cctbx.xray package

Subpackages

• cctbx.xray.observations package
  • Module contents
    • customized_copy()
• cctbx.xray.structure_factors package
  • Submodules
    • cctbx.xray.structure_factors.from_scatterers module
      • from_scatterers
    • cctbx.xray.structure_factors.from_scatterers_direct module
      • from_scatterers_direct
        • from_scatterers_direct.f_calc()
    • cctbx.xray.structure_factors.from_scatterers_direct_parallel module
      • direct_summation_cuda_platform
        • direct_summation_cuda_platform.validate_platform_resources()
      • direct_summation_simple
        • direct_summation_simple.use_alt_parallel
      • fcalc_container
        • fcalc_container.f_calc()
      • pprocess
        • pprocess.prepare_gaussians_symmetries_cell()
        • pprocess.prepare_miller_arrays_for_cuda()
        • pprocess.prepare_scattering_sites_for_cuda()
        • pprocess.print_diagnostics()
        • pprocess.validate_the_inputs()
    • cctbx.xray.structure_factors.from_scatterers_fft module
      • from_scatterers_fft
        • from_scatterers_fft.f_calc()
        • from_scatterers_fft.show_unknown_scatterers()
    • cctbx.xray.structure_factors.global_counters module
      • calls_and_accumulated_time
        • calls_and_accumulated_time.process()
      • show()
    • cctbx.xray.structure_factors.gradient_flags module
      • gradient_flags
    • cctbx.xray.structure_factors.gradients module
      • gradients
    • cctbx.xray.structure_factors.gradients_base module
      • gradients_base
        • gradients_base.check_size()
        • gradients_base.d_target_d_f_calc()
        • gradients_base.d_target_d_fdp()
        • gradients_base.d_target_d_fp()
        • gradients_base.d_target_d_occupancy()
        • gradients_base.d_target_d_u_iso()
        • gradients_base.packed()
    • cctbx.xray.structure_factors.gradients_direct module
      • gradients_direct
        • gradients_direct.d_target_d_site_cart()
        • gradients_direct.d_target_d_site_frac()
        • gradients_direct.d_target_d_u_cart()
        • gradients_direct.d_target_d_u_star()
    • cctbx.xray.structure_factors.gradients_fft module
      • gradients_fft
        • gradients_fft.d_target_d_site_cart()
        • gradients_fft.d_target_d_site_frac()
        • gradients_fft.d_target_d_u_cart()
        • gradients_fft.d_target_d_u_star()
    • cctbx.xray.structure_factors.manager module
      • managed_calculation_base
        • managed_calculation_base.algorithm()
        • managed_calculation_base.manager()
        • managed_calculation_base.miller_set()
        • managed_calculation_base.xray_structure()
      • manager
        • manager.cfft()
        • manager.cos_sin_table()
        • manager.crystal_gridding()
        • manager.d_min()
        • manager.exp_table_one_over_step_size()
        • manager.force_complex()
        • manager.grid_resolution_factor()
        • manager.have_good_timing_estimates()
        • manager.mandatory_grid_factors()
        • manager.max_prime()
        • manager.quality_factor()
        • manager.rfft()
        • manager.sampled_density_must_be_positive()
        • manager.setup_fft()
        • manager.symmetry_flags()
        • manager.tolerance_positive_definite()
        • manager.u_base()
        • manager.wing_cutoff()
    • cctbx.xray.structure_factors.misc module
      • quality_factor_from_any()
  • Module contents
• cctbx.xray.targets package
  • Submodules
    • cctbx.xray.targets.r1 module
      • calc_k()
      • calc_t()
      • target
        • target.gradients_work()
        • target.hessians_work()
        • target.target_work()
  • Module contents
    • shelxl_wght_ls
      • shelxl_wght_ls.gradients_work()
      • shelxl_wght_ls.hessians_work()
      • shelxl_wght_ls.target_work()

Submodules

• cctbx.xray.ext module
• cctbx.xray.minimization module
  • add_gradients()
  • lbfgs
    • lbfgs.apply_shifts()
    • lbfgs.callback_after_step()
    • lbfgs.compute_functional_and_gradients()
    • lbfgs.compute_target()
  • occupancy_penalty_exp
    • occupancy_penalty_exp.functional()
    • occupancy_penalty_exp.gradient()
• cctbx.xray.observation_types module
  • amplitude
  • any
  • intensity
  • reconstructed_amplitude
• cctbx.xray.scatterer module
  • anomalous_scatterer_group
    • anomalous_scatterer_group.copy_to_scatterers_in_place()
    • anomalous_scatterer_group.extract_from_scatterers_in_place()
    • anomalous_scatterer_group.labels_refine()
    • anomalous_scatterer_group.select()
    • anomalous_scatterer_group.show_summary()
  • scatterer
• cctbx.xray.structure module
  • conservative_pair_proxies
  • meaningful_site_cart_differences
    • meaningful_site_cart_differences.max_absolute()
    • meaningful_site_cart_differences.show()
  • scattering_type_registry_params
  • structure
    • structure.add_scatterer()
    • structure.add_scatterers()
    • structure.adjust_occupancy()
    • structure.adjust_u_iso()
    • structure.all_selection()
    • structure.apply_rigid_body_shift()
    • structure.apply_rigid_body_shift_obj()
    • structure.apply_shift()
    • structure.apply_special_position_ops_d_target_d_site()
    • structure.apply_symmetry_sites()
    • structure.apply_symmetry_u_stars()
    • structure.as_cif_block()
    • structure.as_cif_simple()
    • structure.as_emma_model()
    • structure.as_pdb_file()
    • structure.as_py_code()
    • structure.asu_mappings()
    • structure.asymmetric_unit_in_p1()
    • structure.atomic_weights()
    • structure.b_iso_min_max_mean()
    • structure.b_iso_or_b_equiv()
    • structure.by_index_selection()
    • structure.center_of_mass()
    • structure.change_basis()
    • structure.change_hand()
    • structure.closest_distances()
    • structure.concatenate()
    • structure.concatenate_inplace()
    • structure.conservative_pair_proxies()
    • structure.convert_to_anisotropic()
    • structure.convert_to_isotropic()
    • structure.coordinate_degrees_of_freedom_counts()
    • structure.crystal_density()
    • structure.crystal_symmetry()
    • structure.cubic_unit_cell_around_centered_scatterers()
    • structure.customized_copy()
    • structure.deep_copy_scatterers()
    • structure.difference_vectors_cart()
    • structure.discard_scattering_type_registry()
    • structure.distances()
    • structure.element_selection()
    • structure.erase_scatterers()
    • structure.expand_to_p1()
    • structure.extract_u_cart_plus_u_iso()
    • structure.extract_u_iso_or_u_equiv()
    • structure.f_000()
    • structure.from_cif()
    • structure.from_shelx()
    • structure.grads_and_curvs_target_simple()
    • structure.guess_scattering_type_is_a_mixture_of_xray_and_neutron()
    • structure.guess_scattering_type_neutron()
    • structure.hd_selection()
    • structure.intersection_of_scatterers()
    • structure.is_positive_definite_u()
    • structure.is_similar()
    • structure.make_scatterer_labels_shelx_compatible_in_place()
    • structure.max_distance()
    • structure.mean_distance()
    • structure.mean_scattering_density()
    • structure.min_distance()
    • structure.min_u_cart_eigenvalue()
    • structure.n_grad_u_aniso()
    • structure.n_grad_u_iso()
    • structure.n_parameters()
    • structure.n_undefined_multiplicities()
    • structure.non_unit_occupancy_implies_min_distance_sym_equiv_zero()
    • structure.orthorhombic_unit_cell_around_centered_scatterers()
    • structure.pair_asu_table()
    • structure.pair_sym_table_show()
    • structure.pair_sym_table_show_distances()
    • structure.parameter_map()
    • structure.principal_axes_of_inertia()
    • structure.random_remove_sites_selection()
    • structure.random_shift_sites()
    • structure.re_apply_symmetry()
    • structure.replace_scatterers()
    • structure.replace_sites_cart()
    • structure.replace_sites_frac()
    • structure.rms_difference()
    • structure.scale_adp()
    • structure.scale_adps()
    • structure.scatterer_flags()
    • structure.scatterers()
    • structure.scattering_dictionary_as_string()
    • structure.scattering_type_registry()
    • structure.scattering_types()
    • structure.scattering_types_counts_and_occupancy_sums()
    • structure.select()
    • structure.select_inplace()
    • structure.selection_within()
    • structure.set_b_iso()
    • structure.set_custom_inelastic_form_factors()
    • structure.set_fdps()
    • structure.set_fps()
    • structure.set_inelastic_form_factors()
    • structure.set_non_unit_occupancy_implies_min_distance_sym_equiv_zero()
    • structure.set_occupancies()
    • structure.set_scatterer_flags()
    • structure.set_sites_cart()
    • structure.set_sites_frac()
    • structure.set_u_cart()
    • structure.set_u_iso()
    • structure.shake_adp()
    • structure.shake_adp_if_all_equal()
    • structure.shake_fdps()
    • structure.shake_fps()
    • structure.shake_occupancies()
    • structure.shake_sites_in_place()
    • structure.shift_occupancies()
    • structure.shift_sites_in_place()
    • structure.shift_us()
    • structure.show_angles()
    • structure.show_dihedral_angles()
    • structure.show_distances()
    • structure.show_scatterer_flags_summary()
    • structure.show_scatterers()
    • structure.show_special_position_shifts()
    • structure.show_summary()
    • structure.show_u_statistics()
    • structure.site_symmetry_table()
    • structure.sites_cart()
    • structure.sites_frac()
    • structure.sites_mod_positive()
    • structure.sites_mod_short()
    • structure.sort()
    • structure.special_position_indices()
    • structure.structure_factors()
    • structure.switch_to_neutron_scattering_dictionary()
    • structure.tidy_us()
    • structure.translate()
    • structure.truncate_at_pdb_format_precision()
    • structure.unit_cell_content()
    • structure.use_u_aniso()
    • structure.use_u_iso()
• cctbx.xray.target_functors module
  • intensity_correlation
    • intensity_correlation.f_obs()
    • intensity_correlation.use_multiplicities_as_weights()
    • intensity_correlation.weights()
  • least_squares
  • least_squares_residual
  • least_squares_residual_for_amplitude
    • least_squares_residual_for_amplitude.statistical_weighting
    • least_squares_residual_for_amplitude.use_sigmas_as_weights()
  • max_like
  • registry()
  • unified_least_squares_residual
    • unified_least_squares_residual.f_obs()
    • unified_least_squares_residual.obs()
    • unified_least_squares_residual.weighting()
• cctbx.xray.weighting_schemes module
  • amplitude_unit_weighting
    • amplitude_unit_weighting.compute()
  • intensity_quasi_unit_weighting
    • intensity_quasi_unit_weighting.compute()
  • pure_statistical_weighting
    • pure_statistical_weighting.compute()
  • shelx_weighting
    • shelx_weighting.calculated
    • shelx_weighting.compute()
    • shelx_weighting.observed
  • simple_shelx_weighting
    • simple_shelx_weighting.compute()

Module contents