#!/usr/bin/env python

from modeller import *
from modeller.automodel import *
import os

log.verbose()
env=environ()
env.io.atom_files_directory='./'

class myloop(dope_loopmodel):
    def select_loop_atoms(self):
        return selection(self.residue_range('1:','21:'),self.residue_range('22:','23:'),self.residue_range('27:','28:'),self.residue_range('29:','31:'),self.residue_range('32:','36:'),self.residue_range('37:','39:'),self.residue_range('40:','44:'),self.residue_range('45:','48:'),self.residue_range('56:','62:'))

a=myloop(env,
            alnfile='2cpnA_2das1A.ali',
            knowns='2cpn',
            sequence='2das1',
            loop_assess_methods=assess.DOPE
            )

a.md_level = refine.slow
a.loop.md_level = refine.slow

myloop.repeat_optimization=3
a.final_malign3d=True

a.starting_model=1
a.ending_model=1

a.loop.starting_model=1
a.loop.ending_model=10

a.make()