plinder.core.scores.alignment

Load full chain alignments from optional CIGAR shards.

plinder.core.scores.alignment.expand_alignment_cigar(cigar: str, *, query_start: int, target_start: int, source: Literal['foldseek', 'mmseqs'], include_gaps: bool = True, alignment_index: int = 0) → DataFrame

Expand one CIGAR into backend-native residue positions.

MMseqs positions are one-based SEQRES positions. Foldseek positions are zero-based indices over resolved coordinate residues.

plinder.core.scores.alignment.map_chain_alignment(query_entry: str, query_chain: str, target_entry: str, target_chain: str, *, source: Literal['foldseek', 'mmseqs'], search_db: str = 'holo', include_gaps: bool = True, release: PlinderRelease | None = None) → DataFrame

Load and expand full alignments for a pair of label-asym chains.