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protocols::protein_interface_design::filters::DisulfideFilter Class Reference

Filters for structures which could form a disulfide bond across the docking interface. More...

#include <DisulfideFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::DisulfideFilter:
Inheritance graph
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Public Member Functions

 DisulfideFilter ()
 default ctor More...
 
 DisulfideFilter (DisulfideFilter const &df)
 copy ctor More...
 
 DisulfideFilter (core::Size targetResidue)
 Constructor with a single target residue. More...
 
 DisulfideFilter (core::select::residue_selector::ResidueSelectorCOP targetResidues)
 Constructor with multiple target residues. More...
 
bool apply (core::pose::Pose const &pose) const override
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 
core::Real report_sm (core::pose::Pose const &pose) const override
 
protocols::filters::FilterOP clone () const override
 
protocols::filters::FilterOP fresh_instance () const override
 
 ~DisulfideFilter () override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 
std::string name () const override
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
virtual std::string get_type () const
 
std::string get_user_defined_name () const
 
void set_user_defined_name (std::string const &name)
 
virtual void clear ()
 used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Types

typedef protocols::filters::Filter parent
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP targets_
 residues which may participate in the disulfide. More...
 
core::Size rb_jump_
 Which jump defines the interface where the targets lie? More...
 

Static Private Attributes

static const
core::scoring::disulfides::CentroidDisulfidePotential 
potential_
 for calculating centroid disulfide energies More...
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Detailed Description

Filters for structures which could form a disulfide bond across the docking interface.

Use this filter when you are trying to design one docking member so that it forms a disulfide bond to one or more target residues of the other docking partner. The filter does not consider the indentities of the residues involved, only their Cb position.

This filter only applies to centroid poses. Calling it with a full atom pose will result in everything failing.

Author
Spencer Bliven blive.nosp@m.ns@u.nosp@m..wash.nosp@m.ingt.nosp@m.on.ed.nosp@m.u

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::protein_interface_design::filters::DisulfideFilter::DisulfideFilter ( )

default ctor

protocols::protein_interface_design::filters::DisulfideFilter::DisulfideFilter ( DisulfideFilter const &  df)
default

copy ctor

protocols::protein_interface_design::filters::DisulfideFilter::DisulfideFilter ( core::Size  targetResidue)

Constructor with a single target residue.

protocols::protein_interface_design::filters::DisulfideFilter::DisulfideFilter ( core::select::residue_selector::ResidueSelectorCOP  targetResidues)

Constructor with multiple target residues.

targets may come from either binding partner. If no targets are specified for one target, all residues on the interface will be concidered.

protocols::protein_interface_design::filters::DisulfideFilter::~DisulfideFilter ( )
overridedefault

Member Function Documentation

bool protocols::protein_interface_design::filters::DisulfideFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::protein_interface_design::filters::DisulfideFilter::class_name ( )
static
protocols::filters::FilterOP protocols::protein_interface_design::filters::DisulfideFilter::clone ( ) const
inlineoverridevirtual
protocols::filters::FilterOP protocols::protein_interface_design::filters::DisulfideFilter::fresh_instance ( ) const
inlineoverridevirtual
std::string protocols::protein_interface_design::filters::DisulfideFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::protein_interface_design::filters::DisulfideFilter::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual

Parameters recognized:

  • targets. A list of possible target residues, seperated by commas.

Reimplemented from protocols::filters::Filter.

References core::pose::get_resnum_selector(), and targets_.

void protocols::protein_interface_design::filters::DisulfideFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::protein_interface_design::filters::DisulfideFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual
Real protocols::protein_interface_design::filters::DisulfideFilter::report_sm ( core::pose::Pose const &  pose) const
overridevirtual

Member Data Documentation

const core::scoring::disulfides::CentroidDisulfidePotential protocols::protein_interface_design::filters::DisulfideFilter::potential_
staticprivate

for calculating centroid disulfide energies

core::Size protocols::protein_interface_design::filters::DisulfideFilter::rb_jump_
private

Which jump defines the interface where the targets lie?

Referenced by apply(), report(), and report_sm().

core::select::residue_selector::ResidueSelectorCOP protocols::protein_interface_design::filters::DisulfideFilter::targets_
private

residues which may participate in the disulfide.

If either docking partner has no target residues specified, all interface residues will be allowed to disulfide bond.

Referenced by apply(), parse_my_tag(), report(), and report_sm().


The documentation for this class was generated from the following files: