Configuration & Logging

This module defines functions for logging in files, configuring ProDy, and running tests.

confProDy(*args, **kwargs)[source]

Configure ProDy.

Option Default (acceptable values)
auto_bonds False
auto_secondary False
auto_show False
backup False
backup_ext ‘.BAK’
check_updates 0
ligand_xml_save False
local_pdb_folder ‘’ See also pathPDBFolder().
pdb_mirror_path ‘’ See also pathPDBMirror().
selection_warning True
typo_warnings True
verbosity ‘debug’ (‘critical’, ‘debug’, ‘error’, ‘info’, ‘none’, ‘progress’, or ‘warning’)

Usage example:

confProDy('backup', 'backup_ext')
confProDy(backup=True, backup_ext='.bak')

Check PyPI to see if there is a newer ProDy version available. Setting ProDy configuration parameter check_updates to a positive integer will make ProDy automatically check updates, e.g.:

confProDy(check_updates=7) # check at most once a week
confProDy(check_updates=0) # do not auto check updates
confProDy(check_updates=-1) # check at the start of every session
startLogfile(filename, **kwargs)[source]

Start a logfile. If filename does not have an extension. .log will be appended to it.

  • filename – name of the logfile
  • mode – mode in which logfile will be opened, default is “w”
  • backupcount – number of existing filename.log files to backup, default is 1

Close logfile with filename.


Log text using ProDy logger at log level info. Multiple arguments are accepted. Each argument will be converted to string and joined using a white space as delimiter.