# Example for: alignment.malign3d(), alignment.compare_structures()

# This will read all sequences from a sequence file, multiply align
# their 3D structures, and then also compare them using this alignment.

env = environ()

aln = alignment(env, file='toxin.ali', align_codes='all')
aln.malign(gap_penalties_1d=(-600, -400))
aln.malign3d(gap_penalties_3d=(0, 2.0), write_fit=True, write_whole_pdb=False)
aln.write(file='toxin-str.pap', alignment_format='PAP')

# Make two comparisons: no cutoffs, and 3.5A/60 degree cutoffs for RMS, DRMS,
# and dihedral angle comparisons:
aln.compare_structures(rms_cutoffs=[999]*11)
aln.compare_structures(rms_cutoffs=(3.5, 3.5, 60, 60, 60, 60, 60, 60, 60,
                                    60, 60))