tree.txt

FastMDAnalysis/
├── .github/
│   └── workflows/                   # CI config (tests/docs/etc.)
├── assets/                          # Project images/badges/banners
├── docs/                            # Sphinx/RTD documentation sources
├── examples/                        # Example scripts (API/CLI usage)
├── src/
│   └── fastmdanalysis/
│       ├── __init__.py              # Package init: public API surface
│       ├── datasets.py              # Lightweight dataset helpers (e.g., TrpCage)
│       ├── utils.py                 # I/O helpers (load_trajectory, etc.)
│       ├── analysis/
│       │   ├── __init__.py          # Re-export analysis modules
│       │   ├── base.py              # Base analysis class / shared exceptions
│       │   ├── rmsd.py              # RMSD analysis
│       │   ├── rmsf.py              # RMSF analysis
│       │   ├── rg.py                # Radius of gyration
│       │   ├── hbonds.py            # Hydrogen bonds (Baker–Hubbard)
│       │   ├── ss.py                # Secondary structure (DSSP)
│       │   ├── cluster.py           # KMeans/DBSCAN/Hierarchical & plots
│       │   ├── dimred.py            # PCA/MDS/t-SNE wrappers
│       │   └── sasa.py              # Solvent accessible surface area
│       └── cli/
│           ├── __init__.py          # CLI package init
│           ├── _common.py           # Shared CLI parsing/logging/build utilities
│           ├── main.py              # Entry point (subcommands wired here)
│           ├── analyze.py           # Orchestrator: include/exclude analyses, slides
│           └── simple.py            # Legacy single-analysis commands
├── tests/
│   ├── test_cluster_dimred.py       # Dimensionality reduction / clustering tests
│   └── …                            # Other unit tests
├── .gitignore
├── .readthedocs.yaml
├── CONTRIBUTING.md
├── LICENSE
├── README.md
├── STRUCTURE.md
├── pyproject.toml
├── requirements.txt
└── tree.txt                         # This file