pestifer.util package

Various utility modules for Pestifer.

Submodules

• pestifer.util.cacheable_object module
  • CacheableObject
    • CacheableObject.APP_NAME
    • CacheableObject.APP_VERSION
    • CacheableObject.CACHE_COMPRESS
    • CacheableObject.CACHE_PREFIX
    • CacheableObject.VERSION_SCOPE
  • TarBytesFS
    • TarBytesFS.compression
    • TarBytesFS.from_file()
    • TarBytesFS.fs()
    • TarBytesFS.ls()
    • TarBytesFS.open()
    • TarBytesFS.tar_bytes
• pestifer.util.cifutil module
  • CIFdict
  • CIFload()
• pestifer.util.colors module
  • PestiferColorMap
    • PestiferColorMap.hue()
• pestifer.util.coord module
  • build_tmat()
  • coorddf_from_pdb()
  • lawofcos()
  • measure_dihedral()
  • mic_shift()
  • positionN()
• pestifer.util.formatvalidator module
  • FormatValidator
    • FormatValidator.extract()
    • FormatValidator.fullmatch()
    • FormatValidator.pattern
  • extract_from_format()
  • validate_format()
• pestifer.util.gitutil module
  • get_git_origin_url()
• pestifer.util.linkcell module
  • Linkcell
    • Linkcell.cellndx_of_ldx()
    • Linkcell.cellndx_of_point()
    • Linkcell.ldx_of_cellndx()
    • Linkcell.ldx_searchlist_of_ldx()
    • Linkcell.wrap_point()
• pestifer.util.namdrestart module
  • NAMDConfig
    • NAMDConfig.backresolve_lines()
    • NAMDConfig.replace_command()
    • NAMDConfig.var_backresolve()
    • NAMDConfig.write()
  • make_namd_restart_subcommand()
• pestifer.util.patch module
  • PatchApplyError
  • apply_unified_diff()
• pestifer.util.progress module
  • NAMDProgress
  • PDB2PQRProgress
  • PackmolProgress
  • PestiferProgress
    • PestiferProgress.finish()
    • PestiferProgress.go()
    • PestiferProgress.register_update_function()
  • PsfgenProgress
• pestifer.util.pytest_plugin module
  • pytest_addoption()
  • pytest_configure()
• pestifer.util.readme_to_changelog_with_dates module
  • extract_changelog_from_readme()
  • get_git_tag_dates()
  • get_pypi_release_dates()
• pestifer.util.spinner_wrapper module
  • with_spinner()
• pestifer.util.stringthings module
  • ByteCollector
    • ByteCollector.addline()
    • ByteCollector.banner()
    • ByteCollector.comment()
    • ByteCollector.has_statement()
    • ByteCollector.ingest_file()
    • ByteCollector.lastline()
    • ByteCollector.log()
    • ByteCollector.reassign()
    • ByteCollector.reset()
    • ByteCollector.write()
    • ByteCollector.write_file()
  • FileCollector
    • FileCollector.flush()
    • FileCollector.tarball()
  • banner()
  • example_footer()
  • linesplit()
  • my_logger()
  • oxford()
  • parse_filter_expression()
  • plu()
  • raise_clean()
  • striplist()
  • to_latex_math()
• pestifer.util.units module
  • cuA_of_nmolec()
  • nmolec_in_cuA()
• pestifer.util.util module
  • cell_from_xsc()
  • cell_to_xsc()
  • countTime()
  • flatten()
  • hms()
  • hmsf()
  • is_periodic()
  • protect_str_arg()
  • reduce_intlist()
  • remove_argument()
  • replace()
  • running_under_pytest()
  • tarball_walk()
  • write_residue_map()