# Demonstrating ALIGN2D, aligning with variable gap penalty

log.verbose()
env = environ()

env.libs.topology.read(file='$(LIB)/top_heav.lib')

# Read aligned structure(s):
aln = alignment(env)
aln.append(file='toxin.ali', align_codes='2ctx')
aln_block = len(aln)

# Read aligned sequence(s):
aln.append(file='toxin.ali', align_codes='1nbt')
 
# Structure sensitive variable gap penalty sequence-sequence alignment:
aln.align2d(overhang=0, gap_penalties_1d=(-100, 0),
            gap_penalties_2d=(3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0., 0.),
            align_block=aln_block)

aln.write(file='align2d.ali', alignment_format='PIR')
aln.write(file='align2d.pap', alignment_format='PAP',
          alignment_features='INDICES HELIX BETA STRAIGHTNESS ' + \
                             'ACCESSIBILITY CONSERVATION')
aln.check()

# Color the first template structure according to gaps in alignment:
aln = alignment(env)
aln.append(file='align2d.ali', align_codes=('2ctx', '1nbt'),
           alignment_format='PIR', remove_gaps=True)
mdl = model(env)
mdl.read(aln=aln, model_segment=('2ctx', '2ctx'))
mdl.color(aln=aln)
mdl.write(file='2ctx.aln.pdb')

# Color the first template structure according to secondary structure:
mdl.write_data(file='2ctx', output='SSM')
mdl.write(file='2ctx.ssm.pdb')

# Superpose the target structure onto the first template:
mdl2 = model(env)
mdl2.read(aln=aln, model_segment=('1nbt', '1nbt'))
mdl.pick_atoms(aln=aln, atom_types='CA')
mdl.superpose(mdl2, aln)
mdl2.write(file='1nbt.fit.pdb')