LICENSE
MANIFEST.in
README.md
pyproject.toml
src/Auto3D/__init__.py
src/Auto3D/py.typed
src/Auto3D.egg-info/PKG-INFO
src/Auto3D.egg-info/SOURCES.txt
src/Auto3D.egg-info/dependency_links.txt
src/Auto3D.egg-info/entry_points.txt
src/Auto3D.egg-info/requires.txt
src/Auto3D.egg-info/top_level.txt
src/Auto3D/domain/__init__.py
src/Auto3D/domain/clash_relief.py
src/Auto3D/domain/embedding.py
src/Auto3D/domain/filtering.py
src/Auto3D/domain/id_mapping.py
src/Auto3D/domain/ranking.py
src/Auto3D/engines/__init__.py
src/Auto3D/engines/model_factory.py
src/Auto3D/engines/batch_opt/__init__.py
src/Auto3D/engines/batch_opt/batchopt.py
src/Auto3D/engines/batch_opt/fire_optimizer.py
src/Auto3D/engines/batch_opt/model_wrapper.py
src/Auto3D/engines/batch_opt/optimization_engine.py
src/Auto3D/engines/batch_opt/padding.py
src/Auto3D/engines/isomers/__init__.py
src/Auto3D/engines/isomers/base.py
src/Auto3D/engines/isomers/factory.py
src/Auto3D/engines/isomers/omega.py
src/Auto3D/engines/isomers/rdkit_sdf.py
src/Auto3D/engines/isomers/rdkit_smi.py
src/Auto3D/engines/isomers/tautomers.py
src/Auto3D/engines/models/__init__.py
src/Auto3D/engines/models/adapter.py
src/Auto3D/engines/models/ani2xt.py
src/Auto3D/engines/models/ani2xt_no_repulsion.pt
src/Auto3D/engines/models/contract.py
src/Auto3D/engines/models/loading.py
src/Auto3D/engines/models/policy.py
src/Auto3D/engines/models/preflight.py
src/Auto3D/engines/models/species.py
src/Auto3D/entry/SPE.py
src/Auto3D/entry/__init__.py
src/Auto3D/entry/auto3D.py
src/Auto3D/entry/tautomer.py
src/Auto3D/entry/ASE/__init__.py
src/Auto3D/entry/ASE/geometry.py
src/Auto3D/entry/ASE/thermo/__init__.py
src/Auto3D/entry/ASE/thermo/calculator.py
src/Auto3D/entry/ASE/thermo/driver.py
src/Auto3D/entry/ASE/thermo/properties.py
src/Auto3D/entry/ASE/thermo/vibrations.py
src/Auto3D/foundation/__init__.py
src/Auto3D/foundation/config.py
src/Auto3D/foundation/constants.py
src/Auto3D/foundation/exceptions.py
src/Auto3D/foundation/registry.py
src/Auto3D/foundation/results.py
src/Auto3D/foundation/torch_config.py
src/Auto3D/foundation/utils/__init__.py
src/Auto3D/foundation/utils/atomic_io.py
src/Auto3D/foundation/utils/connectivity.py
src/Auto3D/foundation/utils/convergence.py
src/Auto3D/foundation/utils/energy.py
src/Auto3D/foundation/utils/geometry.py
src/Auto3D/foundation/utils/logging_config.py
src/Auto3D/foundation/utils/molprops.py
src/Auto3D/foundation/utils/output_guard.py
src/Auto3D/foundation/utils/reconciliation.py
src/Auto3D/foundation/utils/sdf_io.py
src/Auto3D/foundation/utils/smi_io.py
src/Auto3D/foundation/utils/stereo_check.py
src/Auto3D/foundation/utils/stereochemistry.py
src/Auto3D/orchestration/__init__.py
src/Auto3D/orchestration/chunk_manager.py
src/Auto3D/orchestration/job_layout.py
src/Auto3D/orchestration/processors.py
src/Auto3D/orchestration/workflow.py
src/Auto3D/orchestration/workflow_workers.py
src/Auto3D/orchestration/pipeline/__init__.py
src/Auto3D/orchestration/pipeline/input_checks.py
src/Auto3D/presentation/__init__.py
src/Auto3D/presentation/auto3Dcli.py
src/Auto3D/presentation/cli/__init__.py
src/Auto3D/presentation/cli/app.py
src/Auto3D/presentation/cli/config_schema.py
src/Auto3D/presentation/cli/console.py
src/Auto3D/presentation/cli/errors.py
src/Auto3D/presentation/cli/progress.py
src/Auto3D/presentation/cli/results.py
src/Auto3D/presentation/cli/commands/__init__.py
src/Auto3D/presentation/cli/commands/config.py
src/Auto3D/presentation/cli/commands/models.py
src/Auto3D/presentation/cli/commands/properties.py
src/Auto3D/presentation/cli/commands/run.py
src/Auto3D/presentation/cli/commands/validate.py
tests/test_SPE.py
tests/test_adapter_atom_mask.py
tests/test_adapter_fp64_contract.py
tests/test_ani2xt_atom_energies.py
tests/test_ase_geometry.py
tests/test_ase_torch_config.py
tests/test_atomic_io.py
tests/test_auto3D.py
tests/test_auto3Dcli.py
tests/test_batchopt.py
tests/test_chunk_manager.py
tests/test_cli.py
tests/test_cli_app.py
tests/test_cli_commands_config.py
tests/test_cli_config_schema.py
tests/test_cli_console.py
tests/test_cli_errors.py
tests/test_cli_exit_codes.py
tests/test_cli_models_command.py
tests/test_cli_property_commands.py
tests/test_cli_results.py
tests/test_cli_security.py
tests/test_config.py
tests/test_config_parity.py
tests/test_conftest_isolation_guards.py
tests/test_custom_nnp_contract.py
tests/test_custom_nnp_eager.py
tests/test_durability.py
tests/test_e_tot_units.py
tests/test_element_sets.py
tests/test_embed_params.py
tests/test_filtering.py
tests/test_filtering_thermo_failed.py
tests/test_fire_optimizer.py
tests/test_helpers_pipeline_output.py
tests/test_hessian_invocation_contract.py
tests/test_id_mapping.py
tests/test_import_boundaries.py
tests/test_isomer_engine.py
tests/test_isomer_engine_hardening.py
tests/test_isomers.py
tests/test_job_layout.py
tests/test_layer_boundaries.py
tests/test_lazy_torchani_import.py
tests/test_legacy_yaml_parity.py
tests/test_logging_config.py
tests/test_model_adapter.py
tests/test_model_caching.py
tests/test_model_factory.py
tests/test_model_preflight.py
tests/test_model_wrapper.py
tests/test_mp_start_method.py
tests/test_notebook_properties.py
tests/test_optimization_engine.py
tests/test_optimization_engine_indexing.py
tests/test_optimization_engine_validation.py
tests/test_output_overwrite_gates.py
tests/test_packaging_metadata.py
tests/test_padding.py
tests/test_padding_invariance.py
tests/test_parallel_embed.py
tests/test_pipeline_e2e.py
tests/test_processors.py
tests/test_progress.py
tests/test_public_api.py
tests/test_ranking.py
tests/test_ranking_by_gibbs.py
tests/test_registry.py
tests/test_results.py
tests/test_sdf_isomer_enumeration.py
tests/test_smiles_stereo_warning.py
tests/test_spe_energy_only.py
tests/test_species_conversion.py
tests/test_species_module.py
tests/test_stereo_identity.py
tests/test_stereo_postopt.py
tests/test_stereochemistry_validation.py
tests/test_suite_hygiene.py
tests/test_tauto.py
tests/test_tautomer_select.py
tests/test_tautomer_stereo.py
tests/test_thermo.py
tests/test_thermo_etot_sync.py
tests/test_thermo_helpers.py
tests/test_thermo_imaginary_mode_inversion.py
tests/test_thermo_projection.py
tests/test_thermo_record_assertions.py
tests/test_thermo_reference.py
tests/test_thermo_relative_energies.py
tests/test_thermo_transition_state.py
tests/test_torch_config.py
tests/test_utils.py
tests/test_utils_connectivity.py
tests/test_utils_energy_constants.py
tests/test_utils_geometry.py
tests/test_utils_molprops.py
tests/test_utils_reconciliation.py
tests/test_utils_sdf_io.py
tests/test_utils_smi_io.py
tests/test_utils_stereochemistry.py
tests/test_utils_validation.py
tests/test_validate_run_parity.py
tests/test_validation.py
tests/test_validation_errors.py
tests/test_workflow.py