uniprot

UniProt extraction and injection helpers for structures.

ChainUniprotPair = namedtuple('ChainUniprotPair', ['chain_id', 'uniprot_accession']) module-attribute

Pair of chain id and UniProt accession for mapping purposes.

UniprotSource = Literal['both', 'sifts', 'struct_ref_seq', 'fallback'] module-attribute

From which source to extract UniProt accessions from a structure.

FlattenedUniprotChainMapping dataclass

Collapsed _struct_ref_seq like alignment information for one chain.

Attributes:

uniprot_accession: The UniProt accession.
uniprot_start: The start position of the alignment on the UniProt sequence.
uniprot_end: The end position of the alignment on the UniProt sequence.
chain_id: The chain ID in the 'auth' [chain ID system][protein_quest.structure.chains.ChainIdSystem].
sequence_identity: The sequence identity of the alignment.
aligned_residue_count: The number of aligned residues in the alignment.

add_uniprot_accessions2structure(structure, pdb2uniprot, *, chain_system='auth')

Add UniProt accessions to a structure if they are missing, based on the provided pdb2uniprot mapping.

If structure has UniProt accession that is not in pdb2uniprot, it will be left unchanged. If structure has chain extraction provenance, the chain names from pdb2uniprot will be renamed to match the output chain name in the provenance.

Parameters:

Name	Type	Description	Default
structure	Structure	The gemmi Structure object to add UniProt accessions to.	required
pdb2uniprot	Pdb2UniprotChainsMapping | None	Dictionary mapping PDB ID to structured UniProt chain mappings. If provided, will be used to inject UniProt accessions into the structure if they are missing. If None, the structure is returned unchanged.	required
chain_system	ChainIdSystem	System of chain ids in pdb2uniprot mapping.	'auth'

Returns:

Type	Description
Structure	A gemmi Structure object with UniProt accessions added if they were missing
Structure	or the structure unchanged if all accessions were already present.

apply_chain_provenance_to_uniprot_mappings(mappings, chain_provenance)

Apply chain extraction provenance to a set of UniprotChainMapping.

Parameters:

Name	Type	Description	Default
mappings	set[UniprotChainMapping]	Set of UniprotChainMapping to apply provenance to.	required
chain_provenance	ChainExtractionProvenance	ChainExtractionProvenance to apply to mappings.	required

Returns:

Type	Description
set[UniprotChainMapping]	Set of UniprotChainMapping with chain ids updated based on provenance.

flatten_uniprot_chain_mappings(mappings)

Flatten a set of UniprotChainMapping.

Each (accession, chain) group is collapsed into one record with merged start/end and aligned_residue_count summed across all ranges.

Parameters:

Name	Type	Description	Default
mappings	set[UniprotChainMapping]	Set of UniprotChainMapping.	required

Returns:

Type	Description
set[FlattenedUniprotChainMapping]	Set of flattened per-(accession, chain) records with merged start/end,
set[FlattenedUniprotChainMapping]	summed aligned residue counts, and computed sequence identity.

structure2uniprot_accessions(structure)

Extract UniProt accessions from a gemmi Structure object.

Logs a warning and returns an empty set if no accessions are found in structure.

Parameters:

Name	Type	Description	Default
structure	Structure	The gemmi Structure object to extract UniProt accessions from.	required

Returns:

Type	Description
set[str]	A set of UniProt accessions found in the structure.

structure_to_uniprot(structure, source='both', one_uniprot_per_chain=True)

Extract UniProt chain mappings from a structure.

Parameters:

Name	Type	Description	Default
structure	Structure	The structure containing SIFTS and/or _struct_ref_seq data.	required
source	UniprotSource	UniProt source to read from. sifts: Read from entity sifts_unp_acc values. struct_ref_seq: Read from _struct_ref_seq filtered by _struct_ref records with db_name=UNP. both: Merge SIFTS and struct_ref_seq results. fallback: Return SIFTS when available, otherwise struct_ref_seq.	'both'
one_uniprot_per_chain	bool	If True, return only the best UniProt per chain, based on highest aligned residue count, with ties broken alphabetically by accession. Otherwise, return all UniProt mappings for each chain.	True

Returns:

Type	Description
set[FlattenedUniprotChainMapping]	Set of flattened per-(accession, chain) records with merged start/end,
set[FlattenedUniprotChainMapping]	summed aligned residue counts, and computed sequence identity.

uniprot_chain_mappings_from_sifts(structure)

Extract UniProt chain mappings from SIFTS data.

Parameters:

Name	Type	Description	Default
structure	Structure	The structure containing SIFTS data.	required

Returns:

Type	Description
set[UniprotChainMapping]	Set of UniProt chain mappings with ranges per chain. Empty if no SIFTS data found.

uniprot_chain_mappings_from_struct_ref_seq(structure)

Extract UniProt chain mappings from _struct_ref_seq rows.

Parameters:

Name	Type	Description	Default
structure	Structure	The structure containing _struct_ref and _struct_ref_seq records.	required

Returns:

Type	Description
set[UniprotChainMapping]	Set of UniProt chain mappings with ranges per chain. Empty if no UNP data found.