# Example for: alignment.compare_with(), alignment.append_model()

# Compare two alignments of two proteins each. In this case, the first
# alignment is a sequence-sequence alignment and the second alignment
# is a structure-structure alignment.

from modeller import *
log.level(1, 1, 1, 1, 0)
env = environ()
env.io.atom_files_directory = ['../atom_files']

# Generate and save sequence-sequence alignment:
aln = alignment(env)
for code in ('1fas', '2ctx'):
    mdl = model(env, file=code)
    aln.append_model(mdl=mdl, align_codes=code, atom_files=code)
aln.align(gap_penalties_1d=(-600, -400))
aln.write(file='toxin-seq.ali')

# Generate and save structure-structure alignment:
aln.align3d(gap_penalties_3d=(0, 2.0))
aln.write(file='toxin-str.ali')

# Compare the two pairwise alignments:
aln  = alignment(env, file='toxin-seq.ali', align_codes='all')
aln2 = alignment(env, file='toxin-str.ali', align_codes='all')
aln.compare_with(aln2)