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CHANGELOG.md
CODEOWNERS
CODE_OF_CONDUCT.md
CONTRIBUTORS.md
LICENSE.md
README.md
mkdocs.yml
pixi.lock
pixi.toml
pyproject.toml
.github/workflows/codecov.yml
.github/workflows/docs.yml
.github/workflows/tests.yml
docs/.pages
docs/gen_ref_pages.py
docs/index.md
docs/.overrides/main.html
docs/css/base.css
docs/css/colors.css
docs/css/jupyter.css
docs/css/launchy.css
docs/css/mkdocstrings.css
docs/js/mathjax-config.js
gypsum_dl/MolContainer.py
gypsum_dl/MolObjectHandling.py
gypsum_dl/MyMol.py
gypsum_dl/__init__.py
gypsum_dl/_version.py
gypsum_dl/chem_utils.py
gypsum_dl/parallelizer.py
gypsum_dl/run.py
gypsum_dl/start.py
gypsum_dl/utils.py
gypsum_dl.egg-info/PKG-INFO
gypsum_dl.egg-info/SOURCES.txt
gypsum_dl.egg-info/dependency_links.txt
gypsum_dl.egg-info/entry_points.txt
gypsum_dl.egg-info/requires.txt
gypsum_dl.egg-info/top_level.txt
gypsum_dl/steps/__init__.py
gypsum_dl/steps/conf/Convert2DTo3D.py
gypsum_dl/steps/conf/GenerateAlternate3DNonaromaticRingConfs.py
gypsum_dl/steps/conf/Minimize3D.py
gypsum_dl/steps/conf/PrepareThreeD.py
gypsum_dl/steps/conf/__init__.py
gypsum_dl/steps/io/LoadFiles.py
gypsum_dl/steps/io/ProcessOutput.py
gypsum_dl/steps/io/SaveToPDB.py
gypsum_dl/steps/io/SaveToSDF.py
gypsum_dl/steps/io/Web2DOutput.py
gypsum_dl/steps/io/__init__.py
gypsum_dl/steps/smiles/AddHydrogens.py
gypsum_dl/steps/smiles/DeSaltOrigSmiles.py
gypsum_dl/steps/smiles/DurrantLabFilter.py
gypsum_dl/steps/smiles/EnumerateChiralMols.py
gypsum_dl/steps/smiles/EnumerateDoubleBonds.py
gypsum_dl/steps/smiles/MakeTautomers.py
gypsum_dl/steps/smiles/PrepareSmiles.py
gypsum_dl/steps/smiles/__init__.py
gypsum_dl/steps/smiles/site_structures.smarts
hooks/launchy.py
tests/__init__.py
tests/conftest.py
tests/test_problematic_smiles.py
tests/test_sample.py
tests/files/Pitt_CRC/README.md
tests/files/Pitt_CRC/mpi_gypsum_dl.sh
tests/files/Pitt_CRC/mpi_sample_molecules.json
tests/files/Pitt_CRC/smp_gypsum_dl.sh
tests/files/Pitt_CRC/smp_sample_molecules.json
tests/files/Pitt_CRC/tmp/sample_molecules.json
tests/files/Pitt_CRC/tmp/sample_molecules_multi.json
tests/files/sample/sample_molecules.smi
tests/tmp/.gitignore