OCDocker.Toolbox package

Submodules

• OCDocker.Toolbox.Basetools module
  • redirect_to_tqdm()
• OCDocker.Toolbox.Constants module
  • STANDARD_TEMPERATURE_K
  • ZERO_C_IN_K
  • CAL_TO_J
  • R
  • Rk
  • RJ
  • RJK
  • order
  • cal_to_J()
  • J_to_cal()
  • C_to_K()
  • K_to_C()
  • convert_Ki_Kd_to_dG()
  • convert_dG_to_Ki_Kd()
• OCDocker.Toolbox.Conversion module
  • convert_mols()
  • convert_mols_from_string()
  • kikd_to_deltag()
  • split_and_convert()
• OCDocker.Toolbox.Downloading module
  • DownloadProgressBar
    • DownloadProgressBar.update_to()
  • download_url()
• OCDocker.Toolbox.FilesFolders module
  • empty_docking_digest()
  • ensure_parent_dir()
  • from_hdf5()
  • from_pickle()
  • normalize_path()
  • safe_create_dir()
  • safe_remove_dir()
  • safe_remove_file()
  • to_hdf5()
  • to_pickle()
  • untar()
• OCDocker.Toolbox.IO module
  • lazyread()
  • lazyread_mmap()
  • lazyread_reverse_order()
  • lazyread_reverse_order_mmap()
• OCDocker.Toolbox.Logging module
  • backup_log()
  • clear_past_logs()
  • configure()
  • get_logger()
  • is_rich_enabled()
  • set_level_from_report()
• OCDocker.Toolbox.MoleculeProcessing module
  • build_charmm_to_canonical_map()
  • clean_for_dssp()
  • clean_pdb_file()
  • convert_pdb_charmm_to_canonical()
  • get_rmsd()
  • get_rmsd_matrix()
  • needs_canonical_pdb_fix()
  • split_poses()
• OCDocker.Toolbox.Preparation module
  • PreparationStrategy
    • PreparationStrategy.get_ligand_command()
    • PreparationStrategy.get_receptor_command()
    • PreparationStrategy.prepare_ligand()
    • PreparationStrategy.prepare_receptor()
  • MGLToolsPreparationStrategy
    • MGLToolsPreparationStrategy.get_ligand_command()
    • MGLToolsPreparationStrategy.get_receptor_command()
    • MGLToolsPreparationStrategy.prepare_ligand()
    • MGLToolsPreparationStrategy.prepare_receptor()
  • SPORESPreparationStrategy
    • SPORESPreparationStrategy.get_ligand_command()
    • SPORESPreparationStrategy.get_receptor_command()
    • SPORESPreparationStrategy.prepare_ligand()
    • SPORESPreparationStrategy.prepare_receptor()
  • OpenBabelPreparationStrategy
    • OpenBabelPreparationStrategy.get_ligand_command()
    • OpenBabelPreparationStrategy.get_receptor_command()
    • OpenBabelPreparationStrategy.prepare_ligand()
    • OpenBabelPreparationStrategy.prepare_receptor()
• OCDocker.Toolbox.Printing module
  • print_error()
  • print_error_log()
  • print_info()
  • print_info_log()
  • print_section()
  • print_sorry()
  • print_subsection()
  • print_success()
  • print_success_log()
  • print_warning()
  • print_warning_log()
  • printv()
  • section()
  • subsection()
• OCDocker.Toolbox.Reproducibility module
  • generate_reproducibility_manifest()
  • write_reproducibility_manifest()
  • generate_manifest()
• OCDocker.Toolbox.Running module
  • SubprocessError
  • is_tool_available()
  • run()
• OCDocker.Toolbox.Security module
  • allow_unsafe_runtime()
  • env_flag_enabled()
  • require_trusted_input()
• OCDocker.Toolbox.Validation module
  • is_algorithm_allowed()
  • is_molecule_valid()
  • is_molecule_valid_with_retry()
  • validate_digest_extension()
  • validate_obabel_extension()

Module contents

Toolbox helpers for OCDocker utilities.

Usage:

import OCDocker.Toolbox as octools

Modules

• Basetools: Basic helper utilities.

• Constants: Physical constants and unit conversions.

• Conversion: Molecule conversion utilities.

• Downloading: Download helpers with progress reporting.

• FilesFolders: File and folder utilities.

• IO: Low-level I/O helpers.

• Logging: Logging helpers.

• MoleculeProcessing: Molecule parsing and processing utilities.

• Preparation: Molecule preparation strategies.

• Printing: Printing and verbosity helpers.

• Reproducibility: Environment/version manifest helpers.

• Running: Subprocess and command execution helpers.

• Validation: Input validation utilities.