# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved.  This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use.  This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---

# This script is generated by the Modeller Dialog in Chimera, 
# incorporating the settings from the user interface. User can revise 
# this script and submit the modified one into the Advanced Option panel. 


# Import the Modeller module
from modeller import *
from modeller.automodel import *    


# ---------------------- namelist.dat --------------------------------
# A "namelist.dat" file contains the file names, which was output from 
# the Modeller dialog in Chimera based on user's selection.
# The first line it the name of the target sequence, the remaining 
# lines are name of the template structures
namelist = open( 'namelist.dat', 'r' ).read().split('\n')
tarSeq = namelist[0]
template = tuple( [ x.strip() for x in namelist[1:] if x != '' ] )
# ---------------------- namelist.dat --------------------------------

# This instructs Modeller to display all log output. 
log.verbose()

# create a new Modeller environment
env = environ()

# Directory of atom/PDB/structure files. It is a relative path, inside 
# a temp folder generated by Chimera. User can modify it and add their 
# absolute path containing the structure files.
env.io.atom_files_directory = ['.', './template_struc']