Package Biskit :: Package Dock :: Module settings

Module settings

Settings

This module provides Dock-global settings as fields. Throughout Biskit.Dock a (environment-dependent) parameter such as, e.g., ssh_bin can be addressed as:

>>> import Biskit.Dock.settings as S
>>> bin = S.ssh_bin

However, since a user should not be required to hack python modules, ssh_bin is not actually defined in settings.py. Instead, the value is taken from ~/.biskit/settings_Dock.cfg -- which should have an entry like ssh_bin=/bin/ssh # comment. If this entry (or the config file) is not found, settings.py uses the default value from biskit/external/defaults/settings_Dock.cfg.

If missing, the user configuration file ~/.biskit/settings_Dock.cfg is created automatically during the startup of Biskit (i.e. for any import). The auto-generated file only contains parameters for which the default values don't seem to work (invalid paths or binaries).

See Biskit.SettingsManager

Summary for Biskit users

If you want to change a biskit parameter, do so in ~/.biskit/settings_Dock.cfg

Summary for Biskit developpers

If you want to create a new user-adjustable parameter, do so in biskit/external/defaults/settings_Dock.cfg.

Summary for all

!Dont't touch settings.py!

Classes

[hide private]

Test
Mock test, settings is always executed anyway.

Variables

[hide private]

env = {}

hex_env = {'HEX_ROOT': '/home/Bis/johan/APPLICATIONS/HEX', 'HE...

prosaII_env = {'PROSA_BASE': '/home/Bis/shared/rh73/prosa/prosabas...

Variables Details

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env

Value:

{}

hex_env

Value:

{'HEX_ROOT': '/home/Bis/johan/APPLICATIONS/HEX', 'HEX_CACHE': '/home/B
is/johan/APPLICATIONS/HEX/hex_cache', 'HEX_VERSION': '4b'}

prosaII_env

Value:

{'PROSA_BASE': '/home/Bis/shared/rh73/prosa/prosabase/'}