Optional Parameters

Input/Output

-out <filename>

Option to specify the output file to write hits in oedu format.

[default = sitehopper_hits.oedu]

SiteHopper Search Options

-max_hits <value>

Option to specify the maximum number of hits to write out. Note that if fewer than this value are found, all hits will be written out

[default = 200]

-normalize_and_rescore <bool>

Option to normalize the sitehopper score of hits by the difference in binding site size between query and hit.

[default = false]

-cutoff <float>

Minimum PatchScore to retain in the hit list.

[default = 0.0]

-sequence_cutoff <float>

Only keeps hits that have a protein sequence similarity to the query that is less than this value. This is useful to remove obvious results.

[default = 100.0]

-ncpu <value>

Number of CPU threads to use for the search. Setting this to zero implies use all available. Search requires 1GB available RAM per thread, so this value may be reduced at runtime.

[default = 0]

-use_gpu <bool>

Use NVIDIA GPU as a pre-screen search. This option is only available on Linux platforms with a compatible NVIDIA GPU.

[default = true]

Logging

-log <logfile>

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

[default = sitehopper_search_output.log]

-param <paramfile>

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

[default = sitehopper_search_settings.param]

[ Aliases = -settings ]

-prefix <prefix>

Prefix used to name output files, default is blank

-verbose

Triggers copious logging output