Optional Parameters

Input Options

-map <filename>

Input electron density map from X-ray crystallography, to be used for Iridium score calculation.

-ref <filename>

Reference OEDesignUnit indicating the proper biological unit and relevant binding site.

-site_residue <residue identifier>

Input option to specify a binding site using a single residue specification if apo (or holo). The format is “name:num:insert code:chainid”, e.g. “ASP:25: :A” indicating Aspartic acid 25 in chain A. Note: A blank/whitespace character is used for the insert code, which is a typical use case.

Output Options

-prefix <prefix>

Prefix used to name output files, default is blank

-log <logfile>

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

-verbose : Triggers copious logging output

Enumerate Sites Parameters

-add_interactions

Option to add OEInteractionHints to the design unit(s)

[default = true]

-add_style

Option to add visualization style to the design unit(s)

[default = true]

-collapse_nonsite_alts

Option to deduplicate structures with different alternate locations if those alternate locations are far from the binding site

[default = true]

-duplicate_removal

Option to deduplicate identical structures resulting from symmetry operations

[default = true]

-enum_cofactors_sites

Option to generate design units with sites based on components classified as co-factors

[default = false]

-restrict_to_refsite

Option to skip generating design units for sites identified, that do not match a provided reference design unit

[default = true]

-site_size <value>

Distance from the ligand used to determine the size of the site

[default = 5.0 (angstroms)]

-superpose

Option to superpose generated design units, if multiple. If a reference is provided, the first generated design unit will be superposed onto the reference structure, and subsequent structures onto that one.

[default = true]

-superpose_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)
sitehopper	Superposition based on binding site similarities (sitehopper)