Tutorials

Runnable notebooks with molecular viewers, plots, and exercises. Start with 01–03, then use packing (04) and minimization (05) before FastRelax (06). For a specific operation, use the task index.

In Colab, select Runtime → Change runtime type → T4 GPU, then Run all. The setup cell installs TMol and downloads the example data. The bootstrap supports Python 3.12/3.13, PyTorch 2.11, and CUDA 12.8, including Colab’s 2026.07 runtime. For local execution, follow Installation.

Basics

Tutorial 01 — Working with structures

Tutorial 02 — GPU batching

Tutorial 03 — Scoring and analysis

Tutorial 04 — Packing and mutation scans

Tutorial 05 — Minimization, constraints, and kinematics

Tutorial 06 — FastRelax

Tutorial 07 — Ligands and parameter files

Tutorial 08 — DNA and RNA

Applications

Tutorial 09 — Protein interface analysis

Tutorial 10 — Ligand pose sensitivity

Extending TMol

Tutorial 11 — Extending chemistry and scoring

Tutorial 12 — Explicit FoldForests and torsions

Tutorial 13 — Extending the packer