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CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
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README.md
THIRD_PARTY_NOTICES.txt
pyproject.toml
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.github/workflows/docs_quality.yml
.github/workflows/release.yml
.github/workflows/test.yml
docs/Makefile
docs/add-elem-info.md
docs/all.md
docs/bond-summary.md
docs/cli-conventions.md
docs/conf.py
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/hpc-example.md
docs/index.md
docs/installation.md
docs/irc.md
docs/json-output.md
docs/make.bat
docs/opt.md
docs/path-opt.md
docs/path-search.md
docs/quickstart-all.md
docs/quickstart-scan.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/uma-pysis.md
docs/yaml-reference.md
docs/_static/.gitkeep
docs/_static/custom.css
docs/_static/theme_toggle.js
docs/_templates/.gitkeep
docs/_templates/page.html
docs/ja/add-elem-info.md
docs/ja/all.md
docs/ja/bond-summary.md
docs/ja/cli-conventions.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
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docs/ja/index.md
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docs/ja/path-opt.md
docs/ja/path-search.md
docs/ja/quickstart-all.md
docs/ja/quickstart-scan.md
docs/ja/quickstart-tsopt-freq.md
docs/ja/recipes-common-errors.md
docs/ja/scan.md
docs/ja/scan2d.md
docs/ja/scan3d.md
docs/ja/trj2fig.md
docs/ja/troubleshooting.md
docs/ja/tsopt.md
docs/ja/uma-pysis.md
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docs/reference/commands/add_elem_info.md
docs/reference/commands/all.md
docs/reference/commands/bond_summary.md
docs/reference/commands/dft.md
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examples/1.R.pdb
examples/2.IM.pdb
examples/3.P.pdb
examples/run.sh
pdb2reaction/__init__.py
pdb2reaction/__main__.py
pdb2reaction/_version.py
pdb2reaction/add_elem_info.py
pdb2reaction/advanced_help.py
pdb2reaction/align_freeze_atoms.py
pdb2reaction/all.py
pdb2reaction/bond_changes.py
pdb2reaction/bond_summary.py
pdb2reaction/bool_compat.py
pdb2reaction/cli.py
pdb2reaction/cli_utils.py
pdb2reaction/default_group.py
pdb2reaction/defaults.py
pdb2reaction/dft.py
pdb2reaction/energy_diagram.py
pdb2reaction/extract.py
pdb2reaction/fix_altloc.py
pdb2reaction/freq.py
pdb2reaction/harmonic_constraints.py
pdb2reaction/hessian_cache.py
pdb2reaction/irc.py
pdb2reaction/opt.py
pdb2reaction/path_opt.py
pdb2reaction/path_search.py
pdb2reaction/py.typed
pdb2reaction/scan.py
pdb2reaction/scan2d.py
pdb2reaction/scan3d.py
pdb2reaction/scan_common.py
pdb2reaction/summary_log.py
pdb2reaction/trj2fig.py
pdb2reaction/tsopt.py
pdb2reaction/uma_pysis.py
pdb2reaction/utils.py
pdb2reaction.egg-info/PKG-INFO
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pdb2reaction.egg-info/dependency_links.txt
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pdb2reaction/backends/__init__.py
pdb2reaction/backends/aimnet2.py
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pdb2reaction/backends/mace.py
pdb2reaction/backends/orb.py
pdb2reaction/backends/solvent.py
pdb2reaction/backends/uma.py
pdb2reaction/backends/xtb_alpb_correction.py
pysisyphus/Geometry.py
pysisyphus/LICENSE
pysisyphus/TableFormatter.py
pysisyphus/TablePrinter.py
pysisyphus/__init__.py
pysisyphus/color.py
pysisyphus/config.py
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pysisyphus/plot.py
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pysisyphus/socket_helper.py
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pysisyphus/intcoords/derivatives.py
pysisyphus/intcoords/eval.py
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pysisyphus/intcoords/generate_derivatives.py
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pysisyphus/line_searches/Backtracking.py
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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
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pysisyphus/optimizers/HessianOptimizer.py
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pysisyphus/optimizers/LayerOpt.py
pysisyphus/optimizers/MicroOptimizer.py
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pysisyphus/optimizers/Optimizer.py
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pysisyphus/optimizers/StabilizedQNMethod.py
pysisyphus/optimizers/SteepestDescent.py
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pysisyphus/optimizers/cls_map.py
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pysisyphus/stocastic/FragmentKick.py
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pysisyphus/stocastic/Pipeline.py
pysisyphus/stocastic/__init__.py
pysisyphus/stocastic/align.py
pysisyphus/tsoptimizers/RSIRFOptimizer.py
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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_core_cli_commands.py
scripts/smoke_docs_commands.py
scripts/smoke_dump_trajectories.py
tests/README.md
tests/conftest.py
tests/test_align_math.py
tests/test_all_multiplicity_option.py
tests/test_bond_changes.py
tests/test_bool_compat_cli.py
tests/test_cli_smoke_low_coverage.py
tests/test_cli_utils.py
tests/test_default_group.py
tests/test_defaults.py
tests/test_extract.py
tests/test_summary_log.py
tests/test_utils.py
tests/test_utils_extended.py
tests/smoke/h2.gjf
tests/smoke/input.yaml
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tests/smoke/scan2d_spec.yaml
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tests/smoke/test.md
tests/smoke/ts.gjf
tests/smoke/ts.pdb
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thermoanalysis/LICENSE
thermoanalysis/QCData.py
thermoanalysis/__init__.py
thermoanalysis/config.py
thermoanalysis/constants.py
thermoanalysis/thermo.py