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protocols::loops::filters::LoopAnalyzerFilter Class Reference

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:
Inheritance graph
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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 (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 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

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

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

Member Function Documentation

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.

std::string protocols::loops::filters::LoopAnalyzerFilter::class_name ( )
static
protocols::filters::FilterOP protocols::loops::filters::LoopAnalyzerFilter::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

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

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

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().

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

References class_name().

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().

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

Reimplemented from protocols::filters::Filter.

References class_name().

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().

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

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

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

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().

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: