schrodinger.application.msv.jobs.structure_alignment module

schrodinger.application.msv.jobs.structure_alignment.runStructureAlignment(seq_chain_pairs, transform_coords=True, SeqClass=<class 'schrodinger.protein.sequence.ProteinSequence'>)

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.

Return type:

dict of list of integers using Sequence keys

Returns:

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