LICENSE.md
MANIFEST.in
README.md
pyproject.toml
AutoREACTER/__init__.py
AutoREACTER/arx_cli.py
AutoREACTER/cache.py
AutoREACTER/initialization.py
AutoREACTER/input_parser.py
AutoREACTER/session.py
AutoREACTER/detectors/__init__.py
AutoREACTER/detectors/functional_groups_detector.py
AutoREACTER/detectors/non_monomer_detector.py
AutoREACTER/detectors/reaction_detector.py
AutoREACTER/detectors/functional_groups_library/__init__.py
AutoREACTER/detectors/functional_groups_library/active_centers.py
AutoREACTER/detectors/functional_groups_library/aromatic_groups.py
AutoREACTER/detectors/functional_groups_library/carboxyl_and_carbonyl_groups.py
AutoREACTER/detectors/functional_groups_library/halide_groups.py
AutoREACTER/detectors/functional_groups_library/heterocumulene_groups.py
AutoREACTER/detectors/functional_groups_library/mixed_ab_groups.py
AutoREACTER/detectors/functional_groups_library/nitrogen_groups.py
AutoREACTER/detectors/functional_groups_library/oxygen_groups.py
AutoREACTER/detectors/functional_groups_library/registry.py
AutoREACTER/detectors/functional_groups_library/ring_groups.py
AutoREACTER/detectors/functional_groups_library/silicon_groups.py
AutoREACTER/detectors/functional_groups_library/sulfur_groups.py
AutoREACTER/detectors/functional_groups_library/vinyl_and_alkene_groups.py
AutoREACTER/detectors/reactions_library/__init__.py
AutoREACTER/detectors/reactions_library/cycloaddition_polymers.py
AutoREACTER/detectors/reactions_library/epoxy_polymers.py
AutoREACTER/detectors/reactions_library/metathesis_polymers.py
AutoREACTER/detectors/reactions_library/phenolic_resins.py
AutoREACTER/detectors/reactions_library/polyamides.py
AutoREACTER/detectors/reactions_library/polyanhydrides.py
AutoREACTER/detectors/reactions_library/polybenzimidazoles.py
AutoREACTER/detectors/reactions_library/polycarbonates.py
AutoREACTER/detectors/reactions_library/polyesters.py
AutoREACTER/detectors/reactions_library/polyethers.py
AutoREACTER/detectors/reactions_library/polyimides.py
AutoREACTER/detectors/reactions_library/polysiloxanes.py
AutoREACTER/detectors/reactions_library/polysulfides.py
AutoREACTER/detectors/reactions_library/polythioesters.py
AutoREACTER/detectors/reactions_library/polyureas.py
AutoREACTER/detectors/reactions_library/polyurethanes.py
AutoREACTER/detectors/reactions_library/registry.py
AutoREACTER/detectors/reactions_library/thiol_ene_polymers.py
AutoREACTER/detectors/reactions_library/vinyl_polymers.py
AutoREACTER/reaction_preparation/__init__.py
AutoREACTER/reaction_preparation/deduplication_detector.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/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/prepare_reactions.py
AutoREACTER/reaction_preparation/reaction_processor/reaction_progression.py
AutoREACTER/reaction_preparation/reaction_processor/utils.py
AutoREACTER/reaction_preparation/reaction_processor/walker.py
AutoREACTER/reaction_preparation/reaction_processor/warning_asci.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/advanced_options.md
docs/source/api_reference.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/template-deduplication.md
docs/source/_static/Overview - Copy.png
docs/source/_static/Overview.png
docs/source/_static/autoreacter_overview.png
docs/source/_static/logo.png
docs/source/_static/deep_search_figures/edge_monomers.png
docs/source/_static/deep_search_figures/edge_templates_template.png
docs/source/_static/deep_search_figures/input_monomers.png
docs/source/_static/deep_search_figures/missed_templates_template.png
docs/source/_static/deep_search_figures/w_deep_search.png
docs/source/_static/deep_search_figures/w_o_deep_search.png
docs/source/_static/loop_figures/glycine_templates_template.png
docs/source/_static/loop_figures/loop_monomers.png
docs/source/_static/loop_figures/loop_templates_template.png
docs/source/_static/loop_figures/wo_loop_templates_template.png
docs/source/_static/wild_cards_figures/prior_templates_template.png
docs/source/_static/wild_cards_figures/wild_cards-templates_template.png
examples/EPON862_DETDA_10k_100k.json
examples/epoxy_amine_reaction_iteration.json
examples/example_1.ipynb
examples/example_1.py
examples/hyperbranched.json
examples/input.json
examples/ipn_advanced_workflow.json
examples/polyamide_count_mode_advanced_options.json
examples/polyamide_count_mode_basic.json
examples/polyamide_ratio_mode_basic.json
examples/pu_epoxy_ipn.json
examples/pu_pmma_ipn.json
examples/styrene_wildcards.json
examples/AutoREACTER_outputs/DGEBA_MMA_TEGDMA_IPN_Advanced_Workflow/input.json
examples/AutoREACTER_outputs/EPON862_DETDA_10k_100k/input.json
examples/AutoREACTER_outputs/Hyperbranched_DHBA_10k_100k/input.json
examples/AutoREACTER_outputs/PBAT_Esterification_10k_100k/input.json
examples/AutoREACTER_outputs/PBAT_Esterification_10k_100k/make_pbat_500k_variants.py
examples/AutoREACTER_outputs/PU_Epoxy_IPN/input.json
examples/AutoREACTER_outputs/PU_PMMA_IPN/input.json
examples/AutoREACTER_outputs/PU_PMMA_IPN_100k/input.json
examples/AutoREACTER_outputs/PU_PMMA_IPN_100k_Wildcards/input.json
examples/AutoREACTER_outputs/PU_PMMA_IPN_100k_Wildcards/LAMMPS_input_files/PU_PMMA_IPN_100k_Wildcards_PU_PMMA_IPN_100k_70PU_30PMMA/clear.ipynb
examples/AutoREACTER_outputs/Polyamide_Count_Mode_Advanced/input.json
examples/AutoREACTER_outputs/Polyamide_Count_Mode_Basic/input.json
examples/AutoREACTER_outputs/Styrene_Wildcards/input.json
examples/legacy/example_1.ipynb
examples/legacy/run_AutoREACTER.py
examples/legacy_examples/DGEBA_MMA_IPN.json
examples/legacy_examples/example_1_inputs_count_mode_FF.json
examples/legacy_examples/test_epoxy.json
examples/legacy_examples/test_styrene.json
tests/__init__.py
tests/unit/__init__.py
tests/unit/test_arx_cli.py
tests/unit/test_cache.py
tests/unit/test_initialization.py
tests/unit/test_input_parser.py
tests/unit/test_public_api.py
tests/unit/test_session.py
tests/unit/detectors/__init__.py
tests/unit/detectors/test_functional_groups_detector.py
tests/unit/detectors/test_non_monomer_detector.py
tests/unit/detectors/test_reaction_detector.py
tests/unit/detectors/functional_groups_library/__init__.py
tests/unit/detectors/functional_groups_library/test_active_centers.py
tests/unit/detectors/functional_groups_library/test_carboxyl_and_carbonyl_groups.py
tests/unit/detectors/functional_groups_library/test_heterocumulene_groups.py
tests/unit/detectors/functional_groups_library/test_mixed_ab_groups.py
tests/unit/detectors/functional_groups_library/test_nitrogen_groups.py
tests/unit/detectors/functional_groups_library/test_oxygen_groups.py
tests/unit/detectors/functional_groups_library/test_registry.py
tests/unit/detectors/functional_groups_library/test_ring_groups.py
tests/unit/detectors/functional_groups_library/test_silicon_groups.py
tests/unit/detectors/functional_groups_library/test_sulfur_groups.py
tests/unit/detectors/functional_groups_library/test_vinyl_and_alkene_groups.py
tests/unit/detectors/reactions_library/test_epoxy_polymers.py
tests/unit/detectors/reactions_library/test_polyamides.py
tests/unit/detectors/reactions_library/test_polyanhydrides.py
tests/unit/detectors/reactions_library/test_polycarbonates.py
tests/unit/detectors/reactions_library/test_polyesters.py
tests/unit/detectors/reactions_library/test_polysiloxanes.py
tests/unit/detectors/reactions_library/test_polythioesters.py
tests/unit/detectors/reactions_library/test_polyureas.py
tests/unit/detectors/reactions_library/test_polyurethanes.py
tests/unit/detectors/reactions_library/test_registry.py
tests/unit/detectors/reactions_library/test_thiol_ene_polymers.py
tests/unit/detectors/reactions_library/test_vinyl_polymers.py
tests/unit/reaction_preparation/test_deduplication_detector.py
tests/unit/reaction_preparation/ff_wrapper/test_REACTER_files_builder.py
tests/unit/reaction_preparation/ff_wrapper/test_ff_locator.py
tests/unit/reaction_preparation/ff_wrapper/test_ff_validator.py
tests/unit/reaction_preparation/ff_wrapper/test_ff_wrapper.py
tests/unit/reaction_preparation/ff_wrapper/test_modifiers_molecule_files.py
tests/unit/reaction_preparation/ff_wrapper/test_molecule_3d_preparation.py
tests/unit/reaction_preparation/ff_wrapper/lunar_client/test_config.py
tests/unit/reaction_preparation/ff_wrapper/lunar_client/test_locate_lunar.py
tests/unit/reaction_preparation/ff_wrapper/lunar_client/test_lunar_api_wrapper.py
tests/unit/reaction_preparation/ff_wrapper/lunar_client/test_lunar_executor.py
tests/unit/reaction_preparation/ff_wrapper/lunar_client/test_lunar_utils.py
tests/unit/reaction_preparation/ff_wrapper/lunar_client/test_merge_builder.py
tests/unit/reaction_preparation/reaction_processor/test_prepare_reactions.py
tests/unit/reaction_preparation/reaction_processor/test_reaction_progression.py
tests/unit/reaction_preparation/reaction_processor/test_utils.py
tests/unit/reaction_preparation/reaction_processor/test_walker.py
tests/unit/reaction_preparation/reaction_processor/test_warning_asci.py
tests/unit/sim_setup/test_simulation_setup.py
tests/unit/sim_setup/test_system_property_calculations.py
tests/unit/sim_setup/writers/test_densification_writer.py
tests/unit/sim_setup/writers/test_lammps_settings.py
tests/unit/sim_setup/writers/test_post_eq_writer.py
tests/unit/sim_setup/writers/test_pre_eq_writer.py
tests/unit/sim_setup/writers/test_rxn_first_stage_writer.py
tests/unit/sim_setup/writers/test_rxn_second_stage_writer.py
tests/unit/sim_setup/writers/test_writer.py