ihm_validation

• ihm_validation package
  • Submodules
  • ihm_validation.cx module
    • CxValidation
      • CxValidation.ID
      • CxValidation.assign_ertypes()
      • CxValidation.assign_rtdtypes()
      • CxValidation.check_conditional_flag()
      • CxValidation.driver
      • CxValidation.format_pct_count()
      • CxValidation.get_best_distance_per_restraint()
      • CxValidation.get_best_distances_per_model_group()
      • CxValidation.get_cx_data()
      • CxValidation.get_ertype()
      • CxValidation.get_ertypes()
      • CxValidation.get_ertypes_df()
      • CxValidation.get_ertypes_df_html()
      • CxValidation.get_measured_restraints()
      • CxValidation.get_models()
      • CxValidation.get_number_of_restraint_groups()
      • CxValidation.get_number_of_restraints()
      • CxValidation.get_per_model_satifaction_rates()
      • CxValidation.get_pride_data()
      • CxValidation.get_pride_ids()
      • CxValidation.get_pyhmmer_version()
      • CxValidation.get_raw_restraints()
      • CxValidation.get_residue_pairs_pride()
      • CxValidation.get_restraint_group_chain_type()
      • CxValidation.get_restraint_group_entity_type()
      • CxValidation.get_rtdtype()
      • CxValidation.get_rtdtypes()
      • CxValidation.get_sequences_pride()
      • CxValidation.get_stats_per_model_group()
      • CxValidation.is_restraint_group_satisfied()
      • CxValidation.measure_restraint()
      • CxValidation.plot_distograms_per_model_group()
      • CxValidation.plot_satisfaction_per_ensemble()
      • CxValidation.process_restraint_groups()
      • CxValidation.pyhmmer_alignment_to_map()
      • CxValidation.quality_check()
      • CxValidation.request_pride()
      • CxValidation.save_plots()
      • CxValidation.select_atom_by_asym_id_seq_id_atom_id()
      • CxValidation.validate_all_pride_data()
      • CxValidation.validate_pride_data()
  • ihm_validation.em module
    • EMValidation
      • EMValidation.ID
      • EMValidation.VA_TIMEOUT
      • EMValidation.driver
      • EMValidation.get_chimera_version()
      • EMValidation.get_chimerax_version()
      • EMValidation.get_em_reconstruction_method()
      • EMValidation.get_emdb_data()
      • EMValidation.get_emdb_ids()
      • EMValidation.get_emdb_map()
      • EMValidation.get_emdb_map_images()
      • EMValidation.get_emdb_map_metadata()
      • EMValidation.get_emdb_map_validation()
      • EMValidation.get_emdb_numerical_code()
      • EMValidation.get_level_from_primary_contour()
      • EMValidation.get_map_image()
      • EMValidation.get_mapq_version()
      • EMValidation.get_resolution_estimates()
      • EMValidation.get_va_version()
      • EMValidation.request_emdb()
      • EMValidation.run_va()
      • EMValidation.save_plots()
      • EMValidation.validate_all_emdb_data()
      • EMValidation.validate_emdb_data()
  • ihm_validation.excludedvolume module
    • GetExcludedVolume
      • GetExcludedVolume.get_all_spheres()
      • GetExcludedVolume.get_excluded_volume()
      • GetExcludedVolume.get_nCr()
      • GetExcludedVolume.get_radii()
      • GetExcludedVolume.get_violation_dict()
      • GetExcludedVolume.get_violation_percentage()
      • GetExcludedVolume.get_xyzr()
  • ihm_validation.format_checker module
    • check_all_exception()
    • check_all_log()
    • check_entities_histidines()
    • check_file_exception()
    • check_file_log()
    • check_models()
    • parse_ihm_cif()
  • ihm_validation.futures module
    • CXMSValidator
      • CXMSValidator.ertypes
      • CXMSValidator.ertypes_df
      • CXMSValidator.load_restraint()
      • CXMSValidator.number_of_restraint_groups
      • CXMSValidator.number_of_restraints
      • CXMSValidator.rtdtypes
      • CXMSValidator.validate_ensemble()
      • CXMSValidator.validate_model()
    • StereoChemistryValidator
      • StereoChemistryValidator.validate_model()
    • Validator
      • Validator.dataset
      • Validator.load_restraint()
      • Validator.restraint
      • Validator.validate_ensemble()
      • Validator.validate_model()
    • get_hierarchy_from_atoms()
    • get_hierarchy_from_model()
    • is_model_atomic()
    • is_model_cg()
    • is_model_mixed()
  • ihm_validation.generate_static_html_pages module
    • createdirs()
    • write_html()
  • ihm_validation.get_plots module
    • Plots
      • Plots.plot_quality_at_glance()
      • Plots.save_plots()
  • ihm_validation.ihm_validator module
    • createdirs()
    • load_json_plot()
    • write_html()
    • write_json()
    • write_pdf()
    • write_supplementary_table()
  • ihm_validation.images module
  • ihm_validation.mmcif_io module
    • GetInputInformation
      • GetInputInformation.atomic
      • GetInputInformation.cg
      • GetInputInformation.check_ensembles()
      • GetInputInformation.check_for_em()
      • GetInputInformation.check_sphere()
      • GetInputInformation.dataset_id_type_dic()
      • GetInputInformation.delete_extra_loops()
      • GetInputInformation.deposition_date
      • GetInputInformation.get_RB_flex_dict()
      • GetInputInformation.get_all_asym()
      • GetInputInformation.get_assembly_ID_of_models()
      • GetInputInformation.get_atomic_coverage()
      • GetInputInformation.get_authors()
      • GetInputInformation.get_chain_subunit_dict()
      • GetInputInformation.get_composition()
      • GetInputInformation.get_databases()
      • GetInputInformation.get_dataset_comp()
      • GetInputInformation.get_dataset_details()
      • GetInputInformation.get_dataset_dict()
      • GetInputInformation.get_dataset_length()
      • GetInputInformation.get_dataset_xl_info()
      • GetInputInformation.get_empty_chain_dict()
      • GetInputInformation.get_ensembles()
      • GetInputInformation.get_file_id()
      • GetInputInformation.get_id()
      • GetInputInformation.get_model_assem_dict()
      • GetInputInformation.get_model_id_column()
      • GetInputInformation.get_model_names()
      • GetInputInformation.get_model_rep_dict()
      • GetInputInformation.get_number_of_assemblies()
      • GetInputInformation.get_number_of_chains()
      • GetInputInformation.get_number_of_entities()
      • GetInputInformation.get_number_of_models()
      • GetInputInformation.get_pdb_dev_id()
      • GetInputInformation.get_pdb_id()
      • GetInputInformation.get_primary_citation_info()
      • GetInputInformation.get_protocol_number()
      • GetInputInformation.get_ranked_id_list()
      • GetInputInformation.get_representation()
      • GetInputInformation.get_representation_ID_of_models()
      • GetInputInformation.get_representation_details()
      • GetInputInformation.get_representation_info()
      • GetInputInformation.get_representation_scale()
      • GetInputInformation.get_residues()
      • GetInputInformation.get_residues_subunit_dict()
      • GetInputInformation.get_restraints()
      • GetInputInformation.get_sampling()
      • GetInputInformation.get_software_comp()
      • GetInputInformation.get_software_length()
      • GetInputInformation.get_struc_title()
      • GetInputInformation.has_crosslinking_ms_dataset
      • GetInputInformation.has_em_dataset
      • GetInputInformation.has_sas_dataset
      • GetInputInformation.mmcif_get_lists()
      • GetInputInformation.nocache
      • GetInputInformation.num_models
      • GetInputInformation.pretty_print_scale()
      • GetInputInformation.read_all_references()
      • GetInputInformation.remove_flr()
      • GetInputInformation.sequences
    • IHMVAvailableModes
      • IHMVAvailableModes.DEVELOPMENT
      • IHMVAvailableModes.PRODUCTION
    • get_operational_mode()
  • ihm_validation.molprobity module
    • AtomSiteVariant
      • AtomSiteVariant.get_dumpers()
    • GetMolprobityInformation
      • GetMolprobityInformation.convert
      • GetMolprobityInformation.data
      • GetMolprobityInformation.get_internal_version()
      • GetMolprobityInformation.get_mp_data()
      • GetMolprobityInformation.get_mq_plot_data()
      • GetMolprobityInformation.get_summary_table_stats()
      • GetMolprobityInformation.models
      • GetMolprobityInformation.molprobity_version
      • GetMolprobityInformation.run_molprobity()
      • GetMolprobityInformation.summarize_angles()
      • GetMolprobityInformation.summarize_bonds()
      • GetMolprobityInformation.summarize_clashes()
      • GetMolprobityInformation.summarize_clashscores()
      • GetMolprobityInformation.summarize_mp_data()
      • GetMolprobityInformation.summarize_rama_rota()
      • GetMolprobityInformation.summarize_rama_rota_stats()
      • GetMolprobityInformation.verify_molprobity_installation()
    • MyModelDumper
      • MyModelDumper.dump()
      • MyModelDumper.dump_atoms()
      • MyModelDumper.model_id
  • ihm_validation.molprobity_convert module
    • get_atom_tuple()
    • rota_rama_result_to_tuple()
  • ihm_validation.precision module
    • PRISM
      • PRISM.data
      • PRISM.get_data()
      • PRISM.get_plots()
      • PRISM.prism_version
      • PRISM.pymol_version
      • PRISM.timeout
  • ihm_validation.report module
    • WriteReport
      • WriteReport.clean()
      • WriteReport.create_webdriver()
      • WriteReport.run_cx_validation()
      • WriteReport.run_cx_validation_plots()
      • WriteReport.run_em_validation()
      • WriteReport.run_entry_composition()
      • WriteReport.run_model_quality()
      • WriteReport.run_prism()
      • WriteReport.run_quality_glance()
      • WriteReport.run_sas_validation()
      • WriteReport.run_sas_validation_plots()
      • WriteReport.run_supplementary_table()
  • ihm_validation.sas module
    • SasValidation
      • SasValidation.check_sascif_dicts()
      • SasValidation.findMinDiff()
      • SasValidation.get_Guinier_data()
      • SasValidation.get_atsas_version()
      • SasValidation.get_fit_data()
      • SasValidation.get_fit_r2()
      • SasValidation.get_fits_for_plot()
      • SasValidation.get_intensities()
      • SasValidation.get_number_of_fits()
      • SasValidation.get_parameters_mw_many()
      • SasValidation.get_parameters_vol_many()
      • SasValidation.get_pddf()
      • SasValidation.get_pddf_info()
      • SasValidation.get_pofr()
      • SasValidation.get_pofr_errors()
      • SasValidation.get_pofr_ext()
      • SasValidation.get_pvals()
      • SasValidation.get_rg_and_io()
      • SasValidation.get_rg_for_plot()
      • SasValidation.get_rg_table_many()
      • SasValidation.get_sas_ids()
      • SasValidation.get_sasbdb_ids()
      • SasValidation.get_sascif_dicts()
      • SasValidation.get_sascif_file()
      • SasValidation.get_sasdb_code_fits()
      • SasValidation.get_scan_unit_mult()
      • SasValidation.get_total_number_of_fits()
      • SasValidation.modify_intensity()
  • ihm_validation.sas_plots module
    • SasValidationPlots
      • SasValidationPlots.Guinier_plot_fit_rwt()
      • SasValidationPlots.plot_Guinier()
      • SasValidationPlots.plot_fit_rwt()
      • SasValidationPlots.plot_fits()
      • SasValidationPlots.plot_intensities()
      • SasValidationPlots.plot_intensities_log()
      • SasValidationPlots.plot_kratky()
      • SasValidationPlots.plot_multiple()
      • SasValidationPlots.plot_pddf()
      • SasValidationPlots.plot_pddf_int_rwt()
      • SasValidationPlots.plot_pf()
      • SasValidationPlots.plot_porod_debye()
      • SasValidationPlots.save_plots()
      • SasValidationPlots.set_plot_style()
  • ihm_validation.utility module
    • all_same()
    • calc_optimal_range()
    • cat_list_string()
    • check_for_dataset_type()
    • clean_all()
    • compress_cx_stats()
    • dict_to_JSlist()
    • dict_to_JSlist_rows()
    • encode_img()
    • format_RB_text()
    • format_flex_text()
    • format_list_text()
    • format_range()
    • format_tuple()
    • format_wwpdb_id()
    • format_wwpdb_url()
    • get_RB()
    • get_all_files()
    • get_alphafolddb_link()
    • get_bead_size()
    • get_copy()
    • get_cx_data_fits()
    • get_datasets()
    • get_datasets_summary()
    • get_flex()
    • get_hierarchy_from_atoms()
    • get_hierarchy_from_model()
    • get_key_from_val()
    • get_larget_assembly_model()
    • get_method_name()
    • get_method_type()
    • get_name()
    • get_output_file_html()
    • get_output_file_json()
    • get_output_file_pdf()
    • get_output_file_temp_html()
    • get_python_ihm_version()
    • get_restraints_info()
    • get_rg_data()
    • get_rg_data_fits()
    • get_software()
    • get_subunits()
    • get_supp_file_html()
    • get_supp_file_pdf()
    • get_unique_datasets()
    • get_val_from_key()
    • is_atomic()
    • is_cg()
    • islistempty()
    • load_img()
    • mp_readable_format()
    • order_of_magnitude()
    • parse_ihm_cif()
    • pretty_print_representations()
    • ranges()
    • runInParallel()
    • runInParallel_noargs()
    • summarize_entities()
    • summarize_segments()
    • timeout
      • timeout.handle_timeout()
  • Module contents