Notebook Tutorials

Notebook Tutorials

The notebooks/ directory contains executable examples that complement the wiki pages. Use them when you want to inspect data frames directly, adapt plotting code, or build a reproducible analysis workflow.

Available notebooks

• notebooks/01_quickstart_analysis.ipynb: first complete analysis from Python, including returned result objects and default outputs
• notebooks/02_working_with_results.ipynb: working with FleXgeo2 result data frames in memory
• notebooks/03_reference_comparison.ipynb: comparing an ensemble to a reference model or reference PDB
• notebooks/04_clustering_conformations.ipynb: per-residue and residue-range HDBSCAN clustering
• notebooks/05_cli_to_python_mapping.ipynb: translating command-line examples into Python config objects
• notebooks/06_dmax_library_api.ipynb: computing, inspecting, and retuning dmax

Suggested reading order

Start with 01_quickstart_analysis.ipynb if you are new to FleXgeo2.

Use 05_cli_to_python_mapping.ipynb when you already know the command-line workflow and want to move into Python.

Use 03_reference_comparison.ipynb, 04_clustering_conformations.ipynb, and 06_dmax_library_api.ipynb for focused scientific workflows.

Use 02_working_with_results.ipynb when you want to build custom tables, figures, or downstream analyses from the returned data frames.

Notes

The notebooks may create temporary output directories while running. When adapting examples for your own project, replace temporary paths with project-specific paths such as results/, analysis/results/, or another directory under your working folder.

FleXgeo2 does not write into an output folder that already has files. If you re-run a cell that writes results into the same folder, pass OutputConfig(overwrite=True) or give each run its own folder.