#include <StemFinderFilter.hh>

Inheritance diagram for protocols::simple_filters::StemFinder:

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 () 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
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

◆ StemFinder()

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

References filenames_.

◆ ~StemFinder()

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

overridedefault

Member Function Documentation

◆ add_filename()

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

References filenames_.

◆ apply()

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

overridevirtual

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

Implements protocols::filters::Filter.

References core::pose::Pose::conformation(), core::kinematics::distance(), protocols::simple_filters::dssp(), filenames_, protocols::rosetta_scripts::find_nearest_res(), from_res(), protocols::simple_filters::load_poses(), core::conformation::Residue::name1(), neighbor_distance(), neighbor_separation(), protocols::simple_filters::res_res_min_distance(), core::conformation::Conformation::residue(), rmsd(), core::pose::Pose::size(), stems_are_neighbors(), stems_on_sse(), to_res(), and protocols::simple_filters::TR().

◆ class_name()

std::string protocols::simple_filters::StemFinder::class_name ( )

static

Referenced by protocols::simple_filters::StemFinderFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ filenames()

utility::vector1< std::string > protocols::simple_filters::StemFinder::filenames ( ) const

inline

References filenames_.

◆ fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ from_res() [1/3]

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

References from_res_.

Referenced by apply(), and parse_my_tag().

◆ from_res() [2/3]

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

References from_res_.

◆ from_res() [3/3]

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

References from_res_, and core::pose::make_rid_posenum().

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ neighbor_distance() [1/2]

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

inline

References neighbor_distance_.

Referenced by apply(), and parse_my_tag().

◆ neighbor_distance() [2/2]

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

inline

References neighbor_distance_.

◆ neighbor_separation() [1/2]

core::Size protocols::simple_filters::StemFinder::neighbor_separation ( ) const

inline

References neighbor_separation_.

Referenced by apply(), and parse_my_tag().

◆ neighbor_separation() [2/2]

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

inline

References neighbor_separation_.

◆ 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().

◆ provide_xml_schema()

void protocols::simple_filters::StemFinder::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pose::attributes_for_parse_resnum(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::simple_filters::StemFinderFilterCreator::provide_xml_schema().

◆ report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

◆ report_sm()

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.

◆ rmsd() [1/2]

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

inline

References rmsd_.

Referenced by apply(), and parse_my_tag().

◆ rmsd() [2/2]

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

inline

References rmsd_.

◆ stems_are_neighbors() [1/2]

bool protocols::simple_filters::StemFinder::stems_are_neighbors ( ) const

inline

References stems_are_neighbors_.

Referenced by apply(), and parse_my_tag().

◆ stems_are_neighbors() [2/2]

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

inline

References protocols::match::upstream::b, and stems_are_neighbors_.

◆ stems_on_sse() [1/2]

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

inline

References stems_on_sse_.

Referenced by apply(), and parse_my_tag().

◆ stems_on_sse() [2/2]

void protocols::simple_filters::StemFinder::stems_on_sse ( bool const b )

inline

References protocols::match::upstream::b, and stems_on_sse_.

◆ to_res() [1/3]

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().

◆ to_res() [2/3]

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

References to_res_.

◆ to_res() [3/3]

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

References core::pose::make_rid_posenum(), and to_res_.

Member Data Documentation

◆ filenames_

utility::vector1< std::string > protocols::simple_filters::StemFinder::filenames_

private

Referenced by add_filename(), apply(), filenames(), parse_my_tag(), and StemFinder().

◆ from_res_

core::pose::ResidueIndexDescriptionCOP protocols::simple_filters::StemFinder::from_res_

private

Referenced by from_res(), and parse_my_tag().

◆ neighbor_distance_

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

private

Referenced by neighbor_distance().

◆ neighbor_separation_

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

private

Referenced by neighbor_separation().

◆ rmsd_

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

private

Referenced by rmsd().

◆ stems_are_neighbors_

bool protocols::simple_filters::StemFinder::stems_are_neighbors_

private

Referenced by stems_are_neighbors().

◆ stems_on_sse_

bool protocols::simple_filters::StemFinder::stems_on_sse_

private

Referenced by stems_on_sse().

◆ to_res_

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:

src/protocols/simple_filters/StemFinderFilter.hh
src/protocols/simple_filters/StemFinderFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ StemFinder()

◆ ~StemFinder()

Member Function Documentation

◆ add_filename()

◆ apply()

◆ class_name()

◆ clone()

◆ filenames()

◆ fresh_instance()

◆ from_res() [1/3]

◆ from_res() [2/3]

◆ from_res() [3/3]

◆ name()

◆ neighbor_distance() [1/2]

◆ neighbor_distance() [2/2]

◆ neighbor_separation() [1/2]

◆ neighbor_separation() [2/2]

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ rmsd() [1/2]

◆ rmsd() [2/2]

◆ stems_are_neighbors() [1/2]

◆ stems_are_neighbors() [2/2]

◆ stems_on_sse() [1/2]

◆ stems_on_sse() [2/2]

◆ to_res() [1/3]

◆ to_res() [2/3]

◆ to_res() [3/3]

Member Data Documentation

◆ filenames_

◆ from_res_

◆ neighbor_distance_

◆ neighbor_separation_

◆ rmsd_

◆ stems_are_neighbors_

◆ stems_on_sse_

◆ to_res_