Overview¶
The command line interface includes all of mollib’s functions for processing
and analyzing molecules and molecular data. Mollib can be accessed either
through the mollib
or ml
commands.
$ ml --help
usage: mollib [-h] [-d | -s | -v] [--list-plugins] [--list-settings]
[--version]
...
A molecular processor
optional arguments:
-h, --help show this help message and exit
-d, --debug Print debugging statements
-s, --suppress Suppress all messages, except critical
-v, --verbose Print extra information
--list-plugins List the installed plugins
--list-settings List the available sections for settings
--version Show the program version
commands:
process Process the structure
measure Measure geometries in molecules
hbonds Find and report hydrogen bonds in molecules
pa Singular Value Decomposition of partially aligned NMR data
(RDCs and RACSs)
-h
/--help
- Get basic help information on usage of the command line interface, or one one of the mollib commands.
-d
/--debug
- Display debug messages to the terminal. This is usually only useful to developers or in helping to debug issues.
-s
/--suppress
- Display only errors and critical errors.
-v
/--verbose
- Display informational messages to the terminal. By default, only warning and error messages are displayed.
--version
- Display the version number of the installed mollib.
--list-plugins
Display a list of installed and enabled plugins.
$ ml --list-plugins Installed plugins: process Enabled measure Enabled hydrogenate Enabled hbonds Enabled pa Enabled
--list-settings
Display a list of the settings sections that will be interpreted from configuration files.
$ ml --list-settings Installed settings sections: [settings] [utils.settings] [hydrogens.settings] [hbonds.settings] [statistics.settings] [pa.settings]
Configuration Files¶
Mollib will check for a .mollibrc
configuration file and a configuration
file passed with the -c
filename
/ --config
filename
commandline argument for configuration parameters.
Configuration files customize mollib’s behavior from default values. If a
.mollibrc
file is present and a configuration file is specified in the
commandline, the commandline configuration file will take precedence for
parameters that are mentioned in both.
The following is an example configuration file. Note that only the parameters that need to be changed can be specified in the file.
[settings]
default_pH = 7.0
pKs = {'ASP': {'OD1-OD2': (-1.0, 3.5)},
'GLU': {'OE1-OE2': (-1.0, 4.2)},
'HIS': {'ND1-NE2': (6.6, 14.0)},
'CYS': {'SG': (6.8,)},
'TYR': {'OH': (10.3,)},
'LYS': {'NZ': (10.5, 14.0, 14.0)},
'last': {'O-OXT': (-1.0, 3.3)},
'first': {'N': (7.7, 14.0, 14.0),}
}
[settings.hydrogens]
bond_length = {'N-H': 1.023,
'C-H': 1.117,
'C-C': 1.517,
'N-H2': 1.01,
'O-H': 0.958,
'C-N': 1.488,
'C=O': 1.250,
'C-O': 1.413,
}