Index

A

all_same() (in module ihm_validation.utility) assign_ertypes() (ihm_validation.cx.CxValidation method)

assign_rtdtypes() (ihm_validation.cx.CxValidation method) atomic (ihm_validation.mmcif_io.GetInputInformation property) AtomSiteVariant (class in ihm_validation.molprobity)

C

calc_optimal_range() (in module ihm_validation.utility) cat_list_string() (in module ihm_validation.utility) cg (ihm_validation.mmcif_io.GetInputInformation property) check_all_exception() (in module ihm_validation.format_checker) check_all_log() (in module ihm_validation.format_checker) check_atom_names_chimerax() (in module ihm_validation.format_checker) check_conditional_flag() (ihm_validation.cx.CxValidation method) check_ensembles() (ihm_validation.mmcif_io.GetInputInformation method) check_entities_histidines() (in module ihm_validation.format_checker) check_file_exception() (in module ihm_validation.format_checker) check_file_format() (in module ihm_validation.format_checker) check_file_log() (in module ihm_validation.format_checker)

check_for_dataset_type() (in module ihm_validation.utility) check_for_em() (ihm_validation.mmcif_io.GetInputInformation method) check_models() (in module ihm_validation.format_checker) check_sascif_dicts() (ihm_validation.sas.SasValidation method) check_sphere() (ihm_validation.mmcif_io.GetInputInformation method) clean() (ihm_validation.report.WriteReport method) clean_all() (in module ihm_validation.utility) compress_cx_stats() (in module ihm_validation.utility) convert (ihm_validation.molprobity.GetMolprobityInformation attribute) createdirs() (in module ihm_validation.generate_static_html_pages) (in module ihm_validation.ihm_validator) CXMSValidator (class in ihm_validation.futures) CxValidation (class in ihm_validation.cx)

D

data (ihm_validation.molprobity.GetMolprobityInformation attribute) (ihm_validation.precision.PRISM attribute) dataset (ihm_validation.futures.Validator attribute) dataset_id_type_dic() (ihm_validation.mmcif_io.GetInputInformation method) delete_extra_loops() (ihm_validation.mmcif_io.GetInputInformation method) deposition_date (ihm_validation.mmcif_io.GetInputInformation property)

detect_format() (in module ihm_validation.format_checker) DEVELOPMENT (ihm_validation.mmcif_io.IHMVAvailableModes attribute) dict_to_JSlist() (in module ihm_validation.utility) dict_to_JSlist_rows() (in module ihm_validation.utility) dump() (ihm_validation.molprobity.MyModelDumper method) dump_atoms() (ihm_validation.molprobity.MyModelDumper method)

E

EMValidation (class in ihm_validation.em) encode_img() (in module ihm_validation.utility)

ertypes (ihm_validation.futures.CXMSValidator property) ertypes_df (ihm_validation.futures.CXMSValidator property)

F

FileFormat (class in ihm_validation.format_checker) findMinDiff() (ihm_validation.sas.SasValidation method) format_flex_text() (in module ihm_validation.utility) format_list_text() (in module ihm_validation.utility) format_pct_count() (ihm_validation.cx.CxValidation static method) format_pdb_dev_id() (in module ihm_validation.utility)

format_pdb_id() (in module ihm_validation.utility) format_pdbx_id() (in module ihm_validation.utility) format_range() (in module ihm_validation.utility) format_RB_text() (in module ihm_validation.utility) format_tuple() (in module ihm_validation.utility) format_wwpdb_url() (in module ihm_validation.utility)

G

get_all_asym() (ihm_validation.mmcif_io.GetInputInformation method) get_all_files() (in module ihm_validation.utility) get_all_spheres() (ihm_validation.excludedvolume.GetExcludedVolume method) get_alphafolddb_link() (in module ihm_validation.utility) get_assembly_ID_of_models() (ihm_validation.mmcif_io.GetInputInformation method) get_atom_tuple() (in module ihm_validation.molprobity_convert) get_atomic_coverage() (ihm_validation.mmcif_io.GetInputInformation method) get_atsas_version() (ihm_validation.sas.SasValidation method) get_authors() (ihm_validation.mmcif_io.GetInputInformation method) get_bead_size() (in module ihm_validation.utility) get_best_distance_per_restraint() (ihm_validation.cx.CxValidation method) get_best_distances_per_model_group() (ihm_validation.cx.CxValidation method) get_chain_subunit_dict() (ihm_validation.mmcif_io.GetInputInformation method) get_chimera_version() (ihm_validation.em.EMValidation static method) get_chimerax_version() (ihm_validation.em.EMValidation static method) get_composition() (ihm_validation.mmcif_io.GetInputInformation method) get_copy() (in module ihm_validation.utility) get_cx_data() (ihm_validation.cx.CxValidation method) get_cx_data_fits() (in module ihm_validation.utility) get_data() (ihm_validation.precision.PRISM method) get_databases() (ihm_validation.mmcif_io.GetInputInformation method) get_dataset_comp() (ihm_validation.mmcif_io.GetInputInformation method) get_dataset_details() (ihm_validation.mmcif_io.GetInputInformation method) get_dataset_dict() (ihm_validation.mmcif_io.GetInputInformation method) get_dataset_length() (ihm_validation.mmcif_io.GetInputInformation method) get_dataset_xl_info() (ihm_validation.mmcif_io.GetInputInformation method) get_datasets() (in module ihm_validation.utility) get_datasets_summary() (in module ihm_validation.utility) get_dumpers() (ihm_validation.molprobity.AtomSiteVariant method) get_em_reconstruction_method() (ihm_validation.em.EMValidation static method) get_emdb_data() (ihm_validation.em.EMValidation method) get_emdb_ids() (ihm_validation.em.EMValidation method) get_emdb_map() (ihm_validation.em.EMValidation method) get_emdb_map_images() (ihm_validation.em.EMValidation method) get_emdb_map_metadata() (ihm_validation.em.EMValidation method) get_emdb_map_validation() (ihm_validation.em.EMValidation method) get_emdb_numerical_code() (ihm_validation.em.EMValidation static method) get_empty_chain_dict() (ihm_validation.mmcif_io.GetInputInformation method) get_ensembles() (ihm_validation.mmcif_io.GetInputInformation method) get_ertype() (ihm_validation.cx.CxValidation method) get_ertypes() (ihm_validation.cx.CxValidation method) get_ertypes_df() (ihm_validation.cx.CxValidation method) get_ertypes_df_html() (ihm_validation.cx.CxValidation method) get_excluded_volume() (ihm_validation.excludedvolume.GetExcludedVolume method) get_file_id() (ihm_validation.mmcif_io.GetInputInformation method) get_fit_data() (ihm_validation.sas.SasValidation method) get_fit_r2() (ihm_validation.sas.SasValidation method) get_fits_for_plot() (ihm_validation.sas.SasValidation method) get_flex() (in module ihm_validation.utility) get_Guinier_data() (ihm_validation.sas.SasValidation method) get_hierarchy_from_atoms() (in module ihm_validation.futures) (in module ihm_validation.utility) get_hierarchy_from_model() (in module ihm_validation.futures) (in module ihm_validation.utility) get_id() (ihm_validation.mmcif_io.GetInputInformation method) get_intensities() (ihm_validation.sas.SasValidation method) get_internal_version() (ihm_validation.molprobity.GetMolprobityInformation method) get_key_from_val() (in module ihm_validation.utility) get_level_from_primary_contour() (ihm_validation.em.EMValidation static method) get_map_image() (ihm_validation.em.EMValidation method) get_mapq_version() (ihm_validation.em.EMValidation static method) get_measured_restraints() (ihm_validation.cx.CxValidation method) get_method_name() (in module ihm_validation.utility) get_method_type() (in module ihm_validation.utility) get_model_assem_dict() (ihm_validation.mmcif_io.GetInputInformation method) get_model_id_column() (ihm_validation.mmcif_io.GetInputInformation method) get_model_names() (ihm_validation.mmcif_io.GetInputInformation method) get_model_rep_dict() (ihm_validation.mmcif_io.GetInputInformation method) get_models() (ihm_validation.cx.CxValidation method) get_mp_data() (ihm_validation.molprobity.GetMolprobityInformation method) get_mq_plot_data() (ihm_validation.molprobity.GetMolprobityInformation method) get_name() (in module ihm_validation.utility) get_nCr() (ihm_validation.excludedvolume.GetExcludedVolume method) get_number_of_assemblies() (ihm_validation.mmcif_io.GetInputInformation method) get_number_of_chains() (ihm_validation.mmcif_io.GetInputInformation method) get_number_of_entities() (ihm_validation.mmcif_io.GetInputInformation method) get_number_of_fits() (ihm_validation.sas.SasValidation method) get_number_of_models() (ihm_validation.mmcif_io.GetInputInformation method)

get_number_of_restraint_groups() (ihm_validation.cx.CxValidation method) get_number_of_restraints() (ihm_validation.cx.CxValidation method) get_operational_mode() (in module ihm_validation.mmcif_io) get_output_file_html() (in module ihm_validation.utility) get_output_file_json() (in module ihm_validation.utility) get_output_file_pdf() (in module ihm_validation.utility) get_output_file_temp_html() (in module ihm_validation.utility) get_parameters_mw_many() (ihm_validation.sas.SasValidation method) get_parameters_vol_many() (ihm_validation.sas.SasValidation method) get_pdb_dev_id() (ihm_validation.mmcif_io.GetInputInformation method) get_pdb_id() (ihm_validation.mmcif_io.GetInputInformation method) get_pdbx_id() (ihm_validation.mmcif_io.GetInputInformation method) get_pddf() (ihm_validation.sas.SasValidation method) get_pddf_info() (ihm_validation.sas.SasValidation method) get_per_model_satifaction_rates() (ihm_validation.cx.CxValidation method) get_plots() (ihm_validation.precision.PRISM method) get_pofr() (ihm_validation.sas.SasValidation method) get_pofr_errors() (ihm_validation.sas.SasValidation method) get_pofr_ext() (ihm_validation.sas.SasValidation method) get_pride_data() (ihm_validation.cx.CxValidation method) get_pride_ids() (ihm_validation.cx.CxValidation method) get_primary_citation_info() (ihm_validation.mmcif_io.GetInputInformation method) get_protocol_number() (ihm_validation.mmcif_io.GetInputInformation method) get_pvals() (ihm_validation.sas.SasValidation method) get_pyhmmer_version() (ihm_validation.cx.CxValidation static method) get_python_ihm_version() (in module ihm_validation.utility) get_radii() (ihm_validation.excludedvolume.GetExcludedVolume static method) get_ranked_id_list() (ihm_validation.mmcif_io.GetInputInformation method) get_raw_restraints() (ihm_validation.cx.CxValidation method) get_RB() (in module ihm_validation.utility) get_RB_flex_dict() (ihm_validation.mmcif_io.GetInputInformation method) get_representation() (ihm_validation.mmcif_io.GetInputInformation method) get_representation_details() (ihm_validation.mmcif_io.GetInputInformation method) get_representation_ID_of_models() (ihm_validation.mmcif_io.GetInputInformation method) get_representation_info() (ihm_validation.mmcif_io.GetInputInformation method) get_representation_scale() (ihm_validation.mmcif_io.GetInputInformation method) get_residue_pairs_pride() (ihm_validation.cx.CxValidation method) get_residues() (ihm_validation.mmcif_io.GetInputInformation method) get_residues_subunit_dict() (ihm_validation.mmcif_io.GetInputInformation method) get_resolution_estimates() (ihm_validation.em.EMValidation static method) get_restraint_group_chain_type() (ihm_validation.cx.CxValidation method) get_restraint_group_entity_type() (ihm_validation.cx.CxValidation method) get_restraints() (ihm_validation.mmcif_io.GetInputInformation method) get_restraints_info() (in module ihm_validation.utility) get_rg_and_io() (ihm_validation.sas.SasValidation method) get_rg_data() (in module ihm_validation.utility) get_rg_data_fits() (in module ihm_validation.utility) get_rg_for_plot() (ihm_validation.sas.SasValidation method) get_rg_table_many() (ihm_validation.sas.SasValidation method) get_rtdtype() (ihm_validation.cx.CxValidation method) get_rtdtypes() (ihm_validation.cx.CxValidation method) get_sampling() (ihm_validation.mmcif_io.GetInputInformation method) get_sas_ids() (ihm_validation.sas.SasValidation method) get_sasbdb_ids() (ihm_validation.sas.SasValidation method) get_sascif_dicts() (ihm_validation.sas.SasValidation method) get_sascif_file() (ihm_validation.sas.SasValidation method) get_sasdb_code_fits() (ihm_validation.sas.SasValidation method) get_scan_unit_mult() (ihm_validation.sas.SasValidation static method) get_sequences_pride() (ihm_validation.cx.CxValidation method) get_software() (in module ihm_validation.utility) get_software_comp() (ihm_validation.mmcif_io.GetInputInformation method) get_software_length() (ihm_validation.mmcif_io.GetInputInformation method) get_stats_per_model_group() (ihm_validation.cx.CxValidation method) get_struc_title() (ihm_validation.mmcif_io.GetInputInformation method) get_subunits() (in module ihm_validation.utility) get_summary_table_stats() (ihm_validation.molprobity.GetMolprobityInformation method) get_supp_file_html() (in module ihm_validation.utility) get_supp_file_pdf() (in module ihm_validation.utility) get_total_number_of_fits() (ihm_validation.sas.SasValidation method) get_unique_datasets() (in module ihm_validation.utility) get_va_version() (ihm_validation.em.EMValidation static method) get_val_from_key() (in module ihm_validation.utility) get_violation_dict() (ihm_validation.excludedvolume.GetExcludedVolume method) get_violation_percentage() (ihm_validation.excludedvolume.GetExcludedVolume method) get_xyzr() (ihm_validation.excludedvolume.GetExcludedVolume method) GetExcludedVolume (class in ihm_validation.excludedvolume) GetInputInformation (class in ihm_validation.mmcif_io) GetMolprobityInformation (class in ihm_validation.molprobity) Guinier_plot_fit_rwt() (ihm_validation.sas_plots.SasValidationPlots method)

H

handle_timeout() (ihm_validation.utility.timeout method) has_crosslinking_ms_dataset (ihm_validation.mmcif_io.GetInputInformation property)

has_em_dataset (ihm_validation.mmcif_io.GetInputInformation property) has_sas_dataset (ihm_validation.mmcif_io.GetInputInformation property)

I

ihm_validation module ihm_validation.cx module ihm_validation.em module ihm_validation.excludedvolume module ihm_validation.format_checker module ihm_validation.futures module ihm_validation.generate_static_html_pages module ihm_validation.get_plots module ihm_validation.ihm_validator module ihm_validation.images module ihm_validation.mmcif_io module ihm_validation.molprobity module

ihm_validation.molprobity_convert module ihm_validation.precision module ihm_validation.report module ihm_validation.sas module ihm_validation.sas_plots module ihm_validation.utility module IHMCIF (ihm_validation.format_checker.FileFormat attribute) IHMVAvailableModes (class in ihm_validation.mmcif_io) is_atomic() (in module ihm_validation.utility) is_cg() (in module ihm_validation.utility) is_model_atomic() (in module ihm_validation.futures) is_model_cg() (in module ihm_validation.futures) is_model_mixed() (in module ihm_validation.futures) is_pdb_dev_id() (in module ihm_validation.utility) is_pdb_id() (in module ihm_validation.utility) is_pdbx_id() (in module ihm_validation.utility) is_restraint_group_satisfied() (ihm_validation.cx.CxValidation method) islistempty() (in module ihm_validation.utility)

L

load_img() (in module ihm_validation.utility) load_json_plot() (in module ihm_validation.ihm_validator)

load_restraint() (ihm_validation.futures.CXMSValidator method) (ihm_validation.futures.Validator method)

M

measure_restraint() (ihm_validation.cx.CxValidation method) MMCIF (ihm_validation.format_checker.FileFormat attribute) mmcif_get_lists() (ihm_validation.mmcif_io.GetInputInformation method) model_id (ihm_validation.molprobity.MyModelDumper attribute) models (ihm_validation.molprobity.GetMolprobityInformation property) modify_intensity() (ihm_validation.sas.SasValidation method) module ihm_validation ihm_validation.cx ihm_validation.em ihm_validation.excludedvolume ihm_validation.format_checker ihm_validation.futures ihm_validation.generate_static_html_pages ihm_validation.get_plots ihm_validation.ihm_validator ihm_validation.images ihm_validation.mmcif_io ihm_validation.molprobity ihm_validation.molprobity_convert ihm_validation.precision ihm_validation.report ihm_validation.sas ihm_validation.sas_plots ihm_validation.utility

molprobity_version (ihm_validation.molprobity.GetMolprobityInformation property) mp_readable_format() (in module ihm_validation.utility) MyModelDumper (class in ihm_validation.molprobity)

N

num_models (ihm_validation.mmcif_io.GetInputInformation property)

number_of_restraint_groups (ihm_validation.futures.CXMSValidator property) number_of_restraints (ihm_validation.futures.CXMSValidator property)

O

order_of_magnitude() (in module ihm_validation.utility)

P

parse_ihm_cif() (in module ihm_validation.format_checker) (in module ihm_validation.utility) PDB (ihm_validation.format_checker.FileFormat attribute) plot_distograms_per_model_group() (ihm_validation.cx.CxValidation method) plot_fit_rwt() (ihm_validation.sas_plots.SasValidationPlots method) plot_fits() (ihm_validation.sas_plots.SasValidationPlots method) plot_Guinier() (ihm_validation.sas_plots.SasValidationPlots method) plot_intensities() (ihm_validation.sas_plots.SasValidationPlots method) plot_intensities_log() (ihm_validation.sas_plots.SasValidationPlots method) plot_kratky() (ihm_validation.sas_plots.SasValidationPlots method) plot_multiple() (ihm_validation.sas_plots.SasValidationPlots method) plot_pddf() (ihm_validation.sas_plots.SasValidationPlots method) plot_pddf_int_rwt() (ihm_validation.sas_plots.SasValidationPlots method)

plot_pf() (ihm_validation.sas_plots.SasValidationPlots method) plot_porod_debye() (ihm_validation.sas_plots.SasValidationPlots method) plot_quality_at_glance() (ihm_validation.get_plots.Plots method) plot_satisfaction_per_ensemble() (ihm_validation.cx.CxValidation method) Plots (class in ihm_validation.get_plots) pretty_print_representations() (in module ihm_validation.utility) pretty_print_scale() (ihm_validation.mmcif_io.GetInputInformation method) PRISM (class in ihm_validation.precision) prism_version (ihm_validation.precision.PRISM property) process_restraint_groups() (ihm_validation.cx.CxValidation method) PRODUCTION (ihm_validation.mmcif_io.IHMVAvailableModes attribute) pyhmmer_alignment_to_map() (ihm_validation.cx.CxValidation static method) pymol_version (ihm_validation.precision.PRISM property)

Q

quality_check() (ihm_validation.cx.CxValidation method)

R

ranges() (in module ihm_validation.utility) read_all_references() (ihm_validation.mmcif_io.GetInputInformation method) remove_flr() (ihm_validation.mmcif_io.GetInputInformation method) report_version (ihm_validation.report.WriteReport attribute) request_emdb() (ihm_validation.em.EMValidation static method) request_pride() (ihm_validation.cx.CxValidation static method) restraint (ihm_validation.futures.Validator attribute) rota_rama_result_to_tuple() (in module ihm_validation.molprobity_convert) rtdtypes (ihm_validation.futures.CXMSValidator property) run_cx_validation() (ihm_validation.report.WriteReport method) run_cx_validation_plots() (ihm_validation.report.WriteReport method)

run_em_validation() (ihm_validation.report.WriteReport method) run_entry_composition() (ihm_validation.report.WriteReport method) run_model_quality() (ihm_validation.report.WriteReport method) run_molprobity() (ihm_validation.molprobity.GetMolprobityInformation method) run_prism() (ihm_validation.report.WriteReport method) run_quality_glance() (ihm_validation.report.WriteReport method) run_sas_validation() (ihm_validation.report.WriteReport method) run_sas_validation_plots() (ihm_validation.report.WriteReport method) run_supplementary_table() (ihm_validation.report.WriteReport method) run_va() (ihm_validation.em.EMValidation method) runInParallel() (in module ihm_validation.utility) runInParallel_noargs() (in module ihm_validation.utility)

S

SasValidation (class in ihm_validation.sas) SasValidationPlots (class in ihm_validation.sas_plots) save_plots() (ihm_validation.cx.CxValidation method) (ihm_validation.em.EMValidation method) (ihm_validation.get_plots.Plots method) (ihm_validation.sas_plots.SasValidationPlots method) select_atom_by_asym_id_seq_id_atom_id() (ihm_validation.cx.CxValidation method) sequences (ihm_validation.mmcif_io.GetInputInformation property) set_plot_style() (ihm_validation.sas_plots.SasValidationPlots static method)

StereoChemistryValidator (class in ihm_validation.futures) summarize_angles() (ihm_validation.molprobity.GetMolprobityInformation method) summarize_bonds() (ihm_validation.molprobity.GetMolprobityInformation method) summarize_clashes() (ihm_validation.molprobity.GetMolprobityInformation method) summarize_clashscores() (ihm_validation.molprobity.GetMolprobityInformation method) summarize_entities() (in module ihm_validation.utility) summarize_mp_data() (ihm_validation.molprobity.GetMolprobityInformation method) summarize_rama_rota() (ihm_validation.molprobity.GetMolprobityInformation method) summarize_rama_rota_stats() (ihm_validation.molprobity.GetMolprobityInformation method) summarize_segments() (in module ihm_validation.utility)

T

timeout (class in ihm_validation.utility) (ihm_validation.precision.PRISM attribute)

U

UNKNOWN (ihm_validation.format_checker.FileFormat attribute)

V

VA_TIMEOUT (ihm_validation.em.EMValidation attribute) validate_all_emdb_data() (ihm_validation.em.EMValidation method) validate_all_pride_data() (ihm_validation.cx.CxValidation method) validate_cif_against_dictionary() (in module ihm_validation.format_checker) validate_emdb_data() (ihm_validation.em.EMValidation method) validate_ensemble() (ihm_validation.futures.CXMSValidator method) (ihm_validation.futures.Validator method)

validate_ihmcif() (in module ihm_validation.format_checker) validate_mmcif() (in module ihm_validation.format_checker) validate_model() (ihm_validation.futures.CXMSValidator method) (ihm_validation.futures.StereoChemistryValidator method) (ihm_validation.futures.Validator method) validate_pride_data() (ihm_validation.cx.CxValidation method) Validator (class in ihm_validation.futures) verify_molprobity_installation() (ihm_validation.molprobity.GetMolprobityInformation method)

W

write_html() (in module ihm_validation.generate_static_html_pages) (in module ihm_validation.ihm_validator) write_json() (in module ihm_validation.ihm_validator)

write_pdf() (in module ihm_validation.ihm_validator) write_supplementary_table() (in module ihm_validation.ihm_validator) WriteReport (class in ihm_validation.report)