IHMValidation

Documentation

  • Usage
    • PDB-IHM Validation System
    • Local deployment
      • Building runtime image
      • Running the pipeline
    • Interpreting the reports
  • API
    • ihm_validation package
      • Submodules
      • ihm_validation.cx module
        • CxValidation
      • ihm_validation.em module
        • EMValidation
      • ihm_validation.excludedvolume module
        • GetExcludedVolume
      • 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
        • StereoChemistryValidator
        • Validator
        • 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
      • 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
        • IHMVAvailableModes
        • get_operational_mode()
      • ihm_validation.molprobity module
        • AtomSiteVariant
        • GetMolprobityInformation
        • MyModelDumper
      • ihm_validation.molprobity_convert module
        • get_atom_tuple()
        • rota_rama_result_to_tuple()
      • ihm_validation.precision module
        • PRISM
      • ihm_validation.report module
        • WriteReport
      • ihm_validation.sas module
        • SasValidation
      • ihm_validation.sas_plots module
        • SasValidationPlots
      • 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
      • Module contents

References

  • PDB-IHM Validation System
  • Validation Reports
  • PDB-IHM
  • PDB-IHM Deposition System
IHMValidation
  • Overview: module code

All modules for which code is available

  • 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.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

© Copyright 2025, Arthur Zalevsky, Sai Ganesan, Benjamin M. Webb, Brinda Vallat.

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