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- StringIO(...)
- StringIO([s]) -- Return a StringIO-like stream for reading or writing
- add_occupancy_selection(result, size, selection, hd_special=None)
- apply_twin_fraction(...)
- apply_twin_fraction( (object)amplitude_data_part_one, (object)amplitude_data_part_two, (float)twin_fraction) -> double :
C++ signature :
scitbx::af::shared<double> apply_twin_fraction(scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,double)
- assert_xray_structures_equal(x1, x2, selection=None, sites=True, adp=True, occupancies=True)
- atom_selection(all_chain_proxies, string, allow_empty_selection=False)
- 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)
- create_twin_mate(...)
- create_twin_mate( (miller_index)miller_indices, (object)twin_law_matrix) -> miller_index :
C++ signature :
scitbx::af::shared<cctbx::miller::index<int> > create_twin_mate(scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor>,scitbx::mat3<double>)
- 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)
- extract_tls_and_u_total_from_pdb(f_obs, r_free_flags, xray_structure, tls_selections, tls_groups)
- fmodel_manager(f_obs, xray_structure=None, r_free_flags=None, f_mask=None, f_calc=None, ignore_r_free_flags=False, target_name='ml', hl_coeff=None, use_f_model_scaled=False, update_xray_structure=True, twin_law=None, detwin_mode=None, detwin_map_types=None, alpha_beta_params=None, sf_and_grads_accuracy_params=<libtbx.phil.scope_extract object at 0x25c7f50>, mask_params=None, max_number_of_resolution_bins=None, log=None)
- fmodel_simple(f_obs, xray_structures=None, r_free_flags=None, target_name='ml', bulk_solvent_and_scaling=True, bss_params=None, mask_params=None, twin_laws=None, skip_twin_detection=False, twin_switch_tolerance=2.0)
- 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, allow_empty_selection=False, hydrogens_only=False, one_selection_array=False)
- list_3d_as_bool_selection(list_3d, size)
- miller_array_symmetry_safety_check(miller_array, data_description, working_point_group, symmetry_safety_check, log)
- model_simple(pdb_file_names, log=None, normalization=True, cif_objects=[], crystal_symmetry=None, plain_pairs_radius=5, refinement_flags=None, use_elbow=True, scattering_table=None, d_min=None)
- occupancy_selections(all_chain_proxies, xray_structure, add_water=False, other_individual_selection_strings=None, other_constrained_groups=None, remove_selection=None, as_flex_arrays=True)
- print_header(line, out=None)
- print_programs_start_header(log, text)
- remove_selections(selection, other, size)
- 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)
- setup_scattering_dictionaries(scattering_table, xray_structure, d_min, log=None, all_chain_proxies=None)
- write_pdb_file(xray_structure, pdb_hierarchy, pdb_atoms=None, write_cryst1_record=True, selection=None, atoms_reset_serial=True, out=None)
- xtriage(f_obs)
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