rcsb_search_strucmotif

Find structures containing a 3D STRUCTURAL MOTIF — a geometric arrangement of specific residues — like the one in a reference structure.

This is geometry-based and DIFFERENT from rcsb_search_by_structure (whole-shape similarity) and from rcsb_search_by_seqmotif (sequence pattern). Use it for catalytic triads, binding sites, metal-coordination geometries, etc.

Args: entry_id: Reference PDB entry defining the motif, e.g. "2MNR". residue_ids: 2-10 residues defining the motif, each a dict {"label_asym_id": , "label_seq_id": , "struct_oper_id"?: }. IMPORTANT: these are the mmCIF label identifiers (the internal numbering), which often DIFFER from the author residue numbers seen in papers/the PDB site. If you only have author numbering, resolve the label_asym_id/label_seq_id first (e.g. via rcsb_get_polymer_entity_instances) — author numbers give wrong/no hits. Example (enolase catalytic residues): [{"label_asym_id":"A","label_seq_id":162}, {"label_asym_id":"A","label_seq_id":193}, {"label_asym_id":"A","label_seq_id":219}] backbone_distance_tolerance: Backbone distance tolerance in Å, integer 0-3 (default 1). side_chain_distance_tolerance: Side-chain distance tolerance in Å, integer 0-3 (default 1). angle_tolerance: Angle tolerance in multiples of 20°, integer 0-3 (default 1). rmsd_cutoff: Maximum RMSD of accepted hits (default 2.0). atom_pairing_scheme: ALL, BACKBONE, SIDE_CHAIN (default), or PSEUDO_ATOMS. motif_pruning_strategy: NONE or KRUSKAL (default). return_type: What to return (default "assembly"); see the "Return types and fetching details" note in the server instructions. limit: Max hits (1-100). offset: Number of hits to skip, for paging; pass the response's next_offset back with the same query to fetch the next page. all_hits: Return the COMPLETE result set in one call (for an explicit "ALL ..." request); ignores limit, can't be combined with offset, and is refused above 10000 hits. Ignored when facets is set. attributes: Optional structured filters AND/OR-combined with this match — a list of AttributeFilter {attribute, operator, value, negation?, case_sensitive?} (e.g. restrict to an organism or resolution). See rcsb_search_by_attribute / rcsb_list_pdb_search_attributes for paths and operators. logical_operator: Combine this match and the attribute conditions with "and" (default) or "or". facets: Optional aggregation specs to return a breakdown / distribution instead of hits (see the faceting note in the server instructions for the spec). group_by, group_by_ranking: Collapse redundant polymer_entity hits into clusters, one representative each (needs return_type="polymer_entity") — see the grouping note in the server instructions. sort_by: Attribute path to order the hits by, replacing the default score ordering (each hit's score is still returned); omit to keep it. Only SORTABLE attributes work: those listing exact_match (strings) or equals (numbers/dates) in rcsb_list_pdb_search_attributes; full-text-only attributes (e.g. struct.title) and return_type="mol_definition" are rejected. sort_direction: "asc" (default) or "desc"; applies only when sort_by is set.

Returns: {total_count, returned, offset, has_more, next_offset, hits:[{id, score}], editor}; with facets, instead returns {total_count, facets, editor}.