def _minimize(self):
m1 = self.model.deep_copy()
rama_params = rama_master_phil.fetch().extract(
).ramachandran_plot_restraints
rama_params.favored = 'oldfield'
rama_params.allowed = 'oldfield'
rama_params.outlier = 'oldfield'
m1.set_ramachandran_plot_restraints(rama_params=rama_params)
run2(
restraints_manager=m1.get_restraints_manager(),
pdb_hierarchy=m1.get_hierarchy(),
correct_special_position_tolerance=1.0,
riding_h_manager=None,
ncs_restraints_group_list=
[], # These are actually for NCS CONSTRAINTS!
max_number_of_iterations=500,
number_of_macro_cycles=5,
selection=None,
bond=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True,
parallelity=True,
log=null_out())
m1.set_sites_cart_from_hierarchy(multiply_ncs=True)
return m1
def exercise_1(prefix="tst_model_ramachandran_1"):
""" Make sure that set_ramachandran_plot_restraints() works. """
inp = iotbx.pdb.input(lines=tst_pdb_str, source_info=None)
model = mmtbx.model.manager(model_input=inp)
rama_params = master_phil.fetch().extract().ramachandran_plot_restraints
rama_params.favored = 'oldfield'
rama_params.allowed = 'oldfield'
rama_params.outlier = 'oldfield'
model.set_ramachandran_plot_restraints(rama_params=rama_params)
n = model.get_restraints_manager(
).geometry.ramachandran_manager.get_n_oldfield_proxies()
assert n == 2
rama_params.favored = 'emsley'
rama_params.allowed = 'emsley'
rama_params.outlier = 'emsley'
model.set_ramachandran_plot_restraints(rama_params=rama_params)
n = model.get_restraints_manager(
).geometry.ramachandran_manager.get_n_emsley_proxies()
assert n == 2