LICENSE
README.md
pyproject.toml
src/biochar/__init__.py
src/biochar/constants.py
src/biochar/py.typed
src/biochar.egg-info/PKG-INFO
src/biochar.egg-info/SOURCES.txt
src/biochar.egg-info/dependency_links.txt
src/biochar.egg-info/entry_points.txt
src/biochar.egg-info/requires.txt
src/biochar.egg-info/top_level.txt
src/biochar/charges/__init__.py
src/biochar/charges/ml_charges.py
src/biochar/charges/qm_charges.py
src/biochar/cli/__init__.py
src/biochar/cli/cli.py
src/biochar/cli/condensation_cli.py
src/biochar/cli/md_setup_cli.py
src/biochar/cli/sweep_cli.py
src/biochar/data/__init__.py
src/biochar/data/biochar_data.csv
src/biochar/data/charges_gpr_cm5.json
src/biochar/data/davis-biochar-db.csv
src/biochar/data/temperature_model.json
src/biochar/export/__init__.py
src/biochar/export/gromacs_export.py
src/biochar/export/md_setup.py
src/biochar/models/__init__.py
src/biochar/models/temperature_model.py
src/biochar/pipeline/__init__.py
src/biochar/pipeline/biochar_generator.py
src/biochar/pipeline/carbon_skeleton.py
src/biochar/pipeline/geometry_3d.py
src/biochar/pipeline/heteroatom_assignment.py
src/biochar/pipeline/opls_typing.py
src/biochar/pipeline/protonation.py
src/biochar/pipeline/valence.py
src/biochar/pipeline/validation.py
src/biochar/workflows/__init__.py
src/biochar/workflows/condensation.py
src/biochar/workflows/surface_builder.py
src/biochar/workflows/sweep.py
tests/test_aliphatic_oxygen.py
tests/test_bond_length_validation.py
tests/test_carbon_skeleton_contract.py
tests/test_charge_backends_contract.py
tests/test_charge_neutrality.py
tests/test_clash_tolerance.py
tests/test_cli.py
tests/test_cli_arguments_contract.py
tests/test_condensation.py
tests/test_condensation_contract.py
tests/test_constants_ff.py
tests/test_coverage_gaps.py
tests/test_generation_config.py
tests/test_generator.py
tests/test_geometry_embedding_paths.py
tests/test_gromacs_export.py
tests/test_gromacs_export_contract.py
tests/test_grompp_smoke.py
tests/test_hbond_clash.py
tests/test_hc_control.py
tests/test_heteroatom_assignment_gaps.py
tests/test_md_setup.py
tests/test_md_setup_contract.py
tests/test_ml_charges.py
tests/test_opls_type_map.py
tests/test_opls_typing_ionized.py
tests/test_pah_quality.py
tests/test_parameter_sweep_contract.py
tests/test_ph_integration.py
tests/test_ph_protonation_contract.py
tests/test_protonation.py
tests/test_qm_charges.py
tests/test_surface_builder.py
tests/test_surface_stacking_contract.py
tests/test_sweep.py
tests/test_temperature_model.py
tests/test_temperature_model_contract.py
tests/test_valence.py
tests/test_valence_contract.py
tests/test_validation_extended.py
tests/test_version_consistency.py