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 :doc:`Workflows <workflows/index>`.
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 :doc:`task index <tutorial/recipe_index>` to find a maintained
tutorial, workflow recipe, or API page for a specific operation.

Readers coming from Rosetta or PyRosetta can consult the
:doc:`Rosetta-to-TMol crosswalk <tutorial/rosetta_crosswalk>` alongside the
Tutorials. The crosswalk distinguishes genuine API parallels from capabilities
that TMol does not currently implement.

.. nbgallery::
   :caption: Core interactive tutorials

   tutorial/01_working_with_tmol
   tutorial/02_gpu_batching
   tutorial/03_scoring_and_analysis
   tutorial/04_packing_and_mutation_scan
   tutorial/05_minimization_constraints_kinematics
   tutorial/06_fast_relax
   tutorial/07_ligand_and_params
   tutorial/08_nucleic_acids

.. nbgallery::
   :caption: Integrated case studies

   tutorial/09_protein_interface_hotspot_scan
   tutorial/10_ligand_pose_sensitivity

.. toctree::
   :hidden:

   Task index <tutorial/recipe_index>
   Rosetta-to-TMol crosswalk <tutorial/rosetta_crosswalk>