Example #1
0
    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(),
        }
Example #2
0
 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
Example #3
0
 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
Example #4
0
  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(),
    }