alignment.check() — check alignment for modeling

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/

# 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() = ['../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')

Automatic builds 2017-07-19