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:

Collaboration diagram for protocols::protein_interface_design::filters::DisulfideFilter:

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::Size >	targets_
	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

Definition at line 57 of file DisulfideFilter.hh.

Member Typedef Documentation

typedef protocols::filters::Filter protocols::protein_interface_design::filters::DisulfideFilter::parent

private

Definition at line 60 of file DisulfideFilter.hh.

Constructor & Destructor Documentation

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

default ctor

Definition at line 60 of file DisulfideFilter.cc.

Referenced by clone(), and fresh_instance().

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

copy ctor

Definition at line 67 of file DisulfideFilter.cc.

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

Constructor with a single target residue.

Definition at line 75 of file DisulfideFilter.cc.

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.

Definition at line 84 of file DisulfideFilter.cc.

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

virtual

Definition at line 90 of file DisulfideFilter.cc.

Member Function Documentation

bool protocols::protein_interface_design::filters::DisulfideFilter::apply ( core::pose::Pose const & pose) const

virtual

Returns: Whether a disulfide bond is possible between any of the targets

Implements protocols::filters::Filter.

Definition at line 93 of file DisulfideFilter.cc.

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

virtual protocols::filters::FilterOP protocols::protein_interface_design::filters::DisulfideFilter::clone ( ) const

inlinevirtual

Implements protocols::filters::Filter.

Definition at line 76 of file DisulfideFilter.hh.

References DisulfideFilter().

virtual protocols::filters::FilterOP protocols::protein_interface_design::filters::DisulfideFilter::fresh_instance ( ) const

inlinevirtual

Implements protocols::filters::Filter.

Definition at line 79 of file DisulfideFilter.hh.

References DisulfideFilter().

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
	)