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, proxies=None, i_seqs=None, sigma=0.1): if proxies is None: proxies = adp_restraints.shared_adp_volume_similarity_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")] assert len(i_seqs) > 1 proxies.append(adp_restraints.adp_volume_similarity_proxy(i_seqs=i_seqs, weight=weight)) self.proxies = proxies
def __init__(self, xray_structure, proxies=None, i_seqs=None, sigma=0.1): if proxies is None: proxies = adp_restraints.shared_adp_volume_similarity_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') ] assert len(i_seqs) > 1 proxies.append( adp_restraints.adp_volume_similarity_proxy(i_seqs=i_seqs, weight=weight)) self.proxies = proxies