├── .gitattributes ├── .github ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── CI.yaml │ ├── Lint.yaml │ ├── codeql.yml │ └── integration.yaml ├── .gitignore ├── .lgtm.yml ├── CITATION.cff ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── codecov.yml ├── devtools ├── conda-envs │ ├── basic.yaml │ └── everything.yaml └── design_doc.md ├── qubekit ├── __init__.py ├── _version.py ├── bonded │ ├── __init__.py │ ├── mod_seminario.py │ └── qforce.py ├── charges │ ├── __init__.py │ ├── base.py │ ├── ddec.py │ ├── mbis.py │ ├── solvent_settings │ │ ├── __init__.py │ │ ├── base.py │ │ ├── gaussian.py │ │ └── psi.py │ └── utils.py ├── cli │ ├── __init__.py │ ├── bulk.py │ ├── cli.py │ ├── combine.py │ ├── config.py │ ├── progress.py │ ├── run.py │ ├── utils.py │ └── water_models.py ├── data │ ├── 12-dichloroethene.sdf │ ├── 132-Benzodioxaborole.pdb │ ├── DDEC6_even_tempered_net_atomic_charges.xyz │ ├── DDEC_atomic_Rcubed_moments.xyz │ ├── acetone.mol2 │ ├── acetone.pdb │ ├── acetone.sdf │ ├── bace0.mol │ ├── bace0.pdb │ ├── bace0.sdf │ ├── bace0.xyz │ ├── bace17d_with_fragments.json │ ├── benzene.sdf │ ├── biphenyl.pdb │ ├── biphenyl.sdf │ ├── biphenyl_qdata.txt │ ├── butane.pdb │ ├── capped_leu.pdb │ ├── chloromethane.pdb │ ├── chloromethane.sdf │ ├── chloromethane_hessian.txt │ ├── coumarin_hess_wbo.json │ ├── coumarin_with_rb.json │ ├── cyclohexane.sdf │ ├── cyclohexane.xml │ ├── ethane.sdf │ ├── ethane_hessian.txt │ ├── ethanol_sites.json │ ├── gaussian.fchk │ ├── gaussian.log │ ├── gaussian_gas_example.com │ ├── gaussian_nbo.log │ ├── gaussian_nbo_example.com │ ├── gaussian_solvent_example.com │ ├── integration_workflow.json │ ├── methane.sdf │ ├── methanol.json │ ├── methylamine.json │ ├── missing_names.pdb │ ├── no_sites_fit.json │ ├── pyridine.pdb │ ├── pyridine.sdf │ ├── pyridine.xml │ ├── ring_test.json │ ├── symmetry_fragments.json │ ├── templates │ │ ├── chargemol.txt │ │ ├── gaussian.com │ │ └── optimize.txt │ ├── water.pdb │ └── water.wfx ├── engines │ ├── __init__.py │ ├── base_engine.py │ ├── gaussian_harness.py │ ├── geometry_optimiser.py │ ├── openmm.py │ ├── qcengine.py │ └── torsiondrive.py ├── forcefield │ ├── __init__.py │ ├── force_groups.py │ ├── parameters.py │ └── utils.py ├── fragmentation │ ├── __init__.py │ └── wbo_fragmenter.py ├── molecules │ ├── __init__.py │ ├── components.py │ ├── ligand.py │ ├── protein.py │ └── utils.py ├── nonbonded │ ├── __init__.py │ ├── lennard_jones.py │ ├── protocols.py │ ├── utils.py │ └── virtual_sites.py ├── parametrisation │ ├── __init__.py │ ├── antechamber.py │ ├── base_parametrisation.py │ ├── gromacs.py │ ├── openff.py │ ├── xml.py │ └── xml_protein.py ├── proteins │ ├── __init__.py │ ├── protein_run.py │ └── protein_tools.py ├── tests │ ├── __init__.py │ ├── bonded │ │ ├── __init__.py │ │ ├── qforce_test.py │ │ └── seminario_test.py │ ├── cli │ │ ├── __init__.py │ │ ├── conftest.py │ │ ├── test_bulk.py │ │ ├── test_combine.py │ │ ├── test_config.py │ │ ├── test_run.py │ │ └── test_utils.py │ ├── conftest.py │ ├── engines │ │ ├── __init__.py │ │ ├── gaussian_harness_test.py │ │ ├── geometry_optimiser_test.py │ │ ├── qcengine_test.py │ │ └── torsiondrive_test.py │ ├── fragmentation │ │ ├── __init__.py │ │ └── wbofragmenter_test.py │ ├── ligand │ │ ├── __init__.py │ │ ├── ligand_test.py │ │ └── parametrisation_test.py │ ├── non_bonded │ │ ├── __init__.py │ │ ├── test_charges.py │ │ ├── test_nonbonded.py │ │ └── virtual_sites_test.py │ ├── protein │ │ ├── __init__.py │ │ ├── parametrisation_test.py │ │ └── protein_test.py │ ├── torsions │ │ ├── __init__.py │ │ ├── test_forcebalance.py │ │ └── test_scan.py │ └── workflow │ │ ├── __init__.py │ │ ├── test_helper_stages.py │ │ ├── test_results.py │ │ └── test_workflow.py ├── torsions │ ├── __init__.py │ ├── fitting │ │ ├── __init__.py │ │ └── forcebalance_wrapper.py │ ├── scanning │ │ ├── __init__.py │ │ └── torsion_scanner.py │ └── utils.py ├── utils │ ├── __init__.py │ ├── constants.py │ ├── datastructures.py │ 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