Rosetta  2020.37
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Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::simple_filters::StemFinder Class Reference

#include <StemFinderFilter.hh>

Inheritance diagram for protocols::simple_filters::StemFinder:
Inheritance graph
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Public Member Functions

 StemFinder ()
 
 ~StemFinder () override
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
bool apply (core::pose::Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 
core::Real report_sm (core::pose::Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
core::Real from_res (core::pose::Pose const &pose) const
 
void from_res (core::Real const r)
 
void from_res (core::pose::ResidueIndexDescriptionCOP r)
 
core::Real to_res (core::pose::Pose const &pose) const
 
void to_res (core::Real const r)
 
void to_res (core::pose::ResidueIndexDescriptionCOP r)
 
core::Real rmsd () const
 
void rmsd (core::Real const c)
 
utility::vector1< std::string > filenames () const
 
void add_filename (std::string const &s)
 
bool stems_on_sse () const
 
void stems_on_sse (bool const b)
 
core::Real neighbor_distance () const
 
void neighbor_distance (core::Real const n)
 
void stems_are_neighbors (bool const b)
 
bool stems_are_neighbors () const
 
void neighbor_separation (core::Size const c)
 
core::Size neighbor_separation () const
 
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

core::pose::ResidueIndexDescriptionCOP from_res_
 
core::pose::ResidueIndexDescriptionCOP to_res_
 
core::Real rmsd_
 
utility::vector1< std::string > filenames_
 
bool stems_on_sse_
 
bool stems_are_neighbors_
 
core::Real neighbor_distance_
 
core::Size neighbor_separation_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Constructor & Destructor Documentation

protocols::simple_filters::StemFinder::StemFinder ( )

References filenames_.

protocols::simple_filters::StemFinder::~StemFinder ( )
overridedefault

Member Function Documentation

void protocols::simple_filters::StemFinder::add_filename ( std::string const &  s)

References filenames_.

bool protocols::simple_filters::StemFinder::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::simple_filters::StemFinder::class_name ( )
static
filters::FilterOP protocols::simple_filters::StemFinder::clone ( ) const
inlineoverridevirtual
utility::vector1< std::string > protocols::simple_filters::StemFinder::filenames ( ) const
inline

References filenames_.

filters::FilterOP protocols::simple_filters::StemFinder::fresh_instance ( ) const
inlineoverridevirtual
core::Real protocols::simple_filters::StemFinder::from_res ( core::pose::Pose const &  pose) const

References from_res_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::StemFinder::from_res ( core::Real const  r)
void protocols::simple_filters::StemFinder::from_res ( core::pose::ResidueIndexDescriptionCOP  r)

References from_res_.

std::string protocols::simple_filters::StemFinder::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

core::Real protocols::simple_filters::StemFinder::neighbor_distance ( ) const
inline

References neighbor_distance_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::StemFinder::neighbor_distance ( core::Real const  n)
inline

References neighbor_distance_.

void protocols::simple_filters::StemFinder::neighbor_separation ( core::Size const  c)
inline
core::Size protocols::simple_filters::StemFinder::neighbor_separation ( ) const
inline

References neighbor_separation_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::StemFinder::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References filenames_, from_res(), from_res_, neighbor_distance(), neighbor_separation(), core::pose::parse_resnum(), rmsd(), stems_are_neighbors(), stems_on_sse(), to_res(), to_res_, and protocols::simple_filters::TR().

void protocols::simple_filters::StemFinder::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_filters::StemFinder::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

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

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

core::Real protocols::simple_filters::StemFinder::rmsd ( ) const
inline

References rmsd_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::StemFinder::rmsd ( core::Real const  c)
inline

References core::pack::dunbrack::c, and rmsd_.

void protocols::simple_filters::StemFinder::stems_are_neighbors ( bool const  b)
inline
bool protocols::simple_filters::StemFinder::stems_are_neighbors ( ) const
inline

References stems_are_neighbors_.

Referenced by apply(), and parse_my_tag().

bool protocols::simple_filters::StemFinder::stems_on_sse ( ) const
inline

References stems_on_sse_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::StemFinder::stems_on_sse ( bool const  b)
inline
core::Real protocols::simple_filters::StemFinder::to_res ( core::pose::Pose const &  pose) const

References core::pose::Pose::size(), and to_res_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::StemFinder::to_res ( core::Real const  r)
void protocols::simple_filters::StemFinder::to_res ( core::pose::ResidueIndexDescriptionCOP  r)

References to_res_.

Member Data Documentation

utility::vector1< std::string > protocols::simple_filters::StemFinder::filenames_
private
core::pose::ResidueIndexDescriptionCOP protocols::simple_filters::StemFinder::from_res_
private

Referenced by from_res(), and parse_my_tag().

core::Real protocols::simple_filters::StemFinder::neighbor_distance_
private

Referenced by neighbor_distance().

core::Size protocols::simple_filters::StemFinder::neighbor_separation_
private

Referenced by neighbor_separation().

core::Real protocols::simple_filters::StemFinder::rmsd_
private

Referenced by rmsd().

bool protocols::simple_filters::StemFinder::stems_are_neighbors_
private

Referenced by stems_are_neighbors().

bool protocols::simple_filters::StemFinder::stems_on_sse_
private

Referenced by stems_on_sse().

core::pose::ResidueIndexDescriptionCOP protocols::simple_filters::StemFinder::to_res_
private

Referenced by parse_my_tag(), and to_res().


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