# Demonstrating the use of alignment restraints, only available in
# align2d and salign:
from modeller import *

log.verbose()
env = Environ()

# The special alignment entry '_fix_pos' has to be the last entry in the
# alignment array. Its sequence contains characters blank (or 0), 1, 2, 3,
# and 4 at the restrained alignment positions. The residue-residue score from
# the substitution matrix for these positions will be offset by the scalar
# value FIX_OFFSETS[0..4].
aln = Alignment(env, file='fix_positions.ali', align_codes=('1leh', '3btoA',
                                                            '_fix_pos'))

# fix_offsets specifies the offset corresponding to character ' 1234' in the
# _fix_pos entry in the alignment
# (this offsets unlabeled positions for 0, the ones indicated by 1 by
#  1000, those indicated by 2 by 2000, etc.)
aln.salign(fix_offsets=(0, -10, -20, -30, -40),
           gap_penalties_2d=(0, 0, 0, 0, 0, 0, 0, 0, 0), # Any values are
                                                         # possible here
           local_alignment=False, # Local alignment works, too
           gap_penalties_1d=(-600, -400)) # This is best with the default value
                                          # of gap_penalties_2d

# Write it out, the _fix_pos is erased automatically in salign:
aln.write(file='fix_positions_salign.pap', alignment_format='PAP')