cctbx.omz package

Submodules

• cctbx.omz.bfgs module
  • b_update()
  • h0_scaling()
  • h_update()
  • hg_two_loop_recursion()
  • memory_element
    • memory_element.get()
    • memory_element.rho
    • memory_element.s
    • memory_element.y
• cctbx.omz.cif_refine module
  • extract_from_cif_files
    • extract_from_cif_files.c_obs
    • extract_from_cif_files.edge_list
    • extract_from_cif_files.init_slots_with_none()
    • extract_from_cif_files.non_hydrogen_iselection
    • extract_from_cif_files.non_hydrogen_selection
    • extract_from_cif_files.process()
    • extract_from_cif_files.process_geom_bond()
    • extract_from_cif_files.xray_structure
  • report_fraction_of_negative_observations_if_any()
  • run()
• cctbx.omz.cod_refine module
  • get_master_phil()
  • process()
  • process_continue()
  • remove_tmp_files()
  • run()
  • run_shelx76()
  • run_shelxl()
  • run_smtbx_ls()
  • shelxl_weights()
  • shelxl_weights_a_b()
  • show_cc_r1()
• cctbx.omz.cod_select_and_pickle module
  • cod_data
    • cod_data.c_obs
    • cod_data.cod_id
    • cod_data.edge_list
    • cod_data.f_obs_and_f_calc_agree_well()
    • cod_data.have_bad_sigmas()
    • cod_data.have_close_contacts()
    • cod_data.have_redundant_data()
    • cod_data.have_shelxl_compatible_scattering_types()
    • cod_data.have_sys_absent()
    • cod_data.have_zero_occupancies()
    • cod_data.is_useful()
    • cod_data.non_hydrogen_iselection
    • cod_data.non_hydrogen_selection
    • cod_data.quick_info()
    • cod_data.xray_structure
  • run()
• cctbx.omz.dev module
  • delta_estimation_minus_cos()
  • dynamic_shift_limit_site
    • dynamic_shift_limit_site.pair()
    • dynamic_shift_limit_site.width
  • dynamic_shift_limit_u_iso
    • dynamic_shift_limit_u_iso.d_min
    • dynamic_shift_limit_u_iso.pair()
  • get_master_phil()
  • refinement
    • refinement.approx_curvs()
    • refinement.build_bfgs_memory()
    • refinement.calc_shelxl_wght_ls()
    • refinement.calc_weights_if_needed()
    • refinement.callback_after_step()
    • refinement.classic_lbfgs()
    • refinement.compute_functional_and_gradients()
    • refinement.compute_step()
    • refinement.compute_step_just_grads()
    • refinement.compute_step_using_curvs()
    • refinement.developmental_algorithms()
    • refinement.format_rms_info()
    • refinement.get_active_infos()
    • refinement.get_f_calc()
    • refinement.get_f_cbs()
    • refinement.get_rms_info()
    • refinement.lbfgs_emulation()
    • refinement.line_search()
    • refinement.pack_variables()
    • refinement.plot_samples()
    • refinement.plot_samples_ix()
    • refinement.r1_factor()
    • refinement.setup_bulk_solvent_correction()
    • refinement.show_dests()
    • refinement.show_rms_info()
    • refinement.update_dests_using_bfgs_formula()
    • refinement.update_fgc()
  • run_refinement()
  • shift_limit_pair
    • shift_limit_pair.curv_est_factor
    • shift_limit_pair.curv_est_shift()
    • shift_limit_pair.get()
    • shift_limit_pair.neg
    • shift_limit_pair.pos
  • sign0()
  • xfgc_info
    • xfgc_info.approx_quads
    • xfgc_info.check_strong_wolfe()
    • xfgc_info.curvs
    • xfgc_info.funcl
    • xfgc_info.grads
    • xfgc_info.is_iterate
    • xfgc_info.x
• cctbx.omz.eval_iso_vs_refined module
  • eval_logs()
  • run()
• cctbx.omz.pdb_dev module
  • process()
  • run()
• cctbx.omz.tardy_adaptor module
  • potential_object
    • potential_object.e_pot()
  • sample_e_pot()

Module contents

omz = unique spelling of optimization