LICENSE.md
MANIFEST.in
README.md
pyproject.toml
AutoREACTER/__init__.py
AutoREACTER/_compat.py
AutoREACTER/cache.py
AutoREACTER/initialization.py
AutoREACTER/input_parser.py
AutoREACTER/session.py
AutoREACTER/detectors/__init__.py
AutoREACTER/detectors/detector.py
AutoREACTER/detectors/functional_groups_detector.py
AutoREACTER/detectors/functional_groups_library.py
AutoREACTER/detectors/non_monomer_detector.py
AutoREACTER/detectors/reaction_detector.py
AutoREACTER/detectors/reactions_library.py
AutoREACTER/reaction_preparation/__init__.py
AutoREACTER/reaction_preparation/build_reaction_system.py
AutoREACTER/reaction_preparation/ff_wrapper/REACTER_files_builder.py
AutoREACTER/reaction_preparation/ff_wrapper/__init__.py
AutoREACTER/reaction_preparation/ff_wrapper/ff_locator.py
AutoREACTER/reaction_preparation/ff_wrapper/ff_validator.py
AutoREACTER/reaction_preparation/ff_wrapper/ff_wrapper.py
AutoREACTER/reaction_preparation/ff_wrapper/modifiers_molecule_files.py
AutoREACTER/reaction_preparation/ff_wrapper/molecule_3d_preparation.py
AutoREACTER/reaction_preparation/ff_wrapper/template_builder.py
AutoREACTER/reaction_preparation/ff_wrapper/FF_files/pcff.frc
AutoREACTER/reaction_preparation/ff_wrapper/foyer_client/__init__.py
AutoREACTER/reaction_preparation/ff_wrapper/foyer_client/foyer_api_wrapper.py
AutoREACTER/reaction_preparation/ff_wrapper/foyer_client/foyer_lammps_support.py
AutoREACTER/reaction_preparation/ff_wrapper/lunar_client/__init__.py
AutoREACTER/reaction_preparation/ff_wrapper/lunar_client/config.py
AutoREACTER/reaction_preparation/ff_wrapper/lunar_client/locate_lunar.py
AutoREACTER/reaction_preparation/ff_wrapper/lunar_client/lunar_api_wrapper.py
AutoREACTER/reaction_preparation/ff_wrapper/lunar_client/lunar_executor.py
AutoREACTER/reaction_preparation/ff_wrapper/lunar_client/lunar_utils.py
AutoREACTER/reaction_preparation/ff_wrapper/lunar_client/merge_builder.py
AutoREACTER/reaction_preparation/reaction_processor/__init__.py
AutoREACTER/reaction_preparation/reaction_processor/fragment_comparison.py
AutoREACTER/reaction_preparation/reaction_processor/prepare_reactions.py
AutoREACTER/reaction_preparation/reaction_processor/utils.py
AutoREACTER/reaction_preparation/reaction_processor/walker.py
AutoREACTER/sim_setup/__init__.py
AutoREACTER/sim_setup/simulation_setup.py
AutoREACTER/sim_setup/system_property_calculations.py
AutoREACTER/sim_setup/writers/__init__.py
AutoREACTER/sim_setup/writers/densification_writer.py
AutoREACTER/sim_setup/writers/lammps_settings.py
AutoREACTER/sim_setup/writers/post_eq_writer.py
AutoREACTER/sim_setup/writers/pre_eq_writer.py
AutoREACTER/sim_setup/writers/rxn_first_stage_writer.py
AutoREACTER/sim_setup/writers/rxn_second_stage_writer.py
AutoREACTER/sim_setup/writers/writer.py
docs/source/Draft.md
docs/source/change_log.md
docs/source/conf.py
docs/source/contact.md
docs/source/getting-started.md
docs/source/getting_started_pip_installation.md
docs/source/getting_started_source_installation.md
docs/source/index.rst
docs/source/input-configuration.md
docs/source/overview.md
docs/source/supported-force-fields.md
docs/source/supported-reactions.md
docs/source/_static/Overview.png
docs/source/_static/logo.png
examples/example_1.ipynb
examples/example_1_inputs_count_mode.json
examples/example_1_inputs_count_mode_FF.json
examples/example_1_inputs_ratio_mode.json
examples/run_AutoREACTER.py
tests/test_lunar_api_wrapper.py