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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:
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Collaboration diagram for protocols::protein_interface_design::filters::DisulfideFilter:
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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 (utility::vector1< core::Size > const &targetResidues)
 Constructor with multiple target residues. More...
 
virtual bool apply (core::pose::Pose const &pose) const
 
virtual void report (std::ostream &out, core::pose::Pose const &pose) const
 
virtual core::Real report_sm (core::pose::Pose const &pose) const
 
virtual
protocols::filters::FilterOP 
clone () const
 
virtual
protocols::filters::FilterOP 
fresh_instance () const
 
virtual ~DisulfideFilter ()
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
virtual ~Filter ()
 
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 void apply (core::io::serialization::PipeMap &pmap)
 
virtual void score (core::io::serialization::PipeMap &pmap)
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
 
virtual std::string name () const
 

Private Types

typedef protocols::filters::Filter parent
 

Private Attributes

utility::vector1< core::Sizetargets_
 a list of residues which may participate in the disulfide. More...
 
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

Referenced by clone(), and fresh_instance().

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

copy ctor

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

Constructor with a single target residue.

References targets_.

protocols::protein_interface_design::filters::DisulfideFilter::DisulfideFilter ( utility::vector1< core::Size > const &  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 ( )
virtual

Member Function Documentation

bool protocols::protein_interface_design::filters::DisulfideFilter::apply ( core::pose::Pose const &  pose) const
virtual
virtual protocols::filters::FilterOP protocols::protein_interface_design::filters::DisulfideFilter::clone ( ) const
inlinevirtual
virtual protocols::filters::FilterOP protocols::protein_interface_design::filters::DisulfideFilter::fresh_instance ( ) const
inlinevirtual
void protocols::protein_interface_design::filters::DisulfideFilter::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap ,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &  pose 
)
virtual

Parameters recognized:

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

Reimplemented from protocols::filters::Filter.

References core::pose::get_resnum_list(), targets_, and protocols::protein_interface_design::filters::TR().

void protocols::protein_interface_design::filters::DisulfideFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
virtual
Real protocols::protein_interface_design::filters::DisulfideFilter::report_sm ( core::pose::Pose const &  pose) const
virtual
Returns
The number of disulfides possible

Reimplemented from protocols::filters::Filter.

References protocols::protein_interface_design::movers::DisulfideMover::disulfide_list(), rb_jump_, and targets_.

Member Data Documentation

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

for calculating centroid disulfide energies

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().

utility::vector1<core::Size> protocols::protein_interface_design::filters::DisulfideFilter::targets_
private

a list of 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(), DisulfideFilter(), parse_my_tag(), report(), and report_sm().


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