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)