# Homology modelling by the automodel class

from modeller.automodel import *    # Load the automodel class

log.verbose()
env = environ()

# directories for input atom files
#env.io.atom_files_directory = './:../atom_files'

a = loopmodel(env,
              alnfile  = '1D3Z-1H8C.ali',     # alignment filename
              knowns   = '1H8C',              # codes of the templates
              sequence = '1D3Z')              # code of the target
a.starting_model= 1                 # index of the first model 
a.ending_model  = 1                 # index of the last model
                                    # (determines how many models to calculate)
# Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6
a.repeat_optimization = 3
a.max_molpdf = 1e6

a.loop.starting_model = 1           # First loop model
a.loop.ending_model   = 4           # Last loop model
a.loop.md_level       = refine.very_slow # Loop model refinement level

a.make()                            # do homology modelling