Building an all hydrogen model

This is done by using the allhmodel class rather than automodel. Otherwise, operation is identical. Note that the allhmodel class automatically turns on env.io.hydrogen for you and selects the all-atom topology and radii files.

Example: examples/automodel/model-default-allh.py

from modeller.automodel import *

log.verbose()
env = environ()

env.io.atom_files_directory = './:../atom_files'

a = allhmodel(env, alnfile='alignment.ali', knowns='5fd1', sequence='1fdx')
a.starting_model = a.ending_model = 4

a.make()