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name: structural-bioinformatics description: "Use Biopython Bio.PDB to parse, write, traverse, and analyze PDB, mmCIF, BinaryCIF, PQR, and PDBML structure data." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

Structural Bioinformatics

Use this sub-skill when the task involves macromolecular coordinate structures with Biopython's Bio.PDB: reading or writing structure files, navigating the SMCRA hierarchy, selecting atoms/residues/chains, handling alternate locations or point-mutant disorder, extracting polypeptides, computing contacts or geometry, or superimposing structures.

Route here for

• Parsing PDB, PDBx/mmCIF, BinaryCIF, PQR, and PDBML/XML coordinate files into Structure objects.
• Choosing between PDBParser, MMCIFParser, FastMMCIFParser, BinaryCIFParser, PDBMLParser, PDBIO, and MMCIFIO.
• Traversing Structure -> Model -> Chain -> Residue -> Atom objects and using Selection.unfold_entities.
• Working with residue IDs, hetero residues, waters, insertion codes, atom IDs, altlocs, disordered atoms, and disordered residues.
• Extracting polypeptides and structure-derived sequences with PPBuilder or CaPPBuilder.
• Computing distances, angles, dihedrals, vectors, residue/atom neighborhoods, solvent-exposure-style quantities, or structure superpositions.
• Using PDBList only when an explicitly network-enabled task needs wwPDB downloads.
• Understanding optional structural tools such as DSSP/mkdssp, NACCESS, MSMS-backed residue depth, PSEA, and related executable-dependent workflows.

Route elsewhere

• Sequence object construction, SeqRecord internals, annotations, feature locations, translation, and reverse-complement behavior: use sequence-objects-and-features.
• General sequence/alignment file I/O through SeqIO/AlignIO, including PDB-derived sequence formats such as pdb-atom or pdb-seqres: use file-io-and-format-conversion unless the task needs coordinate objects.
• BLAST/SearchIO semantics, pairwise sequence alignment, phylogenetic tree I/O, or external aligner orchestration: use alignment-search-and-phylogeny.
• Online biological database workflows, Entrez/KEGG/UniProt/ExPASy etiquette, and BioSQL databases: use web-databases-and-biosql.
• Protein structure prediction, docking, de novo design, force fields, or molecular dynamics setup: outside this Biopython repo skill except for simple coordinate parsing/selection utilities.

Operating references

• Start with references/structure-workflows.md for parser choice, SMCRA traversal, writing/selecting, polypeptides, contacts, geometry, superposition, downloads, and optional tools.
• Use references/structure-api-reference.md for verified signatures, object relationships, entity levels, residue/atom ID conventions, and format limits.
• Use references/troubleshooting.md for parser warnings/errors, malformed coordinates, PQR charge/radius issues, mmCIF/PDB ID mismatches, BinaryCIF optional dependencies, writer limits, NeighborSearch, Superimposer, PDBList, and external-tool failures.
• Run scripts/pdb_structure_smoke.py for a safe offline sanity check of PDBParser, SMCRA traversal, atom geometry, NeighborSearch, and PDBIO round-tripping on an embedded tiny PDB fixture.

Guardrails

• Prefer mmCIF/PDBx or BinaryCIF for modern, large, or metadata-heavy structure work; legacy PDB has chain, atom-serial, residue-number, and header limitations.
• Treat PERMISSIVE=True as data-loss-tolerant parsing: warnings may mean atoms or residues were omitted. Use strict parsing when data integrity matters.
• Always decide how to handle disordered atoms/residues before measuring distances, contacts, or superpositions.
• Match superposition atom lists by biological identity and order; Superimposer minimizes RMSD for equal-length lists and mutates the moving atoms when apply is called.
• Do not require downloads, external executables, original repository examples, or repository test data for normal runtime recipes in this sub-skill.