“cmd.align” performs a sequence alignment followed by a structural superposition, and then carries out zero or more cycles of refinement in order to reject outliers.

def align(mobile, target, cutoff=2.0, cycles=5, gap=-10.0,
          extend=-0.5, max_gap=50, object=None,
          matrix="BLOSUM62", mobile_state=0, target_state=0,
          quiet=1, max_skip=0, transform=1, reset=0):

align | api