Find a TMol task

Use this page to find a concise workflow, deep Tutorial, or public API for a common task. Browse the interactive examples when you want a complete walkthrough rather than a lookup table.

Fundamentals, input, and output

Task	Workflow or Tutorial	API and notes
Build a default ParameterDatabase, PackedBlockTypes, or CanonicalOrdering	Structure I/O workflow; Tutorial 01	Database API; I/O API. Most callers receive packed types and ordering through a build context.
Build a pose from PDB	Structure I/O workflow; Tutorial 01	pose_stack_from_pdb() is a compatibility path. Prefer CIF/Biotite when metadata or ligand bonds matter.
Select a residue range from PDB	Tutorial 01	residue_start/residue_end are zero-based, half-open parsed positions, not author residue numbers.
Build a pose from Biotite or mmCIF	Structure I/O workflow; Tutorial 01	Preferred general input path; see the I/O API.
Build from OpenFold, RosettaFold2, or AtomWorks tensors	Integrations; Tutorial 01	Supported adapters have distinct tensor contracts; see the I/O API.
Preserve chain gaps and disconnected regions	Tutorial 01; Tutorial 05	Keep internal gaps disconnected rather than silently turning them into chemical termini.
Batch heterogeneous poses	GPU batching workflow; Tutorial 02	Use PoseStackBuilder.from_poses() for compatible chemistry.
Export Biotite, one PDB, or multiple models	Structure I/O workflow; Tutorial 01	PDB is not a lossless replacement for CIF plus authoritative ligand chemistry.

Kinematics and minimization

Task	Workflow or Tutorial	API and notes
Build an automatic multi-chain, gap-aware forest	Optimization workflow; Tutorial 05	FoldForest.reasonable_fold_forest() follows polymer connectivity and ignores non-polymer connections such as disulfides.
Construct explicit or per-residue-root forests	Tutorial 05	FoldForest.from_edges() uses (edge_type, start_block, end_block, jump_index). Validate root coverage and sentinel padding.
Select named torsions and jumps	Optimization workflow; Tutorial 05	Configure a MoveMap; see the kinematics API.
Run Cartesian or kinematic minimization	Optimization workflow; Tutorial 05	The coordinate models differ. Compare only with matched masks, weights, budgets, and stopping checks.
Run Cartesian, kinematic, or batched FastRelax	Optimization workflow; Tutorial 06	fast_relax() defaults to Cartesian minimization and accepts a compatible kinematic minimizer. It is a smaller Rosetta-inspired routine, not protocol parity.

Scoring and constraints

Task	Workflow or Tutorial	API and notes
Build default, empty, or focused score functions	Scoring workflow; Tutorial 03	See the score API and term map.
Score a pose or backpropagate through coordinates	Scoring workflow; Tutorial 03	Render a module for the current pose layout and call it with coordinates.
Analyze weighted or unweighted block pairs	Scoring workflow; Tutorial 03	Directed accounting can require both matrix orientations for an unordered pair.
Map a protein interface and test selected alanine substitutions	Protein-interface workflow; Case Study 09	Compose author-label masks, both block-pair orientations, and matched local-repacking tasks. Report one-complex score changes, not thermodynamic ΔΔG.
Reweight an interface differentiably	Tutorial 03	Apply an explicit analytical weight tensor before summing and backpropagating.
Add distance, coordinate, or torsion constraints	Optimization workflow; Tutorial 05	See the constraint API. constrain_all_ca() is protein-specific; main-chain restraints follow block declarations.

Packing, design, and preparation

Task	Workflow or Tutorial	API and notes
Construct samplers and repack a fixed sequence	Packing workflow; Tutorial 04	IncludeCurrentSampler deliberately keeps the input conformation as a candidate.
Optimize polar-hydrogen chis or build supported side chains	Structure I/O workflow; Tutorial 01	Use normal preparation or explicitly configure the relevant sampler.
Add extra χ sampling	Packing workflow; Tutorial 04	TMol χ indices are zero-based: 0 is χ1 and 1 is χ2.
Run regional design or a small mutation-score experiment	Packing workflow; Tutorial 04	Compose explicit task masks. TMol has no built-in Rosetta resfile, selector, or mutation-scan protocol layer.
Prepare and inject ligand parameters	Ligand workflow; Tutorial 07	Start from authoritative CIF/MOL2 chemistry. The Rosetta .params writer is syntactic and experimental.
Score controlled ligand-pose decoys and locally refine diagnostic states	Case Study 10	Reuse one ligand-aware context, batch matched rigid-body decoys, and report pose sensitivity rather than docking or binding affinity.
Score or pack DNA/RNA	Nucleic-acid workflow; Tutorial 08	Sugar-pucker sampling and full RosettaDNA/RNA protocols are not implemented.

Availability labels

• Library API means TMol provides a reusable public function or class.

• Workflow recipe means the documentation composes lower-level APIs for the task; it is not a built-in protocol.

• Not available means the Rosetta workflow has no supported TMol implementation.

Readers translating Rosetta workflows should also keep the Rosetta-to-TMol crosswalk open alongside this index.