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:[fragment number:alternate location]”, e.g. “ASP:25: :A:.*: :”, indicating Aspartic acid 25 in chain A, also ensuring both the insert code and alternate location is not set, while the fragment number can be anything (the regex .* fuzzy matcher). The fragment number and alternate location can be left out, in which case they will automatically be replaced by fuzzy matchers. While you could specify ”.*:25: :A”, which would incidate residue 25 in chain A, irrespecive of the residue type, however, we recommend being as explicit as possible.
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)