Modules
		cctbx.adptbx boost cctbx cctbx.crystal iotbx.crystal_symmetry_from_any iotbx.pdb.crystal_symmetry_from_pdb scitbx.python_utils.easy_pickle cctbx.eltbx cctbx.array_family.flex iotbx libtbx scitbx.matrix cctbx.miller mmtbx mmtbx.monomer_library iotbx.mtz mmtbx.solvent.ordered_solvent os iotbx.pdb mmtbx.refinement.print_statistics random iotbx.reflection_file_reader iotbx.reflection_file_utils cctbx.sgtbx sys cctbx.uctbx mmtbx_utils_ext cctbx.xray iotbx.pdb.xray_structure

Classes
		__builtin__.object determine_data_and_flags process_pdb_file_srv   class determine_data_and_flags(__builtin__.object)       Methods defined here: __init__(self, reflection_file_server, parameters=None, data_parameter_scope='', flags_parameter_scope='', data_description=None, working_point_group=None, symmetry_safety_check=None, remark_r_free_flags_md5_hexdigest=None, extract_r_free_flags=True, keep_going=False, log=None) data_as_f_obs(self, f_obs) extract_data(self) extract_flags(self, data, data_description='R-free flags') flags_as_r_free_flags(self, f_obs, r_free_flags, missing_show_max_lines=10) get_r_free_flags(self) verify_r_free_flags_md5_hexdigest(self, ignore_pdb_hexdigest, current, records) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class process_pdb_file_srv(__builtin__.object)       Methods defined here: __init__(self, crystal_symmetry=None, pdb_parameters=None, pdb_interpretation_params=None, stop_for_unknowns=None, log=None, cif_objects=None, cif_parameters=None, mon_lib_srv=None, ener_lib=None) process_pdb_files(self, pdb_file_names=None, raw_records=None) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)

Functions
		StringIO(...) StringIO([s]) -- Return a StringIO-like stream for reading or writing add_occupancy_selection(result, size, selection, hd_special=None) assert_xray_structures_equal(x1, x2, selection=None, sites=True, adp=True, occupancies=True) atom_selection(all_chain_proxies, string) combine_hd_exchangable(hierarchy) correct_drifted_waters(...) correct_drifted_waters( (vec3_double)sites_frac_all, (vec3_double)sites_frac_peaks, (bool)water_selection, (unit_cell)unit_cell) -> None :       C++ signature :         void correct_drifted_waters(scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<bool, scitbx::af::trivial_accessor>,cctbx::uctbx::unit_cell) determine_experimental_phases(reflection_file_server, parameters, log, parameter_scope, working_point_group, symmetry_safety_check, ignore_all_zeros=True) explain_how_to_generate_array_of_r_free_flags(log, flags_parameter_scope) get_atom_selection(pdb_file_name, selection_string, iselection=False) get_atom_selections(all_chain_proxies, xray_structure, selection_strings=None, iselection=True, one_group_per_residue=False, hydrogens_only=False, one_selection_array=False, log=None) list_3d_as_bool_selection(list_3d, size) miller_array_symmetry_safety_check(miller_array, data_description, working_point_group, symmetry_safety_check, log) occupancy_selections(all_chain_proxies, xray_structure, ignore_hydrogens=True, add_water=False, other_individual_selection_strings=None, other_group_selection_strings=None, expect_exangable_hd=False, as_flex_arrays=True) print_header(line, out=None) print_programs_start_header(log, text) select_water_by_distance(...) select_water_by_distance( (vec3_double)sites_frac_all, (std_string)element_symbols_all, (size_t)water_selection_o, (float)dist_max, (float)dist_min_mac, (float)dist_min_sol, (unit_cell)unit_cell) -> size_t :       C++ signature :         scitbx::af::shared<unsigned long> select_water_by_distance(scitbx::af::shared<scitbx::vec3<double> >,scitbx::af::shared<std::string>,scitbx::af::shared<unsigned long>,double,double,double,cctbx::uctbx::unit_cell) set_log(args) write_pdb_file(xray_structure, pdb_hierarchy, pdb_atoms=None, write_cryst1_record=True, selection=None, atoms_reset_serial=True, out=None)

Data
		cif_params = <libtbx.phil.scope object at 0x26ae1f0> data_and_flags = <libtbx.phil.scope object at 0x264ee20> experimental_phases_params = <libtbx.phil.scope object at 0x26ae050> pdb_params = <libtbx.phil.scope object at 0x26ae120>