Optional Parameters

Input Options

-fit_lig <filename>

A file containing a ligand to use as a constraint during the superposition. Should only be used if the input is not an OEDesignUnit

-ref_lig <filename>

A file containing a reference ligand to use as a constraint during the superposition. Should only be used if the input is not an OEDesignUnit

Output Options

-prefix <prefix>

Prefix used to name output files, default is blank. To avoid overwriting input files, all files are automatically use the prefix superposed_ if no prefix is specified.

-log <logfile>

The argument for this flag specifies the name of the log file. This overrides any specified prefix. The default will be superposition_output.log, if no prefix is specified.

-settings <settingsfile>

The argument for this flag specifies the name of the settings file. This overrides any specified prefix. The default will be superposition_settings.param, if no prefix is specified.

-verbose : Triggers copious logging output

Parameters

-method <method>

The method to use for superposition

Method Description
global Global Sequence Alignment to identify CA pairs
site Global Sequence Alignment to identity CA pairs - focusing on the subset in active site
ddm Superposition using the Distance Difference Matrix method (DDM)
sse Superposition using an overlap of Secondary Structure Elements (SSE)