Examples

These ten executable notebooks are in-depth demonstrations with live molecular viewers, selectable structures and atom subsets, result tables, plots, and exercises. For shorter, reusable recipes, see Workflows. Start with Tutorials 01–03. From scoring, branch to packing (04) or minimization (05), then combine both in FastRelax (06). Tutorials 07 and 08 cover specialized ligand and nucleic-acid workflows. Case Studies 09 and 10 bring those primitives together around protein-interface mutation and ligand pose-sensitivity questions.

Use the task index to find a maintained tutorial, workflow recipe, or API page for a specific operation.

Readers coming from Rosetta or PyRosetta can consult the Rosetta-to-TMol crosswalk alongside the Tutorials. The crosswalk distinguishes genuine API parallels from capabilities that TMol does not currently implement.

Core interactive tutorials

Tutorial 01 — Working with TMol

Tutorial 02 — GPU Batching with TMol

Tutorial 03 — Scoring and Analysis

Tutorial 04 — Packing and a Small Mutation Scan

Tutorial 05 — Minimization, Constraints, and Kinematics

Tutorial 06 — FastRelax

Tutorial 07 — Ligands and Parameter Files

Tutorial 08 — Working with DNA and RNA

Integrated case studies

Case Study 09 — Map and Test a Protein Interface

Case Study 10 — Ligand Pose Sensitivity and Local Rescue