├── ethanol.sdf │ │ │ ├── methane.sdf │ │ │ └── methane_multiconformer.sdf │ │ ├── gbsa.offxml │ │ ├── gromacs │ │ │ ├── README.md │ │ │ ├── rb_torsions.gro │ │ │ └── rb_torsions.top │ │ ├── h-bonds.in │ │ ├── hexanol-water.pdb │ │ ├── invalid.gro │ │ ├── invalid.top │ │ ├── invalid_partway_through.top │ │ ├── ions.offxml │ │ ├── lig_CHEMBL3265016-1.pdb │ │ ├── mdp │ │ │ ├── cutoff.mdp │ │ │ ├── cutoff_buck.mdp │ │ │ ├── cutoff_hbonds.mdp │ │ │ ├── default.mdp │ │ │ ├── em.mdp │ │ │ └── reaction-field.mdp │ │ ├── molecules.sdf │ │ ├── no_vdw.offxml │ │ ├── octahedron.pdb │ │ ├── packed-argon.pdb │ │ ├── popc.sdf │ │ ├── run.in │ │ ├── smi_to_sdf.py │ │ ├── system.xml │ │ ├── tip3p.offxml │ │ ├── tip4p.offxml │ │ ├── tip5p.offxml │ │ ├── trim_drug_bank.py │ │ └── water-dimer.pdb │ ├── energy_tests │ │ ├── __init__.py │ │ ├── components │ │ │ ├── __init__.py │ │ │ ├── test_mdconfig.py │ │ │ └── test_smirnoff.py │ │ ├── interop │ │ │ └── amber │ │ │ │ ├── __init__.py │ │ │ │ └── test_energies.py │ │ ├── smirnoff │ │ │ ├── __init__.py │ │ │ └── test_base.py │ │ └── test_energies.py │ ├── interoperability_tests │ │ ├── __init__.py │ │ ├── components │ │ │ ├── __init__.py │ │ │ ├── interchange │ │ │ │ ├── __init__.py │ │ │ │ └── test_combine.py │ │ │ └── test_packmol.py │ │ ├── gromacs │ │ │ ├── __init__.py │ │ │ └── test_systems.py │ │ ├── internal │ │ │ ├── __init__.py │ │ │ ├── test_amber.py │ │ │ └── test_gromacs.py │ │ ├── lammps │ │ │ └── export │ │ │ │ └── __init__.py │ │ ├── serialization │ │ │ └── test_json_roundtrips.py │ │ └── test_openmm.py │ ├── regression_tests │ │ └── components │ │ │ └── test_interchange.py │ ├── test_deprecations.py │ ├── test_issues.py │ └── unit_tests │ │ ├── __init__.py │ │ ├── common │ │ ├── __init__.py │ │ ├── test_nonbonded.py │ │ ├── test_positions.py │ │ └── test_topology.py │ │ ├── components │ │ ├── __init__.py │ │ ├── test_foyer.py │ │ ├── test_interchange.py │ │ ├── test_mbuild.py │ │ ├── test_mdconfig.py │ │ ├── test_packmol.py │ │ ├── test_potentials.py │ │ └── test_toolkit.py │ │ ├── conftest.py │ │ ├── drivers │ │ ├── __init__.py │ │ ├── conftest.py │ │ ├── test_all.py │ │ ├── test_amber.py │ │ ├── test_gromacs.py │ │ ├── test_lammps.py │ │ ├── test_openmm.py │ │ └── test_report.py │ │ ├── interop │ │ ├── __init__.py │ │ ├── amber │ │ │ ├── __init__.py │ │ │ └── export │ │ │ │ ├── __init__.py │ │ │ │ └── test_export.py │ │ ├── gromacs │ │ │ ├── __init__.py │ │ │ ├── _import │ │ │ │ ├── __init__.py │ │ │ │ ├── test_from_files.py │ │ │ │ ├── test_interchange.py │ │ │ │ └── test_topology.py │ │ │ ├── export │ │ │ │ ├── __init__.py │ │ │ │ ├── test_export.py │ │ │ │ ├── test_hmr.py │ │ │ │ └── test_virtual_sites.py │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ └── test_models.py │ │ │ └── test_interchange.py │ │ ├── lammps │ │ │ ├── __init__.py │ │ │ ├── export │ │ │ │ ├── __init__.py │ │ │ │ └── test_lammps.py │ │ │ └── test_provenance.py │ │ ├── openmm │ │ │ ├── __init__.py │ │ │ ├── _import │ │ │ │ ├── __init__.py │ │ │ │ ├── test_compat.py │ │ │ │ ├── test_import.py │ │ │ │ └── test_virtual_sites.py │ │ │ ├── test_constraints.py │ │ │ ├── test_hmr.py │ │ │ ├── test_nonbonded.py │ │ │ ├── test_openmm.py │ │ │ ├── test_topology.py │ │ │ └── test_virtual_sites.py │ │ ├── test_openmm.py │ │ └── test_virtual_sites.py │ │ ├── operations │ │ ├── __init__.py │ │ ├── minimize │ │ │ ├── __init__.py │ │ │ └── test_openmm.py │ │ └── test_combine.py │ │ ├── plugins │ │ ├── __init__.py │ │ └── test_smirnoff_plugins.py │ │ ├── smirnoff │ │ ├── __init__.py │ │ ├── test_base.py │ │ ├── test_charge_assignment_logging.py │ │ ├── test_create.py │ │ ├── test_gbsa.py │ │ ├── test_gromacs.py │ │ ├── test_nonbonded.py │ │ ├── test_valence.py │ │ └── test_virtual_sites.py │ │ ├── test_annotations.py │ │ ├── test_experimental.py │ │ ├── test_lazy_import.py │ │ ├── test_models.py │ │ └── test_pydantic.py │ ├── common │ ├── __init__.py │ ├── _nonbonded.py │ ├── _positions.py │ ├── _topology.py │ └── _valence.py │ ├── components │ ├── __init__.py │ ├── _packmol.py │ ├── _particles.py │ ├── _viz.py │ ├── foyer.py │ ├── interchange.py │ ├── mbuild.py │ ├── mdconfig.py │ ├── nonbonded.py │ ├── potentials.py │ └── toolkit.py │ ├── constants.py │ ├── drivers │ ├── __init__.py │ ├── all.py │ ├── amber.py │ ├── gromacs.py │ ├── lammps.py │ ├── openmm.py │ └── report.py │ ├── exceptions.py │ ├── foyer │ ├── __init__.py │ ├── _base.py │ ├── _create.py │ ├── _guard.py │ ├── _nonbonded.py │ └── _valence.py │ ├── interop │ ├── __init__.py │ ├── _virtual_sites.py │ ├── amber │ │ ├── __init__.py │ │ └── export │ │ │ ├── __init__.py │ │ │ └── _export.py │ ├── common.py │ ├── gromacs │ │ ├── __init__.py │ │ ├── _import │ │ │ ├── __init__.py │ │ │ ├── _import.py │ │ │ ├── _topology.py │ │ │ └── combine.py │ │ ├── _interchange.py │ │ ├── export │ │ │ ├── __init__.py │ │ │ ├── _export.py │ │ │ └── _virtual_sites.py │ │ └── models │ │ │ ├── __init__.py │ │ │ └── models.py │ ├── lammps │ │ ├── __init__.py │ │ └── export │ │ │ ├── __init__.py │ │ │ ├── export.py │ │ │ └── provenance.py │ └── openmm │ │ ├── __init__.py │ │ ├── _gbsa.py │ │ ├── _import │ │ ├── __init__.py │ │ ├── _import.py │ │ ├── _nonbonded.py │ │ ├── _virtual_sites.py │ │ └── compat.py │ │ ├── _nonbonded.py │ │ ├── _positions.py │ │ ├── _topology.py │ │ ├── _valence.py │ │ ├── _virtual_sites.py │ │ └── export │ │ └── __init__.py │ ├── models.py │ ├── operations │ ├── __init__.py │ ├── _combine.py │ └── minimize │ │ ├── __init__.py │ │ └── openmm.py │ ├── plugins │ └── __init__.py │ ├── py.typed │ ├── pydantic.py │ ├── serialization.py │ ├── smirnoff │ ├── __init__.py │ ├── _base.py │ ├── _create.py │ ├── _gbsa.py │ ├── _gromacs.py │ ├── _nonbonded.py │ ├── _valence.py │ └── _virtual_sites.py │ └── warnings.py ├── plugins ├── nonbonded_plugins │ ├── __init__.py │ ├── nonbonded.py │ └── virtual_sites.py ├── py.typed └── pyproject.toml ├── pyproject.toml ├── regression_tests ├── README.md ├── default-comparison-settings.json ├── old-toolkit-env.txt ├── small-molecule │ ├── dataset.smi │ ├── 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-------------------------------------------------------------------------------- 1 | """Interoperability tests with Amber.""" 2 | -------------------------------------------------------------------------------- /openff/interchange/_tests/interoperability_tests/internal/test_amber.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/openff-interchange/HEAD/openff/interchange/_tests/interoperability_tests/internal/test_amber.py -------------------------------------------------------------------------------- /openff/interchange/_tests/interoperability_tests/internal/test_gromacs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/openff-interchange/HEAD/openff/interchange/_tests/interoperability_tests/internal/test_gromacs.py -------------------------------------------------------------------------------- /openff/interchange/_tests/interoperability_tests/lammps/export/__init__.py: -------------------------------------------------------------------------------- 1 | """Tests of LAMMPS exporter.""" 2 | -------------------------------------------------------------------------------- /openff/interchange/_tests/interoperability_tests/serialization/test_json_roundtrips.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/openff-interchange/HEAD/openff/interchange/_tests/interoperability_tests/serialization/test_json_roundtrips.py -------------------------------------------------------------------------------- /openff/interchange/_tests/interoperability_tests/test_openmm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/openff-interchange/HEAD/openff/interchange/_tests/interoperability_tests/test_openmm.py 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/openff/interchange/_tests/unit_tests/drivers/__init__.py: -------------------------------------------------------------------------------- 1 | """Unit tests for drivers.""" 2 | -------------------------------------------------------------------------------- /openff/interchange/_tests/unit_tests/drivers/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/openff-interchange/HEAD/openff/interchange/_tests/unit_tests/drivers/conftest.py -------------------------------------------------------------------------------- /openff/interchange/_tests/unit_tests/drivers/test_all.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/openff-interchange/HEAD/openff/interchange/_tests/unit_tests/drivers/test_all.py -------------------------------------------------------------------------------- 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openff.interchange.plugins.""" 2 | -------------------------------------------------------------------------------- /openff/interchange/_tests/unit_tests/plugins/test_smirnoff_plugins.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/openff-interchange/HEAD/openff/interchange/_tests/unit_tests/plugins/test_smirnoff_plugins.py -------------------------------------------------------------------------------- /openff/interchange/_tests/unit_tests/smirnoff/__init__.py: -------------------------------------------------------------------------------- 1 | """Tests for the openff.interchange.smirnoff module.""" 2 | -------------------------------------------------------------------------------- /openff/interchange/_tests/unit_tests/smirnoff/test_base.py: -------------------------------------------------------------------------------- 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/openff/interchange/interop/amber/export/_export.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/openff-interchange/HEAD/openff/interchange/interop/amber/export/_export.py -------------------------------------------------------------------------------- /openff/interchange/interop/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/openff-interchange/HEAD/openff/interchange/interop/common.py -------------------------------------------------------------------------------- /openff/interchange/interop/gromacs/__init__.py: -------------------------------------------------------------------------------- 1 | """Interfaces with GROMACS.""" 2 | -------------------------------------------------------------------------------- /openff/interchange/interop/gromacs/_import/__init__.py: 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