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CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
THIRD_PARTY_NOTICES.txt
pyproject.toml
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docs/backends.md
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examples/1.R.pdb
examples/2.IM.pdb
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pysisyphus/README.md
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pysisyphus/__init__.py
pysisyphus/_array.py
pysisyphus/config.py
pysisyphus/constants.py
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pysisyphus/xyzloader.py
pysisyphus/calculators/Calculator.py
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pysisyphus/calculators/__init__.py
pysisyphus/cos/ChainOfStates.py
pysisyphus/cos/GrowingChainOfStates.py
pysisyphus/cos/GrowingString.py
pysisyphus/cos/__init__.py
pysisyphus/intcoords/Bend.py
pysisyphus/intcoords/Bend2.py
pysisyphus/intcoords/BondedFragment.py
pysisyphus/intcoords/Cartesian.py
pysisyphus/intcoords/CartesianCoords.py
pysisyphus/intcoords/Coords.py
pysisyphus/intcoords/DLC.py
pysisyphus/intcoords/DistanceFunction.py
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pysisyphus/intcoords/DummyTorsion.py
pysisyphus/intcoords/LinearBend.py
pysisyphus/intcoords/LinearDisplacement.py
pysisyphus/intcoords/OutOfPlane.py
pysisyphus/intcoords/PrimTypes.py
pysisyphus/intcoords/Primitive.py
pysisyphus/intcoords/RedundantCoords.py
pysisyphus/intcoords/RobustTorsion.py
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pysisyphus/intcoords/Stretch.py
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pysisyphus/io/crd.py
pysisyphus/io/hdf5.py
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skills/README.md
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skills/pdb2reaction-cli/all-ts-only.md
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skills/pdb2reaction-cli/extract.md
skills/pdb2reaction-cli/fix-altloc.md
skills/pdb2reaction-cli/freeze-atoms.md
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skills/pdb2reaction-cli/opt.md
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skills/pdb2reaction-install-backends/SKILL.md
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skills/pdb2reaction-install-backends/mace.md
skills/pdb2reaction-install-backends/orb.md
skills/pdb2reaction-install-backends/uma.md
skills/pdb2reaction-install-backends/xtb.md
skills/pdb2reaction-mcp/SKILL.md
skills/pdb2reaction-overview/SKILL.md
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skills/pdb2reaction-structure-io/charge-multiplicity.md
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thermoanalysis/LICENSE
thermoanalysis/QCData.py
thermoanalysis/README.md
thermoanalysis/__init__.py
thermoanalysis/config.py
thermoanalysis/constants.py
thermoanalysis/thermo.py