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 a GPU under Runtime → Change runtime type, then Run all. The shared setup installs a tested TMol release with operators matching Colab’s PyTorch CUDA major and downloads the example data. For local notebooks and supported environments, 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