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CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
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pyproject.toml
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docs/Makefile
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docs/architecture.md
docs/backends.md
docs/bond-summary.md
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docs/conf.py
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docs/python-api.md
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docs/reproducibility.md
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examples/mcp_client_config.json
examples/methyltransferase/complex.parm7
examples/methyltransferase/complex.pdb
examples/methyltransferase/complex.rst7
examples/methyltransferase/pocket.pdb
examples/methyltransferase/r_layered.pdb
examples/methyltransferase/run_all.sh
examples/methyltransferase/run_stepwise.sh
examples/toy_system/ml_region_p.pdb
examples/toy_system/ml_region_r.pdb
examples/toy_system/opt_ase.py
examples/toy_system/p_complex.parm7
examples/toy_system/p_complex.pdb
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examples/toy_system/p_complex_layered.pdb
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examples/toy_system/run.sh
examples/toy_system/test_core.py
hessian_ff/README.md
hessian_ff/__init__.py
hessian_ff/analytical_hessian.py
hessian_ff/constants.py
hessian_ff/forcefield.py
hessian_ff/loaders.py
hessian_ff/prmtop_parmed.py
hessian_ff/system.py
hessian_ff/workflows.py
hessian_ff/native/Makefile
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pysisyphus/Geometry.py
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pysisyphus/README.md
pysisyphus/TablePrinter.py
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pysisyphus/cos/ChainOfStates.py
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pysisyphus/cos/__init__.py
pysisyphus/intcoords/Bend.py
pysisyphus/intcoords/Bend2.py
pysisyphus/intcoords/BondedFragment.py
pysisyphus/intcoords/Cartesian.py
pysisyphus/intcoords/CartesianCoords.py
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pysisyphus/intcoords/DLC.py
pysisyphus/intcoords/DistanceFunction.py
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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
pysisyphus/intcoords/Rotation.py
pysisyphus/intcoords/Stretch.py
pysisyphus/intcoords/Torsion.py
pysisyphus/intcoords/Torsion2.py
pysisyphus/intcoords/Translation.py
pysisyphus/intcoords/__init__.py
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pysisyphus/io/cjson.py
pysisyphus/io/crd.py
pysisyphus/io/hdf5.py
pysisyphus/io/hessian.py
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pysisyphus/io/qcschema.py
pysisyphus/io/xyz.py
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pysisyphus/irc/DWI.py
pysisyphus/irc/EulerPC.py
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pysisyphus/modefollow/NormalMode.py
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pysisyphus/modefollow/lanczos.py
pysisyphus/optimizers/BacktrackingOptimizer.py
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skills/README.md
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skills/mlmm-hpc/SKILL.md
skills/mlmm-hpc/dynamic-dispatch.md
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skills/mlmm-install-backends/aimnet2.md
skills/mlmm-install-backends/ambertools.md
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skills/mlmm-install-backends/env-cuda.md
skills/mlmm-install-backends/mace.md
skills/mlmm-install-backends/orb.md
skills/mlmm-install-backends/uma.md
skills/mlmm-install-backends/xtb.md
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skills/mlmm-overview/SKILL.md
skills/mlmm-structure-io/SKILL.md
skills/mlmm-structure-io/charge-multiplicity.md
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tests/test_freq_active_dof.py
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tests/test_mcp_runner.py
tests/test_mlmm_calc_serial_gap.py
tests/test_mm_parm_preflight.py
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tests/test_preflight.py
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tests/test_write_result_json.py
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thermoanalysis/LICENSE
thermoanalysis/QCData.py
thermoanalysis/README.md
thermoanalysis/__init__.py
thermoanalysis/config.py
thermoanalysis/constants.py
thermoanalysis/thermo.py