result

Module for reformatting/filtering PDB results from UniProtKB SPARQL.

PdbResults = dict[str, set[PdbResult]]

Dictionary with uniprot accessions as keys and sets of PDB results as values.

PdbChainLengthError

Bases: ValueError

Raised when a UniProt chain description does not yield a chain length.

PdbResult dataclass

Result of a PDB search in UniProtKB.

Parameters:

Name	Type	Description	Default
id	str	PDB ID (for example "1H3O").	required
method	str	Method used for the PDB entry (for example "X-ray diffraction").	required
uniprot_chains	str	Chains in UniProt format (for example "A/B=1-42,A/B=50-99").	required
resolution	str | None	Resolution of the PDB entry (for example "2.0" for 2.0 Å). Optional.	None

chain cached property

The first chain from the UniProt chains aka self.uniprot_chains.

chain_length cached property

The length of the chain from the UniProt chains aka self.uniprot_chains.

filter_pdb_results_on_chain_length(pdb_results, min_residues, max_residues, keep_invalid=False)

Filter PDB results based on chain length.

Parameters:

Name	Type	Description	Default
pdb_results	PdbResults	Dictionary with protein IDs as keys and sets of PDB results as values.	required
min_residues	int | None	Minimum number of residues required in the chain mapped to the UniProt accession. If None, no minimum is applied.	required
max_residues	int | None	Maximum number of residues allowed in chain mapped to the UniProt accession. If None, no maximum is applied.	required
keep_invalid	bool	If True, PDB results with invalid chain length (could not be determined) are kept. If False, PDB results with invalid chain length are filtered out. Warnings are logged when length can not be determined.	False

Returns:

Type	Description
PdbResults	Filtered dictionary with protein IDs as keys and sets of PDB results as values.

filter_pdb_results_on_resolution(pdb_results, top)

Filter PDB results to top entries per UniProt accession by resolution.

Entries are ranked by lower resolution first, then higher chain length, and finally deterministic PDB ID ordering.

Parameters:

Name	Type	Description	Default
pdb_results	PdbResults	Dictionary with UniProt accessions mapped to PDB entries.	required
top	int	Maximum number of PDB entries to keep for each accession.	required

Returns:

Type	Description
PdbResults	Filtered dictionary with top-ranked entries per accession.