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

See also

-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

See also

Output Options

-prefix <prefix>

Prefix used to name output files, default is blank. To avoid overwriting input files, all structure files are automatically using 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.

-settings_file <settingsfile>

(Alias: -settings)

The argument for this flag specifies the name of the settings file. This overrides any specified prefix.

-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)

weighted

Superposition using Weighted DDM method

sitehopper

Superposition using SiteHopper

See also

-valid_seqscore <value>

Minimum sequence alignment score for the superposition to be considered valid

[Default=200]

See also

-valid_rmsd <value>

Maximum RMSD threshold for the superposition to be considered valid

[Default=10.0]

See also

-valid_tanimoto <value>

Minimum Tanimoto similarity threshold for the superposition to be considered valid

[Default=0.0]

See also