Command Line Interface

Interactive Help

In addition to this documentation, the command line programs of the OEDocking suite include documentation of their parameters that can be accessed by passing --help to the program as the first argument followed by one of the following options.

  • Options for –help flag

    • simple

      Displays a list of basic command line options for the program with a brief description of their use.

    • all

      Displays a list of all command line options for the program with a brief description of their use.

    • <parameter>

      Provides a detailed description of the specified parameter.

    • defaults

      Lists the default settings for all parameters (or “no default” if there is none).

Parameter Usage

Parameters are entered on the command line by entering the parameter key followed by a value. For example:

prompt> fred -dbase ligands.oeb.gz -rec receptor.oeb.gz

In this case -dbase and -rec are the parameter keys and ligands.oeb.gz and receptor.oeb.gz are the respective values for those parameters.

The parameters can appear on the command line in any order. Thus the example command line above is equivalent to the following command line:

prompt> fred -rec receptor.oeb.gz -dbase ligands.oeb.gz

Parameter names are not case sensitive. Parameter values may or may not be case sensitive, see the documentation for the given parameter.

Parameter Aliases

Some parameters have aliases for the parameter name. Aliases are substitute names that can be used in place of the normal parameter name on the command line, generally as a form of shorthand for the command line. For example, the parameter -dbase has two aliases -database and -in. The following three command lines are thus equivalent

prompt> fred -dbase ligands.oeb.gz -rec receptor.oeb.gz
prompt> fred -database ligands.oeb.gz -rec receptor.oeb.gz
prompt> fred -in ligands.oeb.gz -rec receptor.oeb.gz

Boolean Parameters

Boolean parameters that have a default value of false have a special shorthand on the command line. A boolean parameter with a default value of false can be specified on the command line as a name without a following value, and in this case the value of the parameter will be set to true.

For example -annotate_scores is a boolean flag with a default value of false. The following command lines are thus both valid and equivilant.

prompt> fred -annotate_poses true -dbase ligands.oeb.gz -rec receptor.oeb.gz
prompt> fred -annotate_poses -dbase ligands.oeb.gz -rec receptor.oeb.gz

List Parameters

List parameters are parameters that can have more than one value associated with them (non-list parameters may only have one). Additional values are entered on the command line after the first. For example, -dbase is a list parameter that can be given multiple values as follows:

prompt> fred -dbase ligands1.oeb.gz ligands2.oeb.gz -rec receptor.oeb.gz

In this example the parameter -dbase is set with two values, ligands1.oeb.gz and ligands2.oeb.gz.

List parameters may have any number of values set.

List parameters are documented as follows

-key <value1> [value]...

whereas non-list parameters are documented as

-key <value>

Parameter documentation

Different types have different formatting as follows.

Documentation format Type of parameter
-key <value> Parameter that takes a single value.
-key (X) Parameter with a default value of X
-key <value1> [value2]... List parameter that takes one or more values
-key (X) [value]... List parameter with a default value of X
-key (false) Boolean parameter with a default value of false. This parameter can be set to true by putting the without a following value on the command line.