from modeller import *
from modeller.automodel import *    # Load the automodel class

log.verbose()

# Override the 'special_restraints' and 'user_after_single_model' methods:
class MyModel(automodel):
  def special_restraints(self, aln):
      # Constrain the A and B chains to be identical (but only restrain
      # the C-alpha atoms, to reduce the number of interatomic distances
      # that need to be calculated):
      s1 = selection(self.chains['A']).only_atom_types('CA')
      s2 = selection(self.chains['B']).only_atom_types('CA')
      s3 = selection(self.chains['C']).only_atom_types('CA')
      s4 = selection(self.chains['D']).only_atom_types('CA')
      s5 = selection(self.chains['E']).only_atom_types('CA')
      s6 = selection(self.chains['F']).only_atom_types('CA')
      s7 = selection(self.chains['G']).only_atom_types('CA')
      s8 = selection(self.chains['H']).only_atom_types('CA')
      s9 = selection(self.chains['I']).only_atom_types('CA')
      s10 = selection(self.chains['J']).only_atom_types('CA')
      s11 = selection(self.chains['K']).only_atom_types('CA')
      s12 = selection(self.chains['L']).only_atom_types('CA')
      self.restraints.symmetry.append(symmetry(s1, s2, 1)) 
      self.restraints.symmetry.append(symmetry(s2, s3, 1)) 
      self.restraints.symmetry.append(symmetry(s3, s4, 1)) 
      self.restraints.symmetry.append(symmetry(s4, s5, 1)) 
      self.restraints.symmetry.append(symmetry(s5, s6, 1)) 
      self.restraints.symmetry.append(symmetry(s6, s7, 1))
      self.restraints.symmetry.append(symmetry(s7, s8, 1))
      self.restraints.symmetry.append(symmetry(s8, s9, 1))
      self.restraints.symmetry.append(symmetry(s9, s10, 1))
      self.restraints.symmetry.append(symmetry(s10, s11, 1))   
      self.restraints.symmetry.append(symmetry(s11, s12, 1)) 
  
  def user_after_single_model(self):
      # Report on symmetry violations greater than 1A after building
      # each model:
      self.restraints.symmetry.report(1.0)

env = environ()
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']

# Be sure to use 'MyModel' rather than 'automodel' here!
a = MyModel(env,
            alnfile= 'acr1-mult2.ali',     # alignment filename
            knowns = ('2BYU', '1gme1', '1gme2', '1gme3', '1gme4', '1gme5', '1gme6'),# codes of the templates
            sequence = 'acr1',              # code of the target
            assess_methods=(assess.DOPE,
                            assess.GA341))


a.starting_model= 1                # index of the first model
a.ending_model  = 10               # index of the last model
                                       # (determines how many models to calculate)
a.md_level = refine.slow
a.make()                           # do homology modeling