# Homology modeling by the automodel class
#
# Demonstrates how to refine only a part of the model.
#
# You may want to use the more exhaustive "loop" modeling routines instead.
#
from modeller import *
from modeller.automodel import *    # Load the automodel class

log.verbose()

# Override the 'select_atoms' routine in the 'automodel' class:
# (To build an all-hydrogen model, derive from allhmodel rather than automodel
# here.)
class MyModel(automodel):
    def select_atoms(self):
        # Select residues from chain A (required for multi-chain models):
        return selection(self.residue_range('1:A', '17:A'))

        # Select residues from chain A (required for multi-chain models):
        return selection(self.residue_range('481:A', '534:A'))

        # Select residues from chain B (required for multi-chain models):
        return selection(self.residue_range('560:B', '634:B'))

        # Select residues from chain B (required for multi-chain models):
        return selection(self.residue_range('716:B', '754:B'))

        # Select residues from chain C (required for multi-chain models):
        return selection(self.residue_range('830:C', '852:C'))


env = environ()
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
# selected atoms do not feel the neighborhood
env.edat.nonbonded_sel_atoms = 2

# Be sure to use 'MyModel' rather than 'automodel' here!
a = MyModel(env,
            alnfile  = 'AMPK_final-mult.ali', # alignment filename
            knowns   = ('2Y94', '1Z0M_B', '4F2L', 'AMPK_alpha', 'AMPK_beta', 'AMPK_gamma'),     # codes of the templates
            sequence = 'AMPK_final',assess_methods=(assess.DOPE, assess.GA341))              # code of the target

a.starting_model= 1                # index of the first model
a.ending_model  = 5                # index of the last model
                                   # (determines how many models to calculate)
a.make()                           # do homology modeling