elif o in ("-p", "--write_pdb"):
param_write_pdb = a
elif o in ("-p", "--write_rotated"):
param_write_rotated = a
if len(args) < 3:
print USAGE
print "not enough arguments specified"
sys.exit(1)
param_filename_pdb1 = args[0]
param_filename_pdb2 = args[1]
param_filename_alignment = args[2]
print Experiment.GetHeader()
print Experiment.GetParams()
try:
rmsd, natoms, translation, rotation, iterations = PdbTools.IterativeSuperImposition( param_filename_pdb1,
param_filename_pdb2,
param_filename_alignment,
max_iterations = param_max_iterations,
cutoff = param_cutoff)
except ValueError, msg:
print "# ERROR: %s" % msg
print "rmsd\tna"
print "natoms\tna"
print "iterations\tna"
sys.exit(1)
print "rmsd\t%5.2f" % rmsd
