.gitignore
CHANGELOG.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
THIRD_PARTY_NOTICES.txt
pyproject.toml
.github/workflows/docs.yml
.github/workflows/docs_quality.yml
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.github/workflows/smoke_test.yml
docs/Makefile
docs/add_elem_info.md
docs/all.md
docs/cli_conventions.md
docs/concepts.md
docs/conf.py
docs/define_layer.md
docs/device_hpc.md
docs/dft.md
docs/energy_diagram.md
docs/extract.md
docs/fix_altloc.md
docs/freq.md
docs/getting_started.md
docs/glossary.md
docs/index.md
docs/init.md
docs/irc.md
docs/make.bat
docs/mlmm_calc.md
docs/mlmm_toolkit_overview.png
docs/mm_parm.md
docs/oniom_export.md
docs/oniom_gaussian.md
docs/oniom_import.md
docs/oniom_orca.md
docs/opt.md
docs/path_opt.md
docs/path_search.md
docs/pysis.md
docs/python_api.md
docs/quickstart_all.md
docs/quickstart_scan_spec.md
docs/quickstart_tsopt_freq.md
docs/recipes_common_errors.md
docs/requirements_docs.txt
docs/scan.md
docs/scan2d.md
docs/scan3d.md
docs/trj2fig.md
docs/troubleshooting.md
docs/tsopt.md
docs/yaml_reference.md
docs/_static/custom.css
docs/_static/theme_toggle.js
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docs/ja/add_elem_info.md
docs/ja/all.md
docs/ja/cli_conventions.md
docs/ja/concepts.md
docs/ja/define_layer.md
docs/ja/device_hpc.md
docs/ja/dft.md
docs/ja/energy_diagram.md
docs/ja/extract.md
docs/ja/fix_altloc.md
docs/ja/freq.md
docs/ja/getting_started.md
docs/ja/glossary.md
docs/ja/index.md
docs/ja/init.md
docs/ja/irc.md
docs/ja/mlmm_calc.md
docs/ja/mm_parm.md
docs/ja/oniom_export.md
docs/ja/oniom_gaussian.md
docs/ja/oniom_import.md
docs/ja/oniom_orca.md
docs/ja/opt.md
docs/ja/path_opt.md
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docs/ja/pysis.md
docs/ja/python_api.md
docs/ja/quickstart_all.md
docs/ja/quickstart_scan_spec.md
docs/ja/quickstart_tsopt_freq.md
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docs/ja/scan.md
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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
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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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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
hessian_ff/native/__init__.py
hessian_ff/native/analytical_hessian.py
hessian_ff/native/analytical_hessian_ext.cpp
hessian_ff/native/bonded.py
hessian_ff/native/bonded_ext.cpp
hessian_ff/native/loader.py
hessian_ff/native/nonbonded.py
hessian_ff/native/nonbonded_ext.cpp
hessian_ff/terms/__init__.py
hessian_ff/terms/angle.py
hessian_ff/terms/bond.py
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hessian_ff/tests/test_smoke.py
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hessian_ff/tests/data/small/complex.parm7
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mlmm/__init__.py
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mlmm/energy_diagram.py
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mlmm/fix_altloc.py
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mlmm/harmonic_constraints.py
mlmm/hessian_cache.py
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mlmm/path_opt.py
mlmm/path_search.py
mlmm/preflight.py
mlmm/py.typed
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mlmm/summary_log.py
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pysisyphus/Geometry.py
pysisyphus/LICENSE
pysisyphus/TableFormatter.py
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pysisyphus/__init__.py
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pysisyphus/calculators/FreeEndNEBPot.py
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pysisyphus/calculators/Gaussian16.py
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pysisyphus/calculators/LennardJones.py
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pysisyphus/calculators/NFK.py
pysisyphus/calculators/OBabel.py
pysisyphus/calculators/ONIOMv2.py
pysisyphus/calculators/ORCA.py
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pysisyphus/calculators/OpenMM.py
pysisyphus/calculators/OpenMolcas.py
pysisyphus/calculators/OverlapCalculator.py
pysisyphus/calculators/Psi4.py
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pysisyphus/calculators/SocketCalc.py
pysisyphus/calculators/TIP3P.py
pysisyphus/calculators/TransTorque.py
pysisyphus/calculators/Turbomole.py
pysisyphus/calculators/VRIPot.py
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pysisyphus/calculators/cosmo_data.py
pysisyphus/calculators/parser.py
pysisyphus/cos/AdaptiveNEB.py
pysisyphus/cos/ChainOfStates.py
pysisyphus/cos/FreeEndNEB.py
pysisyphus/cos/FreezingString.py
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pysisyphus/cos/GrowingNT.py
pysisyphus/cos/GrowingString.py
pysisyphus/cos/NEB.py
pysisyphus/cos/SimpleZTS.py
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pysisyphus/cos/stiffness.py
pysisyphus/drivers/__init__.py
pysisyphus/drivers/afir.py
pysisyphus/drivers/barriers.py
pysisyphus/drivers/birkholz.py
pysisyphus/drivers/cluster.py
pysisyphus/drivers/diabatization.py
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pysisyphus/drivers/merge_mol2.py
pysisyphus/drivers/opt.py
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pysisyphus/drivers/pka.py
pysisyphus/drivers/precon_pos_rot.py
pysisyphus/drivers/rates.py
pysisyphus/drivers/replace.py
pysisyphus/drivers/scan.py
pysisyphus/drivers/spectrum.py
pysisyphus/drivers/thermo.py
pysisyphus/dynamics/Gaussian.py
pysisyphus/dynamics/__init__.py
pysisyphus/dynamics/colvars.py
pysisyphus/dynamics/driver.py
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pysisyphus/dynamics/lincs.py
pysisyphus/dynamics/mdp.py
pysisyphus/dynamics/rattle.py
pysisyphus/dynamics/thermostats.py
pysisyphus/dynamics/wigner.py
pysisyphus/intcoords/Bend.py
pysisyphus/intcoords/Bend2.py
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pysisyphus/intcoords/Cartesian.py
pysisyphus/intcoords/CartesianCoords.py
pysisyphus/intcoords/Coords.py
pysisyphus/intcoords/DLC.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/Torsion.py
pysisyphus/intcoords/Torsion2.py
pysisyphus/intcoords/Translation.py
pysisyphus/intcoords/__init__.py
pysisyphus/intcoords/augment_bonds.py
pysisyphus/intcoords/derivatives.py
pysisyphus/intcoords/eval.py
pysisyphus/intcoords/exceptions.py
pysisyphus/intcoords/findiffs.py
pysisyphus/intcoords/generate_derivatives.py
pysisyphus/intcoords/helpers.py
pysisyphus/intcoords/logging_conf.py
pysisyphus/intcoords/mp_derivatives.py
pysisyphus/intcoords/setup.py
pysisyphus/intcoords/setup_fast.py
pysisyphus/intcoords/update.py
pysisyphus/intcoords/valid.py
pysisyphus/interpolate/Geodesic.py
pysisyphus/interpolate/IDPP.py
pysisyphus/interpolate/Interpolator.py
pysisyphus/interpolate/LST.py
pysisyphus/interpolate/Redund.py
pysisyphus/interpolate/__init__.py
pysisyphus/interpolate/helpers.py
pysisyphus/io/__init__.py
pysisyphus/io/aomix.py
pysisyphus/io/cjson.py
pysisyphus/io/crd.py
pysisyphus/io/cube.py
pysisyphus/io/fchk.py
pysisyphus/io/hdf5.py
pysisyphus/io/hessian.py
pysisyphus/io/mol2.py
pysisyphus/io/molden.py
pysisyphus/io/orca.py
pysisyphus/io/pdb.py
pysisyphus/io/psf.py
pysisyphus/io/pubchem.py
pysisyphus/io/qcschema.py
pysisyphus/io/sdf.py
pysisyphus/io/xyz.py
pysisyphus/io/zmat.py
pysisyphus/irc/DWI.py
pysisyphus/irc/DampedVelocityVerlet.py
pysisyphus/irc/Euler.py
pysisyphus/irc/EulerPC.py
pysisyphus/irc/GonzalezSchlegel.py
pysisyphus/irc/IMKMod.py
pysisyphus/irc/IRC.py
pysisyphus/irc/IRCDummy.py
pysisyphus/irc/Instanton.py
pysisyphus/irc/LQA.py
pysisyphus/irc/ModeKill.py
pysisyphus/irc/ParamPlot.py
pysisyphus/irc/RK4.py
pysisyphus/irc/__init__.py
pysisyphus/irc/initial_displ.py
pysisyphus/line_searches/Backtracking.py
pysisyphus/line_searches/HagerZhang.py
pysisyphus/line_searches/LineSearch.py
pysisyphus/line_searches/StrongWolfe.py
pysisyphus/line_searches/__init__.py
pysisyphus/line_searches/interpol.py
pysisyphus/modefollow/NormalMode.py
pysisyphus/modefollow/__init__.py
pysisyphus/modefollow/davidson.py
pysisyphus/modefollow/lanczos.py
pysisyphus/optimizers/BFGS.py
pysisyphus/optimizers/BacktrackingOptimizer.py
pysisyphus/optimizers/ConjugateGradient.py
pysisyphus/optimizers/CubicNewton.py
pysisyphus/optimizers/FIRE.py
pysisyphus/optimizers/HessianOptimizer.py
pysisyphus/optimizers/LBFGS.py
pysisyphus/optimizers/LayerOpt.py
pysisyphus/optimizers/MicroOptimizer.py
pysisyphus/optimizers/NCOptimizer.py
pysisyphus/optimizers/Optimizer.py
pysisyphus/optimizers/PreconLBFGS.py
pysisyphus/optimizers/PreconSteepestDescent.py
pysisyphus/optimizers/QuickMin.py
pysisyphus/optimizers/RFOptimizer.py
pysisyphus/optimizers/RSA.py
pysisyphus/optimizers/StabilizedQNMethod.py
pysisyphus/optimizers/SteepestDescent.py
pysisyphus/optimizers/StringOptimizer.py
pysisyphus/optimizers/__init__.py
pysisyphus/optimizers/closures.py
pysisyphus/optimizers/cls_map.py
pysisyphus/optimizers/exceptions.py
pysisyphus/optimizers/gdiis.py
pysisyphus/optimizers/guess_hessians.py
pysisyphus/optimizers/hessian_updates.py
pysisyphus/optimizers/poly_fit.py
pysisyphus/optimizers/precon.py
pysisyphus/optimizers/restrict_step.py
pysisyphus/stocastic/FragmentKick.py
pysisyphus/stocastic/Kick.py
pysisyphus/stocastic/Pipeline.py
pysisyphus/stocastic/__init__.py
pysisyphus/stocastic/align.py
pysisyphus/tsoptimizers/RSIRFOptimizer.py
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pysisyphus/tsoptimizers/TRIM.py
pysisyphus/tsoptimizers/TSHessianOptimizer.py
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pysisyphus/wavefunction/Basis.py
pysisyphus/wavefunction/DIIS.py
pysisyphus/wavefunction/__init__.py
pysisyphus/wavefunction/build_ext.py
pysisyphus/wavefunction/cart2sph.py
pysisyphus/wavefunction/diabatization.py
pysisyphus/wavefunction/excited_states.py
pysisyphus/wavefunction/gen_ints.py
pysisyphus/wavefunction/helpers.py
pysisyphus/wavefunction/localization.py
pysisyphus/wavefunction/multipole.py
pysisyphus/wavefunction/normalization.py
pysisyphus/wavefunction/pop_analysis.py
pysisyphus/wavefunction/shells.py
pysisyphus/wavefunction/wavefunction.py
pysisyphus/wavefunction/ints/__init__.py
pysisyphus/wavefunction/ints/boys.py
pysisyphus/wavefunction/ints/boys_table_N_64_xasym_27.1_step_0.01.npy
pysisyphus/wavefunction/ints/cart_gto3d.py
pysisyphus/wavefunction/ints/coulomb3d.py
pysisyphus/wavefunction/ints/diag_quadrupole3d.py
pysisyphus/wavefunction/ints/dipole3d.py
pysisyphus/wavefunction/ints/int2c2e3d.py
pysisyphus/wavefunction/ints/int3c2e3d_sph.py
pysisyphus/wavefunction/ints/kinetic3d.py
pysisyphus/wavefunction/ints/ovlp3d.py
pysisyphus/wavefunction/ints/quadrupole3d.py
pysisyphus/wavefunction/ints/self_ovlp3d.py
pysisyphus/wrapper/__init__.py
pysisyphus/wrapper/exceptions.py
pysisyphus/wrapper/jmol.py
pysisyphus/wrapper/mwfn.py
pysisyphus/wrapper/packmol.py
scripts/check_all_scan_contract.py
scripts/check_intro_template.py
scripts/check_markdown_links.py
scripts/generate_reference.py
scripts/run_docs_quality.py
scripts/smoke_docs_commands.py
scripts/smoke_dump_trajectories.py
tests/README.md
tests/conftest.py
tests/test_all_multiplicity_option.py
tests/test_bool_compat_cli.py
tests/test_cli_feature_regressions.py
tests/test_cli_help.py
tests/test_cli_utils.py
tests/test_default_group.py
tests/test_defaults.py
tests/test_e2e_minimal.py
tests/test_error_handling.py
tests/test_extract.py
tests/test_imports.py
tests/test_mm_parm_preflight.py
tests/test_opt.py
tests/test_preflight.py
tests/test_scan_oniom_smoke.py
tests/test_summary_log.py
tests/test_utils.py
tests/smoke/p_complex.parm7
tests/smoke/p_complex.pdb
tests/smoke/p_complex.rst7
tests/smoke/p_complex_layered.pdb
tests/smoke/pocket_p.pdb
tests/smoke/pocket_r.pdb
tests/smoke/r_complex.pdb
tests/smoke/r_complex_layered.pdb
tests/smoke/run.sh
thermoanalysis/LICENSE
thermoanalysis/QCData.py
thermoanalysis/__init__.py
thermoanalysis/config.py
thermoanalysis/constants.py
thermoanalysis/thermo.py