cctbx.examples package

Subpackages

• cctbx.examples.structure_factor_calculus package
  • Submodules
    • cctbx.examples.structure_factor_calculus.site_derivatives module
      • cos_alpha
        • cos_alpha.d2_site()
        • cos_alpha.d_site()
        • cos_alpha.f()
      • d2_cos_alpha_d_site_finite()
      • d_cos_alpha_d_site_finite()
      • exercise()
    • cctbx.examples.structure_factor_calculus.sites_derivatives module
      • cos_alpha
        • cos_alpha.d2_sites()
        • cos_alpha.d_sites()
        • cos_alpha.f()
      • d2_cos_alpha_d_sites_finite()
      • d_cos_alpha_d_sites_finite()
      • exercise()
    • cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives module
      • compare_derivatives()
      • d2_exp_i_hx_d_sites_finite()
      • d_exp_i_hx_d_sites_finite()
      • exercise()
      • exp_i_hx
        • exp_i_hx.d2_sites()
        • exp_i_hx.d2_target_d_sites()
        • exp_i_hx.d_sites()
        • exp_i_hx.d_target_d_sites()
        • exp_i_hx.f()
    • cctbx.examples.structure_factor_calculus.u_star_derivatives module
      • compare_derivatives()
      • d2_debye_waller_d_u_finite()
      • d_debye_waller_d_u_finite()
      • debye_waller
        • debye_waller.d2_u()
        • debye_waller.d_u()
        • debye_waller.f()
      • exercise()
  • Module contents

Submodules

• cctbx.examples.adp_symmetry_constraints module
  • run()
• cctbx.examples.all_axes module
  • list_all_axes()
  • rt_mx_analysis()
  • run()
  • str_ev()
• cctbx.examples.analyze_adp module
  • run()
• cctbx.examples.change_hand_p31 module
  • run()
• cctbx.examples.convert_ccp4_symop_lib module
  • run()
• cctbx.examples.cr2o3_consistency_checks module
  • demo()
• cctbx.examples.cr2o3_primitive_cell module
  • demo()
• cctbx.examples.exp_i_alpha_derivatives module
  • exp_i_alpha_sum
    • exp_i_alpha_sum.d2_alphas()
    • exp_i_alpha_sum.d2_target_d_alphas()
    • exp_i_alpha_sum.d_alphas()
    • exp_i_alpha_sum.d_target_d_alphas()
    • exp_i_alpha_sum.f()
  • least_squares
    • least_squares.da()
    • least_squares.daa()
    • least_squares.dab()
    • least_squares.db()
    • least_squares.dbb()
    • least_squares.f()
• cctbx.examples.f_model_example module
  • f_model_example()
• cctbx.examples.fft_map_electron_density_around_atom module
  • build_xray_structure_with_carbon_along_x()
  • loop_res_fac()
  • rho_stats()
  • run()
• cctbx.examples.find_distances_using_cpp_objects module
  • find_distances()
  • run()
• cctbx.examples.find_sys_abs_equiv_space_groups module
  • run()
• cctbx.examples.g_exp_i_alpha_derivatives module
  • curvatures
  • g_exp_i_alpha_sum
    • g_exp_i_alpha_sum.d2_params()
    • g_exp_i_alpha_sum.d2_target_d_params()
    • g_exp_i_alpha_sum.d_params()
    • g_exp_i_alpha_sum.d_target_d_params()
    • g_exp_i_alpha_sum.f()
  • gradients
  • pack_gradients()
  • pack_parameters()
  • parameters
    • parameters.as_list()
• cctbx.examples.g_exp_i_partial_derivatives module
  • empirical_proof()
  • exercise()
• cctbx.examples.getting_started module
  • run()
• cctbx.examples.hirshfeld_test module
  • run()
• cctbx.examples.le_page_1982_vs_lebedev_2005 module
  • enumerate_reduced_cell_two_folds()
  • run()
  • sample()
• cctbx.examples.lebedev_2005_perturbation module
  • run()
• cctbx.examples.list_non_principal_continuous_shifts module
  • run()
• cctbx.examples.location_part module
  • a_theorem_in_primitive_settings
    • a_theorem_in_primitive_settings.on_new_space_group()
    • a_theorem_in_primitive_settings.on_new_symmetry()
    • a_theorem_in_primitive_settings.verify()
  • run()
  • symmetries_with_both_nonzero_location_and_intrinsic_parts
    • symmetries_with_both_nonzero_location_and_intrinsic_parts.on_new_symmetry()
  • symmetries_with_nonzero_location_parts
    • symmetries_with_nonzero_location_parts.browse()
    • symmetries_with_nonzero_location_parts.on_new_space_group()
    • symmetries_with_nonzero_location_parts.on_new_symmetry()
• cctbx.examples.map_skewness module
  • randomize_phases()
  • run()
  • skewness_calculation()
• cctbx.examples.maximum_subgroups module
  • create_all_subgroups()
  • get_maximal_subgroup()
  • reverse_dict()
  • run_all()
  • run_single()
• cctbx.examples.miller_common_sets module
  • demo()
• cctbx.examples.miller_transform module
  • exercise()
  • run()
• cctbx.examples.neutron_structure_factors module
  • run()
• cctbx.examples.phase_o_phrenia module
  • calculate_exp_i_two_phi_peaks()
  • peak_cluster_reduction()
• cctbx.examples.quartz_structure module
  • run()
• cctbx.examples.random_f_calc module
  • generate_random_f_calc()
  • run()
• cctbx.examples.random_puckers module
  • pentagon_sites_cart()
  • run()
• cctbx.examples.reduced_cell_two_folds module
  • run()
• cctbx.examples.site_symmetry_constraints module
  • run()
• cctbx.examples.site_symmetry_table module
  • demo()
• cctbx.examples.space_group_matrices module
  • run()
• cctbx.examples.space_subgroups module
  • loop_over_super_cells()
  • run()
• cctbx.examples.steve_collins module
  • examples()
• cctbx.examples.structure_factor_derivatives module
  • curvatures
  • gradients
  • pack_gradients()
  • pack_parameters()
  • parameters
    • parameters.as_g_alpha()
    • parameters.as_list()
  • structure_factor
    • structure_factor.as_exp_i_sum()
    • structure_factor.d2_g_alpha_d_params()
    • structure_factor.d2_target_d_params()
    • structure_factor.d_g_alpha_d_params()
    • structure_factor.d_target_d_params()
    • structure_factor.f()
• cctbx.examples.structure_factor_derivatives_2 module
  • curvatures
  • gradients
  • pack_gradients()
  • scatterer_as_g_alpha()
  • scatterer_as_list()
  • scatterer_from_list()
  • structure_factor
    • structure_factor.as_exp_i_sum()
    • structure_factor.d2_g_alpha_d_params()
    • structure_factor.d2_target_d_params()
    • structure_factor.d_g_alpha_d_params()
    • structure_factor.d_target_d_params()
    • structure_factor.f()
  • structure_factors
    • structure_factors.d2_target_d_params()
    • structure_factors.d_target_d_params()
    • structure_factors.f()
    • structure_factors.fs()
• cctbx.examples.structure_factor_derivatives_3 module
  • gradients
  • pack_gradients()
  • scatterer_as_list()
  • scatterer_from_list()
  • structure_factor
    • structure_factor.d2_target_d_params()
    • structure_factor.d2f_d_params()
    • structure_factor.d_target_d_params()
    • structure_factor.df_d_params()
    • structure_factor.f()
  • structure_factors
    • structure_factors.d2_target_d_params()
    • structure_factors.d_target_d_params()
    • structure_factors.f()
    • structure_factors.fs()
• cctbx.examples.structure_factor_derivatives_4 module
  • structure_factor
    • structure_factor.d2_target_d_params()
    • structure_factor.d2_target_d_params_diag()
    • structure_factor.d2f_d_params()
    • structure_factor.d2f_d_params_diag()
    • structure_factor.d_target_d_params()
    • structure_factor.df_d_params()
    • structure_factor.f()
  • structure_factors
    • structure_factors.d2_target_d_params()
    • structure_factors.d2_target_d_params_diag()
    • structure_factors.d2_target_d_params_diag_cpp()
    • structure_factors.d_target_d_params()
    • structure_factors.f()
    • structure_factors.fs()
• cctbx.examples.sub_group_graph module
  • run()
• cctbx.examples.symops_530 module
  • run()
• cctbx.examples.trigonal_r_vs_tetragonal_i module
  • run()
• cctbx.examples.unit_cell_minimizers module
  • gradients()
  • hessian()
  • refinery
    • refinery.functional()
    • refinery.gradients()
    • refinery.hessian()
    • refinery.run_lbfgs_raw()
    • refinery.run_lbfgsb()
    • refinery.unit_cell()
  • residual()
  • run()
  • show_fit()
• cctbx.examples.unit_cell_refinement module
  • gradients()
  • refinery
    • refinery.callback_after_step()
    • refinery.compute_functional_and_gradients()
    • refinery.unit_cell()
  • residual()
  • run()
  • show_fit()
• cctbx.examples.view_fft_map module

Module contents