CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README.md
THIRD_PARTY_NOTICES.txt
pyproject.toml
docs/add-elem-info.md
docs/all.md
docs/architecture.md
docs/backends.md
docs/bond-summary.md
docs/cif.md
docs/cli-conventions.md
docs/dft.md
docs/energy-diagram.md
docs/extract.md
docs/fix-altloc.md
docs/freeze-atoms.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/mcp_server.md
docs/opt.md
docs/output-layout.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/reproducibility.md
docs/scan.md
docs/scan2d.md
docs/scan3d.md
docs/sp.md
docs/trj2fig.md
docs/troubleshooting.md
docs/tsopt.md
docs/uma-pysis.md
docs/yaml-reference.md
docs/ja/add-elem-info.md
docs/ja/all.md
docs/ja/architecture.md
docs/ja/backends.md
docs/ja/bond-summary.md
docs/ja/cif.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/freeze-atoms.md
docs/ja/freq.md
docs/ja/getting-started.md
docs/ja/glossary.md
docs/ja/hpc-example.md
docs/ja/index.md
docs/ja/installation.md
docs/ja/irc.md
docs/ja/json-output.md
docs/ja/mcp_server.md
docs/ja/opt.md
docs/ja/output-layout.md
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/reproducibility.md
docs/ja/scan.md
docs/ja/scan2d.md
docs/ja/scan3d.md
docs/ja/sp.md
docs/ja/trj2fig.md
docs/ja/troubleshooting.md
docs/ja/tsopt.md
docs/ja/uma-pysis.md
docs/ja/yaml-reference.md
docs/reference/commands/add_elem_info.md
docs/reference/commands/all.md
docs/reference/commands/bond_summary.md
docs/reference/commands/dft.md
docs/reference/commands/energy_diagram.md
docs/reference/commands/extract.md
docs/reference/commands/fix_altloc.md
docs/reference/commands/freq.md
docs/reference/commands/index.md
docs/reference/commands/irc.md
docs/reference/commands/opt.md
docs/reference/commands/path_opt.md
docs/reference/commands/path_search.md
docs/reference/commands/scan.md
docs/reference/commands/scan2d.md
docs/reference/commands/scan3d.md
docs/reference/commands/sp.md
docs/reference/commands/trj2fig.md
docs/reference/commands/tsopt.md
examples/1.R.pdb
examples/2.IM.pdb
examples/3.P.pdb
examples/mcp_client_config.json
examples/pdb2reaction_colab.ipynb
examples/run.sh
examples/aromatic_claisen/product.xyz
examples/aromatic_claisen/reactant.xyz
pdb2reaction/__init__.py
pdb2reaction/__main__.py
pdb2reaction/_version.py
pdb2reaction/py.typed
pdb2reaction.egg-info/PKG-INFO
pdb2reaction.egg-info/SOURCES.txt
pdb2reaction.egg-info/dependency_links.txt
pdb2reaction.egg-info/entry_points.txt
pdb2reaction.egg-info/requires.txt
pdb2reaction.egg-info/top_level.txt
pdb2reaction/backends/__init__.py
pdb2reaction/backends/_determinism.py
pdb2reaction/backends/aimnet2.py
pdb2reaction/backends/base.py
pdb2reaction/backends/custom.py
pdb2reaction/backends/mace.py
pdb2reaction/backends/orb.py
pdb2reaction/backends/solvent.py
pdb2reaction/backends/uma.py
pdb2reaction/backends/xtb_alpb_correction.py
pdb2reaction/cli/__init__.py
pdb2reaction/cli/app.py
pdb2reaction/cli/bool_compat.py
pdb2reaction/cli/common_options.py
pdb2reaction/cli/decorators.py
pdb2reaction/cli/default_group.py
pdb2reaction/cli/help_pages.py
pdb2reaction/core/__init__.py
pdb2reaction/core/defaults.py
pdb2reaction/core/logging.py
pdb2reaction/core/output.py
pdb2reaction/core/pes_composition.py
pdb2reaction/core/result_commit.py
pdb2reaction/core/utils.py
pdb2reaction/domain/__init__.py
pdb2reaction/domain/add_elem_info.py
pdb2reaction/domain/bond_changes.py
pdb2reaction/domain/bond_summary.py
pdb2reaction/domain/residue_data.py
pdb2reaction/io/__init__.py
pdb2reaction/io/altloc.py
pdb2reaction/io/charge.py
pdb2reaction/io/energy_diagram.py
pdb2reaction/io/hessian_cache.py
pdb2reaction/io/path_mode_cache.py
pdb2reaction/io/pdb_fix.py
pdb2reaction/io/plotly_image.py
pdb2reaction/io/structure_formats.py
pdb2reaction/io/summary.py
pdb2reaction/io/trj2fig.py
pdb2reaction/io/xyz_trajectory.py
pdb2reaction/mcp/__init__.py
pdb2reaction/mcp/_runner.py
pdb2reaction/mcp/_tools.py
pdb2reaction/mcp/server.py
pdb2reaction/workflows/__init__.py
pdb2reaction/workflows/_all_helpers.py
pdb2reaction/workflows/_outcomes.py
pdb2reaction/workflows/_path_yaml_helpers.py
pdb2reaction/workflows/_run_session.py
pdb2reaction/workflows/align_freeze.py
pdb2reaction/workflows/all.py
pdb2reaction/workflows/dft.py
pdb2reaction/workflows/extract.py
pdb2reaction/workflows/freq.py
pdb2reaction/workflows/irc.py
pdb2reaction/workflows/opt.py
pdb2reaction/workflows/path_opt.py
pdb2reaction/workflows/path_search.py
pdb2reaction/workflows/restraints.py
pdb2reaction/workflows/scan.py
pdb2reaction/workflows/scan2d.py
pdb2reaction/workflows/scan3d.py
pdb2reaction/workflows/scan_common.py
pdb2reaction/workflows/sp.py
pdb2reaction/workflows/tsopt.py
pysisyphus/Geometry.py
pysisyphus/LICENSE
pysisyphus/TablePrinter.py
pysisyphus/__init__.py
pysisyphus/_array.py
pysisyphus/config.py
pysisyphus/constants.py
pysisyphus/elem_data.py
pysisyphus/helpers.py
pysisyphus/helpers_pure.py
pysisyphus/linalg.py
pysisyphus/normal_modes.py
pysisyphus/tr_projection.py
pysisyphus/xyzloader.py
pysisyphus/calculators/Calculator.py
pysisyphus/calculators/Dimer.py
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
pysisyphus/intcoords/DummyImproper.py
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
pysisyphus/intcoords/Rotation.py
pysisyphus/intcoords/Stretch.py
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/helpers.py
pysisyphus/intcoords/logging_conf.py
pysisyphus/intcoords/setup.py
pysisyphus/intcoords/setup_fast.py
pysisyphus/intcoords/update.py
pysisyphus/intcoords/valid.py
pysisyphus/io/__init__.py
pysisyphus/io/cjson.py
pysisyphus/io/crd.py
pysisyphus/io/hdf5.py
pysisyphus/io/hessian.py
pysisyphus/io/mol2.py
pysisyphus/io/pdb.py
pysisyphus/io/qcschema.py
pysisyphus/io/xyz.py
pysisyphus/io/zmat.py
pysisyphus/irc/DWI.py
pysisyphus/irc/EulerPC.py
pysisyphus/irc/IRC.py
pysisyphus/irc/Instanton.py
pysisyphus/irc/__init__.py
pysisyphus/modefollow/NormalMode.py
pysisyphus/modefollow/__init__.py
pysisyphus/modefollow/lanczos.py
pysisyphus/optimizers/BacktrackingOptimizer.py
pysisyphus/optimizers/HessianOptimizer.py
pysisyphus/optimizers/LBFGS.py
pysisyphus/optimizers/Optimizer.py
pysisyphus/optimizers/RFOptimizer.py
pysisyphus/optimizers/StringOptimizer.py
pysisyphus/optimizers/__init__.py
pysisyphus/optimizers/checkpoint.py
pysisyphus/optimizers/closures.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/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
pysisyphus/tsoptimizers/RSPRFOptimizer.py
pysisyphus/tsoptimizers/TRIM.py
pysisyphus/tsoptimizers/TSHessianOptimizer.py
pysisyphus/tsoptimizers/__init__.py
skills/README.md
skills/colab-local-gpu-runtime/SKILL.md
skills/colab-local-gpu-runtime/agents/openai.yaml
skills/colab-local-gpu-runtime/references/colab-connection.md
skills/colab-local-gpu-runtime/scripts/setup.ps1
skills/colab-local-gpu-runtime/scripts/start.ps1
skills/colab-local-gpu-runtime/scripts/status.ps1
skills/colab-local-gpu-runtime/scripts/stop.ps1
skills/pdb2reaction-architecture/SKILL.md
skills/pdb2reaction-cli/SKILL.md
skills/pdb2reaction-cli/add-elem-info.md
skills/pdb2reaction-cli/all-endpoint-mep.md
skills/pdb2reaction-cli/all-scan-list.md
skills/pdb2reaction-cli/all-ts-only.md
skills/pdb2reaction-cli/all.md
skills/pdb2reaction-cli/bond-summary.md
skills/pdb2reaction-cli/dft.md
skills/pdb2reaction-cli/energy-diagram.md
skills/pdb2reaction-cli/extract.md
skills/pdb2reaction-cli/fix-altloc.md
skills/pdb2reaction-cli/freeze-atoms.md
skills/pdb2reaction-cli/freq.md
skills/pdb2reaction-cli/irc.md
skills/pdb2reaction-cli/opt.md
skills/pdb2reaction-cli/path-opt.md
skills/pdb2reaction-cli/path-search.md
skills/pdb2reaction-cli/scan.md
skills/pdb2reaction-cli/scan2d.md
skills/pdb2reaction-cli/scan3d.md
skills/pdb2reaction-cli/sp.md
skills/pdb2reaction-cli/trj2fig.md
skills/pdb2reaction-cli/tsopt.md
skills/pdb2reaction-env-detect/SKILL.md
skills/pdb2reaction-hpc/SKILL.md
skills/pdb2reaction-hpc/dynamic-dispatch.md
skills/pdb2reaction-install-backends/SKILL.md
skills/pdb2reaction-install-backends/aimnet2.md
skills/pdb2reaction-install-backends/core.md
skills/pdb2reaction-install-backends/dft.md
skills/pdb2reaction-install-backends/env-cuda.md
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
skills/pdb2reaction-structure-io/SKILL.md
skills/pdb2reaction-structure-io/charge-multiplicity.md
skills/pdb2reaction-structure-io/cif.md
skills/pdb2reaction-structure-io/gjf.md
skills/pdb2reaction-structure-io/pdb.md
skills/pdb2reaction-structure-io/xyz.md
skills/pdb2reaction-ts-strategy/SKILL.md
skills/pdb2reaction-workflows-output/SKILL.md
skills/pdb2reaction-workflows-output/summary-json.md
tests/README.md
tests/conftest.py
tests/test_active_map_invalidation.py
tests/test_advanced_help.py
tests/test_align_math.py
tests/test_all_calculator_lease.py
tests/test_all_dry_run_help.py
tests/test_all_helpers.py
tests/test_all_manifest_integration.py
tests/test_all_multiplicity_option.py
tests/test_all_path_tangent.py
tests/test_all_postprocessing_contract.py
tests/test_all_run_ownership.py
tests/test_all_scan_contract_checker.py
tests/test_array_shim_equivalence.py
tests/test_backend_model_load_announcement.py
tests/test_backend_selection_and_adapters.py
tests/test_bond_changes.py
tests/test_bool_compat_cli.py
tests/test_bundled_pysis_policy.py
tests/test_bundled_pysisyphus_regressions.py
tests/test_cli_passthrough_safety.py
tests/test_cli_smoke_low_coverage.py
tests/test_cli_start_header.py
tests/test_cli_utils.py
tests/test_colab_notebook.py
tests/test_custom_calc_file.py
tests/test_cycle_limit_defaults.py
tests/test_default_group.py
tests/test_defaults.py
tests/test_determinism.py
tests/test_dft_config_validation.py
tests/test_dimer_constraints.py
tests/test_dmf_calculator_contract.py
tests/test_docs_command_contract.py
tests/test_docs_command_smoke.py
tests/test_docs_deploy_workflow.py
tests/test_docs_link_contract.py
tests/test_dry_run_footer_contract.py
tests/test_energy_plateau_stall.py
tests/test_error_envelope.py
tests/test_example_scripts_contract.py
tests/test_extract.py
tests/test_freeze_noncart_geometry.py
tests/test_frequency_zero_cutoff.py
tests/test_gpu_kernel_parity.py
tests/test_help_grouping.py
tests/test_hessian_cache_handoff.py
tests/test_hessian_method_contract.py
tests/test_hessian_optimizer_internal_partial.py
tests/test_import_graph.py
tests/test_irc_endpoint_hessian_guard.py
tests/test_irc_input_validation.py
tests/test_irc_never_stop.py
tests/test_mcp_runner.py
tests/test_mcp_tools.py
tests/test_mep_threshold_flags.py
tests/test_normal_modes_lowering.py
tests/test_opt_error_output.py
tests/test_opt_flatten_mass_unweight.py
tests/test_opt_result_provenance.py
tests/test_optimizer_checkpoint.py
tests/test_optimizer_trial_safeguards.py
tests/test_orb_analytical_hessian_guard.py
tests/test_orb_precision_alias.py
tests/test_output_adapter.py
tests/test_path_search_reference_merge.py
tests/test_path_semantics.py
tests/test_pdb_fix.py
tests/test_plotly_image_timeout.py
tests/test_precision_dispatch.py
tests/test_reject_uphill_flag.py
tests/test_release_metadata_contract.py
tests/test_release_workflow.py
tests/test_restrained_pes_contract.py
tests/test_result_commit.py
tests/test_rfo_uphill_rejection.py
tests/test_run_session.py
tests/test_scan3d_csv_provenance.py
tests/test_scan_precedence.py
tests/test_scan_validation_regressions.py
tests/test_scientific_outcomes.py
tests/test_silent_noop_warnings.py
tests/test_skill_command_smoke.py
tests/test_smoke_cli_contract.py
tests/test_solvent_pes_composition.py
tests/test_sp.py
tests/test_stop_plateau_flag.py
tests/test_structure_formats.py
tests/test_summary_log.py
tests/test_symmetrize.py
tests/test_thermo_policy.py
tests/test_thermo_symmetry_number.py
tests/test_thermochemistry_golden.py
tests/test_tr_projection.py
tests/test_tr_projection_default.py
tests/test_tsopt_input_validation.py
tests/test_tsopt_soft_imaginary_warning.py
tests/test_tsopt_terminal_phva.py
tests/test_uma_workers_analytical.py
tests/test_utils.py
tests/test_utils_extended.py
tests/test_write_result_json.py
tests/test_xtb_alpb_parsers.py
tests/test_xyz_trajectory.py
thermoanalysis/LICENSE
thermoanalysis/QCData.py
thermoanalysis/__init__.py
thermoanalysis/config.py
thermoanalysis/constants.py
thermoanalysis/thermo.py