.gitignore
.readthedocs.yaml
README.md
pyproject.toml
.github/workflows/python-publish.yml
docs/Makefile
docs/make.bat
docs/requirements.txt
docs/images/elaborations_fig_tight.svg
docs/source/conf.py
docs/source/configurations.rst
docs/source/definitions.rst
docs/source/index.rst
docs/source/reaction_constants.rst
docs/source/retrosynthesis.rst
docs/source/running_an_example.rst
docs/source/running_on_HPC.rst
docs/source/user_guide_w_aizynth.rst
docs/source/_static/css/custom.css
examples/add_reaction/add_reaction_example.ipynb
examples/add_reaction/check_new_rxn_smirks_3March2025.ipynb
examples/fairydust/configure_fairydust.ipynb
examples/fairydust/additional_rxn_options_examples/Alpha_alkylation_of_ester_amide_toAlpha_alkylation_of_ester_amide_alcohol.ipynb
examples/fairydust/additional_rxn_options_examples/ester_amidation_to_amidation.ipynb
examples/fairydust/fairydust_example_data/Alpha_alkylation_of_ester_amide_examples.csv
examples/fairydust/fairydust_example_data/ester_amidation_examples.csv
examples/fairydust/fairydust_example_data/formation_of_urea_examples.csv
examples/fairydust/fairydust_example_data/urea_formation_from_imidazole_tests.csv
examples/run_syndirella_example/run_example.ipynb
examples/run_syndirella_example/run_manual_example.ipynb
examples/run_syndirella_example/syndirella_input_example_automatic.csv
examples/run_syndirella_example/syndirella_input_example_manual.csv
examples/run_syndirella_example/fragments/A71EV2A_combined.sdf
examples/run_syndirella_example/fragments/metadata.csv
examples/run_syndirella_example/fragments/templates/Ax0310a_apo-desolv.pdb
examples/run_syndirella_example/fragments/templates/Ax0926a_apo-desolv.pdb
examples/run_syndirella_example/fragments/templates/Ax1346a_apo-desolv.pdb
hpc/job_list.txt
hpc/prep_csvs_jobs.ipynb
hpc/run_jobs.sh
hpc/scaffolds_354.sdf
hpc/syndirella_master.csv
hpc/template.sh
hpc/jobs/job0.sh
hpc/jobs/job1.sh
hpc/jobs/job2.sh
hpc/jobs/job3.sh
hpc/jobs/job4.sh
hpc/syndirella_input/syndirella_input0.csv
hpc/syndirella_input/syndirella_input1.csv
hpc/syndirella_input/syndirella_input2.csv
hpc/syndirella_input/syndirella_input3.csv
hpc/syndirella_input/syndirella_input4.csv
logos/Full.png
logos/Simple.png
logos/Wand.png
syndirella/__init__.py
syndirella/__main__.py
syndirella/cli.py
syndirella/cli_defaults.py
syndirella/justretroquery.py
syndirella/pipeline.py
syndirella/syndirella_input_template.csv
syndirella/syndirella_manual_input_template.csv
syndirella.egg-info/PKG-INFO
syndirella.egg-info/SOURCES.txt
syndirella.egg-info/dependency_links.txt
syndirella.egg-info/entry_points.txt
syndirella.egg-info/requires.txt
syndirella.egg-info/top_level.txt
syndirella/aizynth/AiZynthManager.py
syndirella/aizynth/__init__.py
syndirella/constants/ADDITIONAL_RXN_OPTIONS.json
syndirella/constants/REACTANT_FILTER_CONSTANTS.json
syndirella/constants/RXN_SMIRKS_CONSTANTS.json
syndirella/constants/__init__.py
syndirella/constants/uspto_template_lookup.json.gz
syndirella/database/Arthor.py
syndirella/database/DatabaseSearch.py
syndirella/database/Postera.py
syndirella/database/__init__.py
syndirella/route/Cobbler.py
syndirella/route/CobblerBench.py
syndirella/route/CobblersWorkshop.py
syndirella/route/Library.py
syndirella/route/Reaction.py
syndirella/route/SMARTSHandler.py
syndirella/route/SmirksLibraryManager.py
syndirella/route/__init__.py
syndirella/slipper/Slipper.py
syndirella/slipper/SlipperFitter.py
syndirella/slipper/__init__.py
syndirella/slipper/_placement_data.py
syndirella/slipper/flatness.py
syndirella/slipper/intra_geometry.py
syndirella/slipper/stats.py
syndirella/slipper/slipper_synthesizer/Labeler.py
syndirella/slipper/slipper_synthesizer/SlipperSynthesizer.py
syndirella/slipper/slipper_synthesizer/__init__.py
syndirella/tests/__init__.py
syndirella/tests/test_add_reaction.py
syndirella/tests/test_additional_routes.py
syndirella/tests/test_arthor_integration.py
syndirella/tests/test_error_handling.py
syndirella/tests/test_full_cli.py
syndirella/tests/test_inputs.py
syndirella/tests/test_justretroquery.py
syndirella/tests/test_pipeline_mocked.py
syndirella/tests/test_pipeline_real.py
syndirella/tests/test_placements.py
syndirella/tests/test_route_handling.py
syndirella/tests/test_template_loader.py
syndirella/tests/inputs/test_error_handling/CHIKV_Mac_combined.sdf
syndirella/tests/inputs/test_error_handling/cx0270a_apo-desolv.pdb
syndirella/tests/inputs/test_error_handling/no_synthesis_route.csv
syndirella/tests/inputs/test_error_handling/single_elab_reactant.csv
syndirella/tests/inputs/test_inputs/A71EV2A_combined.sdf
syndirella/tests/inputs/test_inputs/metadata.csv
syndirella/tests/inputs/test_inputs/templates/Ax0310a_apo-desolv.pdb
syndirella/tests/inputs/test_inputs/templates/Ax0487a_apo-desolv.pdb
syndirella/tests/inputs/test_inputs/templates/Ax0926a_apo-desolv.pdb
syndirella/tests/inputs/test_inputs/templates/Ax1346a_apo-desolv.pdb
syndirella/tests/inputs/test_inputs/templates/Ax1431a_apo-desolv.pdb
syndirella/tests/inputs/test_inputs/templates/Ax1445a_apo-desolv.pdb
syndirella/tests/inputs/test_inputs/templates/Ax1775a_apo-desolv.pdb
syndirella/tests/inputs/test_inputs/templates/Ax1776a_apo-desolv.pdb
syndirella/tests/inputs/test_inputs/templates/Ax1778a_apo-desolv.pdb
syndirella/tests/inputs/test_inputs/templates/Ax1779a_apo-desolv.pdb
syndirella/tests/outputs/test_pipeline/VKQJXGLAYUFNNG-UHFFFAOYSA-N/VKQJXGLAYUFNNG-UHFFFAOYSA-N_aizynth_analysis.json
syndirella/utils/__init__.py
syndirella/utils/check_inputs.py
syndirella/utils/classifier.py
syndirella/utils/error.py
syndirella/utils/fairy.py
syndirella/utils/structure_outputs.py
syndirella/utils/template_loader.py
syndirella/utils/version.py