alignment.expand() -- put all models into alignment

root_name = <str:1>	'undf'	root of a filename for filename construction
file_id = <str:1>	'default'	file id for filename construction
expand_control = <int:5>	9999 9999 1 10 0	for controlling EXPAND_ALIGNMENT
file_ext = <str:1>	''	file extension for filename construction

Description:

file_id, root_name, expand_control, file_ext, and file_id are used to construct atom filenames for all the models (see modfile.default()). The elements of expand_control are, in order, the first and last values of id1, the first and last values of id2, and the number of sequences to remove from the end of the current alignment before adding the new sequences. All the models covered by expand_control are added to the alignment, using the last sequence in the original alignment as the guide. This allows easy multiple superposition of all the templates and models after comparative modeling.

Example: examples/commands/expand_alignment.py

# Example for: alignment.expand()

# This will add models to the alignment.

env = environ()
aln = alignment(env, file='toxin.ali', align_codes=('2ctx', '2abx'))
aln.expand(expand_control=(9999, 9999, 1, 3, 0),
           root_name='2abx', file_id='.B', file_ext = '')
aln.write(file='toxin-expand.ali')