plinder.data.interface_apo

Pair each protein-interface side with deposited non-interacting chains.

class plinder.data.interface_apo.InterfaceApoSelectionConfig(max_per_side: int = 5, min_sequence_identity: float = 0.95, min_query_coverage: float = 0.8, min_target_coverage: float = 0.8)

Bases: object

Similarity thresholds and maximum links for each interface side.

max_per_side: int = 5

min_sequence_identity: float = 0.95

min_query_coverage: float = 0.8

min_target_coverage: float = 0.8

plinder.data.interface_apo.build_interface_apo_candidate_manifest(entry_chains: DataFrame | str | Path, *, biounit_chains: DataFrame | str | Path, entry_metadata: DataFrame | str | Path) → DataFrame

Choose a protein-contact-free assembly instance for each candidate chain.

plinder.data.interface_apo.build_interface_apo_query_manifest(interfaces: DataFrame | str | Path) → DataFrame

Return one query row for each side of every protein interface.

plinder.data.interface_apo.write_interface_apo_structure_table(mmseqs_alignments: str | Path, *, foldseek_alignments: str | Path, queries: DataFrame | str | Path, candidates: DataFrame | str | Path, output_path: str | Path, config: InterfaceApoSelectionConfig | None = None, scratch_dir: str | Path | None = None, threads: int = 1, memory_limit: str = '7GB') → Path

Write ranked protein-contact-free chain links for interface sides.