# Example for: model.transfer_xyz()

# This will build a model for a given sequence by copying
# coordinates from aligned templates. When the templates
# have the same sequence as the target, this procedure ensures
# that the new model corresponds to the MODELLER topology library.

from modeller import *

env = environ()
env.io.atom_files_directory = ['.', '../atom_files']
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

# Read the sequence and calculate its topology:
aln = alignment(env, file='toxin.ali', align_codes=('2ctx', '2nbt'))
aln.malign3d(fit=False)
aln.append(file='toxin.ali', align_codes='1fas')
mdl = model(env)
mdl.generate_topology(aln['1fas'])
# Assign the average of the equivalent template coordinates to MODEL:
mdl.transfer_xyz(aln)
# Get the remaining undefined coordinates from internal coordinates:
mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')

# Write the final MODEL coordinates to a PDB file:
mdl.write(file='1fas.ini')