def __init__(self, *args, **kwds):
super(restrained_crystal_structure_builder,
self).__init__(*args, **kwds)
geom = geometry_restraints
adp = adp_restraints
self._proxies = {}
self._proxies = {
'bond':
geometry_restraints.shared_bond_simple_proxy(),
'angle':
geometry_restraints.shared_angle_proxy(),
'dihedral':
geometry_restraints.shared_dihedral_proxy(),
'planarity':
geometry_restraints.shared_planarity_proxy(),
'chirality':
geometry_restraints.shared_chirality_proxy(),
'bond_similarity':
geometry_restraints.shared_bond_similarity_proxy(),
'adp_similarity':
adp_restraints.shared_adp_similarity_proxy(),
'rigid_bond':
adp_restraints.shared_rigid_bond_proxy(),
'isotropic_adp':
adp_restraints.shared_isotropic_adp_proxy(),
'fixed_u_eq_adp':
adp_restraints.shared_fixed_u_eq_adp_proxy(),
'adp_u_eq_similarity':
adp_restraints.shared_adp_u_eq_similarity_proxy(),
'adp_volume_similarity':
adp_restraints.shared_adp_volume_similarity_proxy(),
}
def __init__(self, xray_structure, u_eq_ideal, proxies=None, i_seqs=None, sigma=0.1):
if proxies is None:
proxies = adp_restraints.shared_fixed_u_eq_adp_proxy()
weight = 1 / (sigma * sigma)
if i_seqs is None:
i_seqs = [i for i, s in enumerate(xray_structure.scatterers()) if s.scattering_type not in ("H", "D")]
for i_seq in i_seqs:
proxies.append(adp_restraints.fixed_u_eq_adp_proxy(i_seqs=(i_seq,), weight=weight, u_eq_ideal=u_eq_ideal))
self.proxies = proxies
def __init__(self,
xray_structure,
u_eq_ideal,
proxies=None,
i_seqs=None,
sigma=0.1):
if proxies is None:
proxies = adp_restraints.shared_fixed_u_eq_adp_proxy()
weight = 1 / (sigma * sigma)
if i_seqs is None:
i_seqs = [
i for i, s in enumerate(xray_structure.scatterers())
if s.scattering_type not in ('H', 'D')
]
for i_seq in i_seqs:
proxies.append(
adp_restraints.fixed_u_eq_adp_proxy(i_seqs=(i_seq, ),
weight=weight,
u_eq_ideal=u_eq_ideal))
self.proxies = proxies
def __init__(self, *args, **kwds):
super(restrained_crystal_structure_builder, self).__init__(*args, **kwds)
geom = geometry_restraints
adp = adp_restraints
self._proxies = {}
self._proxies = {
'bond': geometry_restraints.shared_bond_simple_proxy(),
'angle': geometry_restraints.shared_angle_proxy(),
'dihedral': geometry_restraints.shared_dihedral_proxy(),
'planarity': geometry_restraints.shared_planarity_proxy(),
'chirality': geometry_restraints.shared_chirality_proxy(),
'bond_similarity': geometry_restraints.shared_bond_similarity_proxy(),
'adp_similarity': adp_restraints.shared_adp_similarity_proxy(),
'rigid_bond': adp_restraints.shared_rigid_bond_proxy(),
'isotropic_adp': adp_restraints.shared_isotropic_adp_proxy(),
'fixed_u_eq_adp': adp_restraints.shared_fixed_u_eq_adp_proxy(),
'adp_u_eq_similarity': adp_restraints.shared_adp_u_eq_similarity_proxy(),
'adp_volume_similarity': adp_restraints.shared_adp_volume_similarity_proxy(),
}
