LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
agave_chem/__init__.py
agave_chem/main.py
agave_chem.egg-info/PKG-INFO
agave_chem.egg-info/SOURCES.txt
agave_chem.egg-info/dependency_links.txt
agave_chem.egg-info/not-zip-safe
agave_chem.egg-info/requires.txt
agave_chem.egg-info/top_level.txt
agave_chem/datafiles/__init__.py
agave_chem/datafiles/models/__init__.py
agave_chem/datafiles/models/supervised_albert_model/__init__.py
agave_chem/datafiles/models/supervised_albert_model/config.json
agave_chem/datafiles/models/supervised_albert_model/model.safetensors
agave_chem/datafiles/models/supervised_albert_model/supervised_albert_model.pt
agave_chem/datafiles/smirks_patterns/__init__.py
agave_chem/datafiles/smirks_patterns/reaction_classes.json
agave_chem/datafiles/smirks_patterns/smirks_patterns_with_children.json.gz
agave_chem/mappers/__init__.py
agave_chem/mappers/data_classes.py
agave_chem/mappers/reaction_mapper.py
agave_chem/mappers/types.py
agave_chem/mappers/identical_fragments/__init__.py
agave_chem/mappers/identical_fragments/identical_fragment_mapper.py
agave_chem/mappers/mcs/__init__.py
agave_chem/mappers/mcs/mcs_mapper.py
agave_chem/mappers/neural/__init__.py
agave_chem/mappers/neural/constants.py
agave_chem/mappers/neural/model.py
agave_chem/mappers/neural/neural_mapper.py
agave_chem/mappers/neural/tokenizer.py
agave_chem/mappers/template/__init__.py
agave_chem/mappers/template/parallel_template_mapper.py
agave_chem/mappers/template/template_mapper.py
agave_chem/scoring/__init__.py
agave_chem/scoring/scoring.py
agave_chem/utils/__init__.py
agave_chem/utils/chem_utils.py
agave_chem/utils/constants.py
agave_chem/utils/graph_utils.py
agave_chem/utils/logging_config.py
agave_chem/utils/reaction_balancing.py
agave_chem/utils/symmetry_classes.py
tests/integration/test_mcs_mapper_integration.py
tests/integration/test_template_mapper_integration.py
tests/unit/test_albert_mapper_supervised_unit.py
tests/unit/test_albert_mapper_unsupervised_unit.py
tests/unit/test_bench_utils_sync.py
tests/unit/test_chem_utils_unit.py
tests/unit/test_cli_utils_unit.py
tests/unit/test_compile_speed_table.py
tests/unit/test_differing_atoms.py
tests/unit/test_elo_rating.py
tests/unit/test_filter_reactions.py
tests/unit/test_generate_child_smarts.py
tests/unit/test_graph_utils_unit.py
tests/unit/test_identical_fragment_mapper_unit.py
tests/unit/test_layer_head_identification_unit.py
tests/unit/test_main_unit.py
tests/unit/test_mcs_mapper_unit.py
tests/unit/test_models_unit.py
tests/unit/test_neural_mapper_unit.py
tests/unit/test_reaction_balancing_unit.py
tests/unit/test_supervised_training_unit.py
tests/unit/test_template_mapper_classification_unit.py
tests/unit/test_template_mapper_offset_unit.py
tests/unit/test_unsupervised_training_unit.py
tests/unit/test_workflow_models_unit.py
workflows/benchmarking/_bench_utils.py
workflows/benchmarking/benchmark.py
workflows/benchmarking/benchmark_agave_chem.py
workflows/benchmarking/benchmark_chython.py
workflows/benchmarking/benchmark_localmapper.py
workflows/benchmarking/benchmark_rxnmapper.py
workflows/benchmarking/benchmark_rxnmapper_v2.py
workflows/benchmarking/run_external_benchmarks.py
workflows/compare_mappers/combine_results.py
workflows/compare_mappers/compile_speed_table.py
workflows/compare_mappers/elo_rating.py
workflows/compare_mappers/filter_reactions.py
workflows/compare_mappers/run_agavechem.py
workflows/compare_mappers/run_chython.py
workflows/compare_mappers/run_localmapper.py
workflows/compare_mappers/run_rxnmapper.py
workflows/compare_mappers/run_rxnmapper_v2.py
workflows/compare_mappers/viz_utils.py
workflows/model_training_scripts/albert_mapper_supervised_training.py
workflows/model_training_scripts/albert_mapper_unuspervised_training.py
workflows/model_training_scripts/attention_target_builder.py
workflows/model_training_scripts/cli_utils.py
workflows/model_training_scripts/layer_head_identification.py
workflows/model_training_scripts/supervised_training.py
workflows/model_training_scripts/unsupervised_training.py
workflows/template_processing/generate_child_smarts_from_smirks.py
workflows/template_processing/generate_nucleophilic_substitution_reactions.py
workflows/training_data_generation/map_reactions.py