protocols::simple_filters::NonSequentialNeighborsFilter Class Reference

#include <NonSequentialNeighborsFilter.hh>

Inheritance diagram for protocols::simple_filters::NonSequentialNeighborsFilter:

Public Member Functions
	NonSequentialNeighborsFilter ()
bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...
filters::FilterOP	clone () const override
filters::FilterOP	fresh_instance () const override
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...
core::Real	compute (core::pose::Pose const &pose) const
	~NonSequentialNeighborsFilter () override
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	distance_threshold () const
void	distance_threshold (core::Real const r)
core::Size	neighbor_cutoff () const
void	neighbor_cutoff (core::Size const n)
bool	bound () const
void	bound (bool const b)
core::Size	resnum () const
void	resnum (core::Size const s)
void	jump (core::Size const j)
core::Size	jump () const
core::Size	residue_neighbors (core::pose::Pose const &pose, core::Size const resi) 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::Real	distance_threshold_
core::Size	neighbor_cutoff_
bool	bound_
core::Size	resnum_
core::Size	jump_

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

Constructor & Destructor Documentation

NonSequentialNeighborsFilter()

protocols::simple_filters::NonSequentialNeighborsFilter::NonSequentialNeighborsFilter

(

)

~NonSequentialNeighborsFilter()

protocols::simple_filters::NonSequentialNeighborsFilter::~NonSequentialNeighborsFilter ( )

overridedefault

Member Function Documentation

apply()

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

overridevirtual

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

Implements protocols::filters::Filter.

References compute().

bound() [1/2]

bool protocols::simple_filters::NonSequentialNeighborsFilter::bound ( ) const

inline

References bound_.

Referenced by compute(), protocols::task_operations::ProteinCore::operator()(), and parse_my_tag().

bound() [2/2]

void protocols::simple_filters::NonSequentialNeighborsFilter::bound ( bool const  b )

inline

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

class_name()

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

static

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

clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::simple_filters::NonSequentialNeighborsFilter::compute

(

core::pose::Pose const &

pose

)

const

References protocols::rigid::RigidBodyTransMover::apply(), bound(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), jump(), residue_neighbors(), resnum(), core::pose::Pose::size(), protocols::rigid::RigidBodyTransMover::step_size(), and protocols::simple_filters::TR().

Referenced by apply(), protocols::task_operations::ProteinCore::operator()(), report(), and report_sm().

distance_threshold() [1/2]

core::Real protocols::simple_filters::NonSequentialNeighborsFilter::distance_threshold ( ) const

inline

References distance_threshold_.

Referenced by protocols::task_operations::ProteinCore::operator()(), parse_my_tag(), and residue_neighbors().

distance_threshold() [2/2]

void protocols::simple_filters::NonSequentialNeighborsFilter::distance_threshold ( core::Real const  r )

inline

References distance_threshold_.

fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

jump() [1/2]

core::Size protocols::simple_filters::NonSequentialNeighborsFilter::jump ( ) const

inline

References jump_.

Referenced by compute(), and parse_my_tag().

jump() [2/2]

void protocols::simple_filters::NonSequentialNeighborsFilter::jump ( core::Size const  j )

inline

References jump_.

Referenced by protocols::task_operations::ProteinCore::operator()().

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

neighbor_cutoff() [1/2]

core::Size protocols::simple_filters::NonSequentialNeighborsFilter::neighbor_cutoff ( ) const

inline

References neighbor_cutoff_.

Referenced by protocols::task_operations::ProteinCore::operator()(), parse_my_tag(), and residue_neighbors().

neighbor_cutoff() [2/2]

void protocols::simple_filters::NonSequentialNeighborsFilter::neighbor_cutoff ( core::Size const  n )

inline

References neighbor_cutoff_.

parse_my_tag()

void protocols::simple_filters::NonSequentialNeighborsFilter::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 bound(), distance_threshold(), jump(), neighbor_cutoff(), resnum(), and protocols::simple_filters::TR().

provide_xml_schema()

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

static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

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

report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

report_sm()

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

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

residue_neighbors()

core::Size protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors	(	core::pose::Pose const &	pose,
		core::Size const	resi
	)		const

References core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), core::kinematics::distance(), distance_threshold(), core::conformation::Residue::nbr_atom(), neighbor_cutoff(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by compute().

resnum() [1/2]

core::Size protocols::simple_filters::NonSequentialNeighborsFilter::resnum ( ) const

inline

References resnum_.

Referenced by compute(), protocols::task_operations::ProteinCore::operator()(), and parse_my_tag().

resnum() [2/2]

void protocols::simple_filters::NonSequentialNeighborsFilter::resnum ( core::Size const  s )

inline

References resnum_.

Member Data Documentation

bound_

bool protocols::simple_filters::NonSequentialNeighborsFilter::bound_

private

Referenced by bound().

distance_threshold_

core::Real protocols::simple_filters::NonSequentialNeighborsFilter::distance_threshold_

private

Referenced by distance_threshold().

jump_

core::Size protocols::simple_filters::NonSequentialNeighborsFilter::jump_

private

Referenced by jump().

neighbor_cutoff_

core::Size protocols::simple_filters::NonSequentialNeighborsFilter::neighbor_cutoff_

private

Referenced by neighbor_cutoff().

resnum_

core::Size protocols::simple_filters::NonSequentialNeighborsFilter::resnum_

private

Referenced by resnum().

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

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