Alignment.check() — check alignment for modeling

check(io=None)

This command evaluates an alignment to be used for comparative modeling, by calling Alignment.check_structure_structure() and Alignment.check_sequence_structure().

Example: examples/commands/read_alignment.py

# Example for: Alignment.append(), Alignment.write(),
#              Alignment.check()

# Read an alignment, write it out in the 'PAP' format, and
# check the alignment of the N-1 structures as well as the
# alignment of the N-th sequence with each of the N-1 structures.

from modeller import *

log.level(output=1, notes=1, warnings=1, errors=1, memory=0)
env = Environ()
env.io.atom_files_directory = ['../atom_files']

aln = Alignment(env)
aln.append(file='toxin.ali', align_codes='all')
aln.write(file='toxin.pap', alignment_format='PAP')
aln.write(file='toxin.fasta', alignment_format='FASTA')
aln.check()