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)