Configuration & Logging

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

• confProDy()

• checkUpdates()

• startLogfile()

• closeLogfile()

• plog()

prody.confProDy(*args, **kwargs)

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	‘’
pdb_mirror_path	‘’
selection_warning	True
typo_warnings	True
verbosity	‘debug’ (‘critical’, ‘debug’, ‘error’, ‘info’, ‘none’, ‘progress’, or ‘warning’)

Usage example:

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

prody.checkUpdates()

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

prody.startLogfile(filename, **kwargs)

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

Parameters:

• 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

prody.closeLogfile(filename)

Close logfile with filename.

prody.plog(*text)

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.