sifts

SIFTS mmCIF helpers.

These helpers operate on _pdbx_sifts_unp_segments category in mmCIF files, which are used to map PDB chains to UniProt accessions and residue ranges.

uniprot_chain_mappings_from_cif(block, best_only=True, strip_isoform=True)

Extract UniProt chain mappings from raw _pdbx_sifts_unp_segments rows.

Parameters:

Name	Type	Description	Default
block	Block	mmCIF block containing _pdbx_sifts_unp_segments rows.	required
best_only	bool	If True, only return rows where best_mapping is y.	True
strip_isoform	bool	If True, strip isoform suffixes from UniProt accessions (e.g. O00255-1 -> O00255).	True

Returns:

Type	Description
UniprotChainMappings	Set of UniProt chain mappings with ranges per chain. Empty if no SIFTS
UniprotChainMappings	segment data is found. Returned chains use label system.

uniprot_chain_mappings_to_cif(mappings, block)

Write minimal _pdbx_sifts_unp_segments rows to an mmCIF block.

The emitted category only contains the subset consumed by uniprot_chain_mappings_from_cif().

Parameters:

Name	Type	Description	Default
mappings	UniprotChainMappings	UniProt chain mappings in label chain-id system.	required
block	Block	mmCIF block to update.	required