protocols::simple_filters::ResidueIEFilter Class Reference

#include <ResidueIEFilter.hh>

Inheritance diagram for protocols::simple_filters::ResidueIEFilter:

Collaboration diagram for protocols::simple_filters::ResidueIEFilter:

Public Member Functions
	ResidueIEFilter ()
	ResidueIEFilter (utility::vector1< core::Size > const resnums, std::string const restype, core::scoring::ScoreFunctionCOP scorefxn, core::scoring::ScoreType const score_type, core::Real const threshold, bool const whole_pose=false, bool const whole_interface=false, core::Size const rb_jump=1, core::Real const interface_distance_cutoff=8.0, core::Real max_penalty=0.0, core::Real penalty_factor=1.0)
	ResidueIEFilter (ResidueIEFilter const &init)
bool	apply (core::pose::Pose const &pose) const
	Returns true if the given pose passes the filter, false otherwise. More...
filters::FilterOP	clone () const
filters::FilterOP	fresh_instance () const
void	report (std::ostream &out, core::pose::Pose const &pose) const
core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...
core::Real	compute (core::pose::Pose const &pose) const
virtual	~ResidueIEFilter ()
void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
utility::vector1< core::Size >	resnums () const
core::scoring::ScoreFunctionOP	scorefxn () const
core::scoring::ScoreType	score_type () const
core::Real	threshold () const
void	resnums (utility::vector1< core::Size > const &rn)
void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)
void	score_type (core::scoring::ScoreType score_type)
void	threshold (core::Real const th)
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 Attributes
utility::vector1< core::Size >	resnums_
std::string	restype_
core::scoring::ScoreFunctionOP	scorefxn_
core::scoring::ScoreType	score_type_
core::Real	threshold_
bool	whole_pose_
bool	whole_interface_
core::Size	rb_jump_
core::Real	interface_distance_cutoff_
core::Real	max_penalty_
core::Real	penalty_factor_
bool	use_resE_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Detailed Description

Definition at line 30 of file ResidueIEFilter.hh.

Constructor & Destructor Documentation

protocols::simple_filters::ResidueIEFilter::ResidueIEFilter ( )

inline

Definition at line 33 of file ResidueIEFilter.hh.

Referenced by clone(), and fresh_instance().

protocols::simple_filters::ResidueIEFilter::ResidueIEFilter	(	utility::vector1< core::Size > const	resnums,
		std::string const	restype,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::scoring::ScoreType const	score_type,
		core::Real const	threshold,
		bool const	whole_pose = false,
		bool const	whole_interface = false,
		core::Size const	rb_jump = 1,
		core::Real const	interface_distance_cutoff = 8.0,
		core::Real	max_penalty = 0.0,
		core::Real	penalty_factor = 1.0
	)

Definition at line 43 of file ResidueIEFilter.cc.

References score_type_, scorefxn_, core::scoring::total_score, and use_resE_.

protocols::simple_filters::ResidueIEFilter::ResidueIEFilter

(

ResidueIEFilter const &

init)

Definition at line 80 of file ResidueIEFilter.cc.

References scorefxn_.

protocols::simple_filters::ResidueIEFilter::~ResidueIEFilter ( )

virtual

Definition at line 137 of file ResidueIEFilter.cc.

Member Function Documentation

bool protocols::simple_filters::ResidueIEFilter::apply ( core::pose::Pose const &  pose) const

virtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

Definition at line 177 of file ResidueIEFilter.cc.

References compute(), and max_penalty_.

filters::FilterOP protocols::simple_filters::ResidueIEFilter::clone ( ) const

inlinevirtual

Implements protocols::filters::Filter.

Definition at line 42 of file ResidueIEFilter.hh.

References ResidueIEFilter().

Referenced by parse_my_tag().

core::Real protocols::simple_filters::ResidueIEFilter::compute

(

core::pose::Pose const &

pose)

const

Definition at line 205 of file ResidueIEFilter.cc.

References protocols::simple_filters::EnergyPerResidueFilter::compute(), core::pose::Pose::conformation(), core::graph::Node::const_edge_list_end(), core::scoring::EnergyEdge::dot(), core::graph::Edge::get_node(), core::graph::Edge::get_other_ind(), interface_distance_cutoff_, core::conformation::Residue::is_protein(), core::chemical::ResidueType::name3(), core::conformation::Conformation::num_chains(), penalty_factor_, rb_jump_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), resnums_, restype_, score_type_, scorefxn_, threshold_, core::pose::Pose::total_residue(), core::pose::Pose::update_residue_neighbors(), use_resE_, whole_interface_, and whole_pose_.

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

filters::FilterOP protocols::simple_filters::ResidueIEFilter::fresh_instance ( ) const

inlinevirtual

Implements protocols::filters::Filter.

Definition at line 45 of file ResidueIEFilter.hh.

References ResidueIEFilter().

void protocols::simple_filters::ResidueIEFilter::parse_my_tag ( utility::tag::TagPtr const  tag, protocols::moves::DataMap &  data, filters::Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &  pose  )

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 140 of file ResidueIEFilter.cc.

References clone(), protocols::moves::DataMap::get(), core::pose::get_resnum_list(), interface_distance_cutoff_, max_penalty_, core::pose::Pose::num_jump(), penalty_factor_, rb_jump_, resnums_, restype_, score_type_, core::scoring::score_type_from_name(), scorefxn_, threshold_, use_resE_, whole_interface_, and whole_pose_.

void protocols::simple_filters::ResidueIEFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 187 of file ResidueIEFilter.cc.

References compute(), and restype_.

core::Real protocols::simple_filters::ResidueIEFilter::report_sm ( core::pose::Pose const &  ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

Definition at line 195 of file ResidueIEFilter.cc.

References compute().

utility::vector1< core::Size > protocols::simple_filters::ResidueIEFilter::resnums

(

)

const

Definition at line 128 of file ResidueIEFilter.cc.

References resnums_.

void protocols::simple_filters::ResidueIEFilter::resnums

(

utility::vector1< core::Size > const &

rn)

Definition at line 133 of file ResidueIEFilter.cc.

References resnums_.

core::scoring::ScoreType protocols::simple_filters::ResidueIEFilter::score_type

(

)

const

Definition at line 108 of file ResidueIEFilter.cc.

References score_type_.

Referenced by score_type().

void protocols::simple_filters::ResidueIEFilter::score_type

(

core::scoring::ScoreType

score_type)

Definition at line 113 of file ResidueIEFilter.cc.

References score_type(), and score_type_.

core::scoring::ScoreFunctionOP protocols::simple_filters::ResidueIEFilter::scorefxn

(

)

const

Definition at line 98 of file ResidueIEFilter.cc.

References scorefxn_.

Referenced by scorefxn().

void protocols::simple_filters::ResidueIEFilter::scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn)

Definition at line 103 of file ResidueIEFilter.cc.

References scorefxn(), and scorefxn_.

core::Real protocols::simple_filters::ResidueIEFilter::threshold

(

)

const

Definition at line 118 of file ResidueIEFilter.cc.

References threshold_.

void protocols::simple_filters::ResidueIEFilter::threshold

(

core::Real const

th)

Definition at line 123 of file ResidueIEFilter.cc.

References threshold_.

Member Data Documentation

core::Real protocols::simple_filters::ResidueIEFilter::interface_distance_cutoff_

private

Definition at line 71 of file ResidueIEFilter.hh.

Referenced by compute(), and parse_my_tag().

core::Real protocols::simple_filters::ResidueIEFilter::max_penalty_

private

Definition at line 72 of file ResidueIEFilter.hh.

Referenced by apply(), and parse_my_tag().

core::Real protocols::simple_filters::ResidueIEFilter::penalty_factor_

private

Definition at line 73 of file ResidueIEFilter.hh.

Referenced by compute(), and parse_my_tag().

core::Size protocols::simple_filters::ResidueIEFilter::rb_jump_

private

Definition at line 70 of file ResidueIEFilter.hh.

Referenced by compute(), and parse_my_tag().

utility::vector1<core::Size> protocols::simple_filters::ResidueIEFilter::resnums_

mutableprivate

Definition at line 63 of file ResidueIEFilter.hh.

Referenced by compute(), parse_my_tag(), and resnums().

std::string protocols::simple_filters::ResidueIEFilter::restype_

private

Definition at line 64 of file ResidueIEFilter.hh.

Referenced by compute(), parse_my_tag(), and report().

core::scoring::ScoreType protocols::simple_filters::ResidueIEFilter::score_type_

private

Definition at line 66 of file ResidueIEFilter.hh.

Referenced by compute(), parse_my_tag(), ResidueIEFilter(), and score_type().

core::scoring::ScoreFunctionOP protocols::simple_filters::ResidueIEFilter::scorefxn_

private

Definition at line 65 of file ResidueIEFilter.hh.

Referenced by compute(), parse_my_tag(), ResidueIEFilter(), and scorefxn().

core::Real protocols::simple_filters::ResidueIEFilter::threshold_

private

Definition at line 67 of file ResidueIEFilter.hh.

Referenced by compute(), parse_my_tag(), and threshold().

bool protocols::simple_filters::ResidueIEFilter::use_resE_

private

Definition at line 74 of file ResidueIEFilter.hh.

Referenced by compute(), parse_my_tag(), and ResidueIEFilter().

bool protocols::simple_filters::ResidueIEFilter::whole_interface_

private

Definition at line 69 of file ResidueIEFilter.hh.

Referenced by compute(), and parse_my_tag().

bool protocols::simple_filters::ResidueIEFilter::whole_pose_

private

Definition at line 68 of file ResidueIEFilter.hh.

Referenced by compute(), and parse_my_tag().

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

• src/protocols/simple_filters/ResidueIEFilter.hh
• src/protocols/simple_filters/ResidueIEFilter.cc