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- __builtin__.object
-
- manager
- xh_connectivity_table
class manager(__builtin__.object) |
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Methods defined here:
- __init__(self, xray_structure, pdb_hierarchy, processed_pdb_files_srv=None, restraints_manager=None, ias_xray_structure=None, refinement_flags=None, ias_manager=None, wilson_b=None, tls_groups=None, anomalous_scatterer_groups=None, log=None)
- add_hydrogens(self, element='H', neutron=False)
- add_ias(self, fmodel=None, ias_params=None, file_name=None, build_only=False)
- add_solvent(self, solvent_xray_structure, atom_name='O', residue_name='HOH', chain_id=' ', refine_occupancies=False, refine_adp=None)
- adp_statistics(self)
- deep_copy(self)
- energies_adp(self, iso_restraints, compute_gradients, use_hd)
- extract_ncs_groups(self)
- extract_water_residue_groups(self)
- geometry_minimization(self, max_number_of_iterations=500, number_of_macro_cycles=5, selection=None, bond=False, nonbonded=False, angle=False, dihedral=False, chirality=False, planarity=False, rmsd_bonds_termination_cutoff=0, rmsd_angles_termination_cutoff=0)
- geometry_statistics(self, ignore_hd)
- hd_group_selections(self)
- idealize_h(self, xh_bond_distance_deviation_limit=0, show=True)
- isolated_atoms_selection(self)
- number_of_ordered_solvent_molecules(self)
- remove_ias(self)
- remove_solvent(self)
- renumber_water(self)
- reset_adp_for_hydrogens(self)
- reset_adp_of_hd_sites_to_be_equal(self)
- reset_coordinates_for_exchangable_hd(self)
- restraints_manager_energies_sites(self, geometry_flags=None, custom_nonbonded_function=None, compute_gradients=False, gradients=None, disable_asu_cache=False)
- rms_b_iso_or_b_equiv_bonded(self)
- scale_adp(self, scale_max, scale_min)
- select(self, selection)
- set_refine_individual_adp(self, selection_iso=None, selection_aniso=None)
- set_refine_individual_sites(self, selection=None)
- show_adp_statistics(self, prefix='', padded=False, pdb_deposition=False, out=None)
- show_geometry_statistics(self, ignore_hd, message='', out=None)
- show_groups(self, rigid_body=None, tls=None, out=None, text='Information about rigid groups')
- show_occupancy_statistics(self, out=None, text='')
- show_rigid_bond_test(self, out=None)
- solvent_selection(self)
- write_pdb_file(self, out=None, selection=None, xray_structure=None)
- xh_connectivity_table(self)
- xray_structure_macromolecule(self)
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class xh_connectivity_table(__builtin__.object) |
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Methods defined here:
- __init__(self, geometry, xray_structure)
- # XXX need angle information as well
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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