Module structure_alignment

Runs protein multiple structure alignment using "ska" backend. This will realign sequences in the provided alignment, and optionally transform coordinates of associated chains. Structureless sequences are ignored.

Parameters:

• seq_chain_pairs (list of (ProteinSequence, schrodinger.structure._Chain) tuples) - Pairs of MSV sequences associated with Maestro chains.
• transform_coords (bool) - Tells whether transform structure coordinates.

Returns: dict of list of integers using Sequence keys

Dictionary of gaps for aligned sequences. The dictionary can be empty if this function fails.