LoopAnalyzerFilter examines loop structures and packages extra scores into a Job object; maybe you can filter on its "LAM score" (not yet implemented) More...

#include <LoopAnalyzerFilter.hh>

Inheritance diagram for protocols::loops::filters::LoopAnalyzerFilter:

[legend]

Public Member Functions
	LoopAnalyzerFilter ()

	LoopAnalyzerFilter (protocols::loops::Loops const &loops, bool const tracer=false)
	loops is the loops object to say what to analyze. tracer controls whether output is dumped to a tracer or a Job object (for output with the Pose). More...

	~LoopAnalyzerFilter () override

	LoopAnalyzerFilter (LoopAnalyzerFilter const &rhs)

bool	apply (core::pose::Pose const &pose) const override
	returns true if the structure passes the filter, false otherwise More...

core::Real	report_sm (core::pose::Pose const &pose) const override
	required for reporting score values More...

void	report (std::ostream &os, core::pose::Pose const &pose) const override
	allows printing data to a stream More...

std::string	get_name () const

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Filter in Rosetta Scripts) More...

protocols::filters::FilterOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::filters::FilterOP	clone () const override
	required in the context of the parser/scripting scheme More...

void	set_loops (protocols::loops::LoopsCOP loops)
	set loops object, because public setters/getters are a rule More...

protocols::loops::LoopsCOP const &	get_loops (void) const
	get loops object, because public setters/getters are a rule More...

void	set_use_tracer (bool tracer)
	set tracer bool, because public setters/getters are a rule More...

bool	get_use_tracer (void) const
	get tracer bool, because public setters/getters are a rule More...

std::string	name () const override

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string 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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	class_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Attributes
protocols::loops::LoopsCOP	loops_
	used to store a copy of the input loops More...

bool	tracer_
	output to tracer or PDB/silent file More...

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

Detailed Description

LoopAnalyzerFilter examines loop structures and packages extra scores into a Job object; maybe you can filter on its "LAM score" (not yet implemented)

Constructor & Destructor Documentation

◆ LoopAnalyzerFilter() [1/3]

protocols::loops::filters::LoopAnalyzerFilter::LoopAnalyzerFilter ( )

◆ LoopAnalyzerFilter() [2/3]

protocols::loops::filters::LoopAnalyzerFilter::LoopAnalyzerFilter	(	protocols::loops::Loops const &	loops,
		bool const	tracer = `false`
	)

loops is the loops object to say what to analyze. tracer controls whether output is dumped to a tracer or a Job object (for output with the Pose).

◆ ~LoopAnalyzerFilter()

protocols::loops::filters::LoopAnalyzerFilter::~LoopAnalyzerFilter ( )

overridedefault

◆ LoopAnalyzerFilter() [3/3]

protocols::loops::filters::LoopAnalyzerFilter::LoopAnalyzerFilter ( LoopAnalyzerFilter const & rhs )

Member Function Documentation

◆ apply()

bool protocols::loops::filters::LoopAnalyzerFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

returns true if the structure passes the filter, false otherwise

Calculates a bunch of loop-geometry related score terms and dumps them to tracer / Job object for output with the Pose.

Implements protocols::filters::Filter.

◆ class_name()

std::string protocols::loops::filters::LoopAnalyzerFilter::class_name ( )

static

Referenced by get_name(), protocols::loops::filters::LoopAnalyzerFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::loops::filters::LoopAnalyzerFilter::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ fresh_instance()

protocols::filters::FilterOP protocols::loops::filters::LoopAnalyzerFilter::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ get_loops()

protocols::loops::LoopsCOP const & protocols::loops::filters::LoopAnalyzerFilter::get_loops ( void ) const

get loops object, because public setters/getters are a rule

References loops_.

Referenced by report_sm().

◆ get_name()

std::string protocols::loops::filters::LoopAnalyzerFilter::get_name ( ) const

References class_name().

◆ get_use_tracer()

bool protocols::loops::filters::LoopAnalyzerFilter::get_use_tracer ( void ) const

inline

get tracer bool, because public setters/getters are a rule

References tracer_.

Referenced by report_sm().

◆ name()

std::string protocols::loops::filters::LoopAnalyzerFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::loops::filters::LoopAnalyzerFilter::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Filter in Rosetta Scripts)

Reimplemented from protocols::filters::Filter.

References protocols::loop_modeling::utilities::parse_loops_from_tag(), set_loops(), and set_use_tracer().

◆ provide_xml_schema()

void protocols::loops::filters::LoopAnalyzerFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::loop_modeling::utilities::append_subelement_and_attributes_for_parse_loops_from_tag(), class_name(), and protocols::filters::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::loops::filters::LoopAnalyzerFilterCreator::provide_xml_schema().

◆ report()

void protocols::loops::filters::LoopAnalyzerFilter::report	(	std::ostream &	os,
		core::pose::Pose const &	pose
	)		const

overridevirtual

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

◆ report_sm()

core::Real protocols::loops::filters::LoopAnalyzerFilter::report_sm ( core::pose::Pose const & pose ) const

overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References protocols::analysis::LoopAnalyzerMover::apply(), get_loops(), protocols::analysis::LoopAnalyzerMover::get_total_score(), get_use_tracer(), and protocols::loops::TR().

◆ set_loops()

void protocols::loops::filters::LoopAnalyzerFilter::set_loops ( protocols::loops::LoopsCOP loops )

set loops object, because public setters/getters are a rule

getters, setters/////////////

getters, setters/////////////////////

References loops_.

Referenced by parse_my_tag().

◆ set_use_tracer()

void protocols::loops::filters::LoopAnalyzerFilter::set_use_tracer ( bool tracer )

inline

set tracer bool, because public setters/getters are a rule

References protocols::frag_picker::tracer(), and tracer_.

Referenced by parse_my_tag().

Member Data Documentation

◆ loops_

protocols::loops::LoopsCOP protocols::loops::filters::LoopAnalyzerFilter::loops_

private

used to store a copy of the input loops

Referenced by get_loops(), and set_loops().

◆ tracer_

bool protocols::loops::filters::LoopAnalyzerFilter::tracer_

private

output to tracer or PDB/silent file

Referenced by get_use_tracer(), and set_use_tracer().

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

src/protocols/analysis/LoopAnalyzerFilter.hh
src/protocols/analysis/LoopAnalyzerFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ LoopAnalyzerFilter() [1/3]

◆ LoopAnalyzerFilter() [2/3]

◆ ~LoopAnalyzerFilter()

◆ LoopAnalyzerFilter() [3/3]

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ fresh_instance()

◆ get_loops()

◆ get_name()

◆ get_use_tracer()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ set_loops()

◆ set_use_tracer()

Member Data Documentation

◆ loops_

◆ tracer_