DENSS

DENSS.__init__

Submodules

• DENSS.denss
  • B2u()
  • NumbaDeprecationWarning
  • NumbaPendingDeprecationWarning
  • P2Rg()
  • PDB
    • PDB.add_ImplicitH()
    • PDB.calculate_distance_matrix()
    • PDB.calculate_unique_volume()
    • PDB.generate_pdb_from_defaults()
    • PDB.lookup_unique_volume()
    • PDB.read_cif()
    • PDB.read_pdb()
    • PDB.remove_atomalt()
    • PDB.remove_atoms_from_object()
    • PDB.remove_by_atomname()
    • PDB.remove_by_atomnum()
    • PDB.remove_by_atomtype()
    • PDB.remove_by_chain()
    • PDB.remove_by_resname()
    • PDB.remove_by_resnum()
    • PDB.remove_waters()
    • PDB.write()
  • PDB2MRC
    • PDB2MRC.calc_F_with_modified_params()
    • PDB2MRC.calc_I_with_modified_params()
    • PDB2MRC.calc_chi2()
    • PDB2MRC.calc_penalty()
    • PDB2MRC.calc_rho_with_modified_params()
    • PDB2MRC.calc_score_with_modified_params()
    • PDB2MRC.calculate_average_radii()
    • PDB2MRC.calculate_excluded_volume()
    • PDB2MRC.calculate_excluded_volume_in_A3()
    • PDB2MRC.calculate_global_B()
    • PDB2MRC.calculate_hydration_shell()
    • PDB2MRC.calculate_invacuo_density()
    • PDB2MRC.calculate_structure_factors()
    • PDB2MRC.initialize_penalties()
    • PDB2MRC.load_data()
    • PDB2MRC.make_grids()
    • PDB2MRC.minimize_parameters()
    • PDB2MRC.run_all()
    • PDB2MRC.save_Iq_calc()
    • PDB2MRC.save_fit()
    • PDB2MRC.scale_radii()
    • PDB2MRC.set_radii()
  • PDB2SAS
    • PDB2SAS.calc_I()
    • PDB2SAS.calc_debye()
    • PDB2SAS.calc_form_factors()
  • Sasrec
    • Sasrec.Bt()
    • Sasrec.Ct()
    • Sasrec.Ct2()
    • Sasrec.Et()
    • Sasrec.Ft()
    • Sasrec.Gmn()
    • Sasrec.I0errf()
    • Sasrec.Icerrt()
    • Sasrec.Ish2I0()
    • Sasrec.Ish2Iq()
    • Sasrec.Ish2P()
    • Sasrec.Ish2Q()
    • Sasrec.Ish2Qr()
    • Sasrec.Ish2Vc()
    • Sasrec.Ish2Vp()
    • Sasrec.Ish2avgr()
    • Sasrec.Ish2lc()
    • Sasrec.Ish2mwVc()
    • Sasrec.Ish2mwVp()
    • Sasrec.Ish2rg()
    • Sasrec.Perrt()
    • Sasrec.Qerrf()
    • Sasrec.St()
    • Sasrec.Vcerrf()
    • Sasrec.Vperrf()
    • Sasrec.Yt()
    • Sasrec.avgrerrf()
    • Sasrec.calc_chi2()
    • Sasrec.create_lowq()
    • Sasrec.estimate_Vp_etal()
    • Sasrec.extrapolate()
    • Sasrec.gamma0()
    • Sasrec.lcerrf()
    • Sasrec.mwVcerrf()
    • Sasrec.mwVperrf()
    • Sasrec.optimize_alpha()
    • Sasrec.rgerrf()
    • Sasrec.rgerrfold()
    • Sasrec.shannon_channels()
    • Sasrec.update()
  • abs2()
  • abs2_fast()
  • align()
  • align2xyz()
  • align_multiple()
  • average_pairs()
  • average_two()
  • binary_average()
  • calc_chi2()
  • calc_fsc()
  • calc_rg_I0_by_guinier()
  • calc_rg_by_guinier_first_2_points()
  • calc_rg_by_guinier_peak()
  • calc_rho0()
  • calc_uniform_shell()
  • cap_heights()
  • center_of_circle_from_sphere_intersection()
  • center_rho()
  • center_rho_roll()
  • check_if_raw_data()
  • chi2()
  • clean_up_data()
  • coarse_then_fine_alignment()
  • create_lowq()
  • denss_3DFs()
  • direct_I2P()
  • ecdf()
  • equation_of_plane_from_sphere_intersection()
  • estimate_dmax()
  • estimate_side_from_pdb()
  • euler2matrix()
  • euler_grid_search()
  • filter_P()
  • find_nearest_i()
  • formfactor()
  • fsc2res()
  • generate_enantiomers()
  • grid_center()
  • inertia_tensor()
  • largest_indices()
  • loadDatFile()
  • loadFitFile()
  • loadOldFitFile()
  • loadOutFile()
  • loadProfile()
  • map
  • minimize_rho()
  • minimize_rho_score()
  • multi_average_two()
  • myabs()
  • mybinmean()
  • mybinmean_optimized()
  • myfftn()
  • myifftn()
  • myirfftn()
  • mylog()
  • mymean()
  • myones()
  • myrfftn()
  • mysqrt()
  • mystd()
  • mysum()
  • myzeros()
  • myzeros_like()
  • object
  • pad_rho()
  • parse_arguments()
  • partial
    • partial.args
    • partial.func
    • partial.keywords
  • pdb2F_multigauss()
  • pdb2F_simple_gauss_by_radius()
  • pdb2map_FFT()
  • pdb2map_multigauss()
  • pdb2map_simple_gauss_by_radius()
  • pdb2support_SES()
  • pdb2support_fast()
  • pdb2support_vdW()
  • principal_axes()
  • principal_axis_alignment()
  • range
    • range.count()
    • range.index()
    • range.start
    • range.step
    • range.stop
  • read_mrc()
  • real_space_correlation_coefficient()
  • realspace_formfactor()
  • realspace_gaussian_formfactor()
  • reciprocalspace_gaussian_formfactor()
  • reconstruct_abinitio_from_scattering_profile()
  • regrid_Iq()
  • rho2rg()
  • rho_overlap_score()
  • rotate_coordinates()
  • running_mean()
  • select_best_enantiomer()
  • select_best_enantiomers()
  • shrinkwrap_by_density_value()
  • shrinkwrap_by_volume()
  • sigmoid()
  • sigmoid_find_x_value_given_y()
  • sphere()
  • sphere_radius_from_volume()
  • sphere_volume_from_radius()
  • spherical_cap_volume()
  • spherical_to_euler()
  • store_parameters_as_string()
  • str
    • str.capitalize()
    • str.casefold()
    • str.center()
    • str.count()
    • str.encode()
    • str.endswith()
    • str.expandtabs()
    • str.find()
    • str.format()
    • str.format_map()
    • str.index()
    • str.isalnum()
    • str.isalpha()
    • str.isascii()
    • str.isdecimal()
    • str.isdigit()
    • str.isidentifier()
    • str.islower()
    • str.isnumeric()
    • str.isprintable()
    • str.isspace()
    • str.istitle()
    • str.isupper()
    • str.join()
    • str.ljust()
    • str.lower()
    • str.lstrip()
    • str.maketrans()
    • str.partition()
    • str.removeprefix()
    • str.removesuffix()
    • str.replace()
    • str.rfind()
    • str.rindex()
    • str.rjust()
    • str.rpartition()
    • str.rsplit()
    • str.rstrip()
    • str.split()
    • str.splitlines()
    • str.startswith()
    • str.strip()
    • str.swapcase()
    • str.title()
    • str.translate()
    • str.upper()
    • str.zfill()
  • transform_rho()
  • u2B()
  • v2B()
  • write_mrc()
  • write_xplor()
  • zip
  • zoom_rho()
  • Submodules
    • DENSS.denss.resources
      • Submodules
    • DENSS.denss.scripts
      • Submodules
  • Submodules
    • DENSS.denss.core
      • B2u()
      • P2Rg()
      • PDB
      • PDB2MRC
      • PDB2SAS
      • Sasrec
      • abs2()
      • abs2_fast()
      • align()
      • align2xyz()
      • align_multiple()
      • average_pairs()
      • average_two()
      • binary_average()
      • calc_chi2()
      • calc_fsc()
      • calc_rg_I0_by_guinier()
      • calc_rg_by_guinier_first_2_points()
      • calc_rg_by_guinier_peak()
      • calc_rho0()
      • calc_uniform_shell()
      • cap_heights()
      • center_of_circle_from_sphere_intersection()
      • center_rho()
      • center_rho_roll()
      • check_if_raw_data()
      • chi2()
      • clean_up_data()
      • coarse_then_fine_alignment()
      • create_lowq()
      • denss_3DFs()
      • direct_I2P()
      • ecdf()
      • equation_of_plane_from_sphere_intersection()
      • estimate_dmax()
      • estimate_side_from_pdb()
      • euler2matrix()
      • euler_grid_search()
      • filter_P()
      • find_nearest_i()
      • formfactor()
      • fsc2res()
      • generate_enantiomers()
      • grid_center()
      • inertia_tensor()
      • largest_indices()
      • loadDatFile()
      • loadFitFile()
      • loadOldFitFile()
      • loadOutFile()
      • loadProfile()
      • minimize_rho()
      • minimize_rho_score()
      • multi_average_two()
      • myabs()
      • mybinmean()
      • mybinmean_optimized()
      • myfftn()
      • myifftn()
      • myirfftn()
      • mylog()
      • mymean()
      • myones()
      • myrfftn()
      • mysqrt()
      • mystd()
      • mysum()
      • myzeros()
      • myzeros_like()
      • pad_rho()
      • pdb2F_multigauss()
      • pdb2F_simple_gauss_by_radius()
      • pdb2map_FFT()
      • pdb2map_multigauss()
      • pdb2map_simple_gauss_by_radius()
      • pdb2support_SES()
      • pdb2support_fast()
      • pdb2support_vdW()
      • principal_axes()
      • principal_axis_alignment()
      • read_mrc()
      • real_space_correlation_coefficient()
      • realspace_formfactor()
      • realspace_gaussian_formfactor()
      • reciprocalspace_gaussian_formfactor()
      • reconstruct_abinitio_from_scattering_profile()
      • regrid_Iq()
      • rho2rg()
      • rho_overlap_score()
      • rotate_coordinates()
      • running_mean()
      • select_best_enantiomer()
      • select_best_enantiomers()
      • shrinkwrap_by_density_value()
      • shrinkwrap_by_volume()
      • sigmoid()
      • sigmoid_find_x_value_given_y()
      • sphere()
      • sphere_radius_from_volume()
      • sphere_volume_from_radius()
      • spherical_cap_volume()
      • spherical_to_euler()
      • transform_rho()
      • u2B()
      • v2B()
      • write_mrc()
      • write_xplor()
      • zoom_rho()
    • DENSS.denss.core-orig
    • DENSS.denss.options
      • parse_arguments()
      • store_parameters_as_string()
    • DENSS.denss.options-orig
• DENSS.resources
  • Submodules
    • DENSS.resources.resources

Submodules

• DENSS.DenssDriver
  • DenssLoghandler
    • DenssLoghandler.emit()
  • UserCancel
  • run_denss()
• DENSS.DenssFitData
  • DenssFitDataDialog
    • DenssFitDataDialog.apply()
    • DenssFitDataDialog.body()
    • DenssFitDataDialog.create_figure()
    • DenssFitDataDialog.get_sasrec()
    • DenssFitDataDialog.show()
  • fit_data_plot()
• DENSS.DenssGui
  • DenssGuiDialog
    • DenssGuiDialog.add_dnd_bind()
    • DenssGuiDialog.apply_fit_data()
    • DenssGuiDialog.ask_cancel()
    • DenssGuiDialog.body()
    • DenssGuiDialog.buttonbox()
    • DenssGuiDialog.create_figure()
    • DenssGuiDialog.denss_fit_data()
    • DenssGuiDialog.denss_thread()
    • DenssGuiDialog.draw_curve()
    • DenssGuiDialog.illustrate_dmax()
    • DenssGuiDialog.is_ready()
    • DenssGuiDialog.ok()
    • DenssGuiDialog.on_fig_dnd()
    • DenssGuiDialog.on_file_entry()
    • DenssGuiDialog.on_folder_entry()
    • DenssGuiDialog.on_input()
    • DenssGuiDialog.prepare_from_args()
    • DenssGuiDialog.run_denss_thread()
    • DenssGuiDialog.show()
    • DenssGuiDialog.show_denss_manager()
    • DenssGuiDialog.show_ed_viewer()
    • DenssGuiDialog.submit_to_denss_manager()
    • DenssGuiDialog.update_button_states()
    • DenssGuiDialog.update_guide_message()
    • DenssGuiDialog.update_progress_text()
  • ProgressLoghandler
    • ProgressLoghandler.emit()
  • StdoutRedirector
    • StdoutRedirector.flush()
    • StdoutRedirector.write()
• DENSS.DenssManager
  • DenssManager
    • DenssManager.accept_job()
    • DenssManager.decide_num_workers()
    • DenssManager.error_callback()
    • DenssManager.success_callback()
    • DenssManager.terminate()
  • JobInfo
  • activate_manager()
  • get_list()
  • get_table()
  • print_table()
  • submit()
  • terminate_manager_impl()
• DENSS.DenssManagerDialog
  • DenssManagerDialog
    • DenssManagerDialog.apply()
    • DenssManagerDialog.body()
    • DenssManagerDialog.buttonbox()
    • DenssManagerDialog.cancel_all_jobs()
    • DenssManagerDialog.cancel_job()
    • DenssManagerDialog.cancel_job_impl()
    • DenssManagerDialog.refresh()
    • DenssManagerDialog.show()
    • DenssManagerDialog.submit_jobs()
    • DenssManagerDialog.update_geometry()
    • DenssManagerDialog.update_table()
  • format_duration()
  • format_time()
  • get_ch2_fg_color()
  • get_state_color()
  • get_state_text()
  • show_manager_dialog()
  • terminate_manager()
• DENSS.DenssUtils
  • fit_data()
  • fit_data_bc()
  • fit_data_impl()
  • get_argparser()
  • get_denss_log_items()
  • get_denssfolder()
  • get_dmax_with_datgnom()
  • get_outfolder()
  • run_denss_impl()
  • run_denss_impl_dummy()
  • run_pdb2mrc()
• DENSS.DmaxDependency
  • collect_dependecy_data()
  • run_datgnom()
  • run_denss_for_survey()
  • run_denss_varying_dmax()
• DENSS.DmaxEstimation
  • demo()
  • estimate_dmax()
  • illustrate_dmax()
  • plot_input()
• DENSS.update-custom-codes
• DENSS.update-denss