Task index

Find a guide, runnable notebook, or API for a specific operation.

Fundamentals, input, and output

Task	Guide or tutorial	API and notes
Build a default ParameterDatabase, PackedBlockTypes, or CanonicalOrdering	Structure I/O guide; 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 guide; 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 guide; Tutorial 01	Preferred general input path; see the I/O API.
Build from OpenFold, RoseTTAFold2, or AtomWorks tensors	Integrations; Tutorial 01	Use Atom37 or map another named layout to canonical tensors; see the model input tutorial.
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 guide; Tutorial 02	Use PoseStackBuilder.from_poses() for compatible chemistry.
Export Biotite, one PDB, or multiple models	Structure I/O guide; Tutorial 01	PDB is not a lossless replacement for CIF plus authoritative ligand chemistry.
Build a stable chemistry subset or inspect packed block-type metadata	Tutorial 11	Keep the source ParameterDatabase immutable; a subset is only safe when the complete input alphabet is known.

Kinematics and minimization

Task	Guide or tutorial	API and notes
Build an automatic multi-chain, gap-aware forest	Optimization guide; 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 guide; Tutorial 05	Configure a MoveMap; see the kinematics API.
Run Cartesian or kinematic minimization	Optimization guide; Tutorial 05	The coordinate models differ. Compare only with matched masks, weights, budgets, and stopping checks.
Run Cartesian, kinematic, or batched FastRelax	Optimization guide; Tutorial 06	fast_relax() defaults to Cartesian minimization and accepts a compatible kinematic minimizer.
Couple chains with an explicit jump or construct a dandelion forest	Tutorial 12	Validate edge coverage and contiguous ordinary-jump indices before coordinate operations.
Perturb rigid-body jump DOFs or assign named torsions	Tutorial 12	These are coordinate transformations, not docking, minimization, or idealization protocols.

Scoring and constraints

Task	Guide or tutorial	API and notes
Build default, empty, or focused score functions	Scoring guide; Tutorial 03	See the score API and term map.
Score a pose or backpropagate through coordinates	Scoring guide; Tutorial 03	Render a module for the current pose layout and call it with coordinates.
Analyze weighted or unweighted block pairs	Scoring guide; Tutorial 03	Directed accounting can require both matrix orientations for an unordered pair.
Map a protein interface and test selected alanine substitutions	Protein-interface guide; Tutorial 09	Compose author-label masks, both block-pair orientations, and matched local-repacking tasks.
Reweight an interface differentiably	Tutorial 03	Apply an explicit analytical weight tensor before summing and backpropagating.
Add distance, coordinate, or torsion constraints	Optimization guide; Tutorial 05	See the constraint API. constrain_all_ca() is protein-specific; main-chain restraints follow block declarations.
Construct a focused score function or derive modified score parameters	Tutorial 11	Change weights to alter term contributions; derive a new immutable database only when changing the underlying parameter model.

Packing, design, and preparation

Task	Guide or tutorial	API and notes
Construct samplers and repack a fixed sequence	Packing guide; Tutorial 04	IncludeCurrentSampler deliberately keeps the input conformation as a candidate.
Optimize polar-hydrogen chis or build supported side chains	Structure I/O guide; Tutorial 01	Use normal preparation or explicitly configure the relevant sampler.
Add extra χ sampling	Packing guide; 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 guide; Tutorial 04	Compose explicit task masks.
Subclass PackerPalette, audit rotamer candidates, or export a rotamer ensemble	Tutorial 13	Candidate enumeration is deterministic for a fixed task; annealing is a separate stochastic assignment search.
Prepare and inject ligand parameters	Ligand guide; Tutorial 07	Start from authoritative CIF/MOL2 chemistry. .tmol is the only parameter format.
Score controlled ligand-pose decoys and locally refine diagnostic states	Tutorial 10	Reuse one ligand-aware context, batch matched rigid-body decoys, and compare scores with ligand displacement.
Score or pack DNA/RNA	Nucleic-acid guide; Tutorial 08	The packer samples glycosidic and hydroxyl-proton chi; sugar pucker stays fixed.