#include <ResidueBurialFilter.hh>

Inheritance diagram for protocols::simple_filters::ResidueBurialFilter:

Public Member Functions
	ResidueBurialFilter ()

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...

core::Size	compute (core::pose::Pose const &pose) const

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

core::pack::task::TaskFactoryOP	task_factory () const

void	task_factory (core::pack::task::TaskFactoryOP tf)

	~ResidueBurialFilter () 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	residue_fraction_buried () const

void	residue_fraction_buried (core::Real const r)

std::string	residue () const

void	residue (std::string const &s)

core::Size	neighbors () const

void	neighbors (core::Size const n)

core::Real	distance_threshold () const

void	distance_threshold (core::Real const r)

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	Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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
std::string	residue_

core::Size	neighbors_

core::Real	distance_threshold_

core::pack::task::TaskFactoryOP	task_factory_

core::Real	residue_fraction_buried_
	used to determine which residues to check for burial dynamically. All designable residues will be checked, and if any of them is buried, returns true More...

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

Constructor & Destructor Documentation

protocols::simple_filters::ResidueBurialFilter::ResidueBurialFilter ( )

protocols::simple_filters::ResidueBurialFilter::~ResidueBurialFilter ( )

overridedefault

Member Function Documentation

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

overridevirtual

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

Implements protocols::filters::Filter.

References apply(), compute(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), distance_threshold(), core::conformation::Residue::name3(), neighbors(), neighbors_, core::pose::parse_resnum(), residue(), core::pose::Pose::residue(), protocols::simple_filters::residue_burial_filter_tracer(), residue_fraction_buried(), protocols::rosetta_scripts::residue_packer_states(), task_factory(), and core::id::to_string().

Referenced by apply().

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

static

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

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

overridevirtual

Implements protocols::filters::Filter.

core::Size protocols::simple_filters::ResidueBurialFilter::compute ( core::pose::Pose const & pose ) const

counts the number of residues to target_residue_ across all chains in the pose, other than the one containing target_residue_

References 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::Conformation::num_chains(), core::pose::parse_resnum(), residue(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), protocols::simple_filters::residue_burial_filter_tracer(), and core::pose::Pose::size().

Referenced by apply(), report(), and report_sm().

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

inline

References distance_threshold_.

Referenced by apply().

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

inline

References distance_threshold_.

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

overridevirtual

Implements protocols::filters::Filter.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

core::Size protocols::simple_filters::ResidueBurialFilter::neighbors ( ) const

inline

References neighbors_.

Referenced by apply().

void protocols::simple_filters::ResidueBurialFilter::neighbors ( core::Size const n )

inline

References neighbors_.

void protocols::simple_filters::ResidueBurialFilter::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 distance_threshold_, neighbors_, core::pack::task::parse_task_operations(), residue(), protocols::simple_filters::residue_burial_filter_tracer(), residue_fraction_buried(), and task_factory().

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

static

References core::pack::task::attributes_for_parse_task_operations(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

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

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), core::conformation::Residue::name3(), core::pose::parse_resnum(), residue(), core::pose::Pose::residue(), and task_factory().

core::Real protocols::simple_filters::ResidueBurialFilter::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(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), and task_factory().

std::string protocols::simple_filters::ResidueBurialFilter::residue ( ) const

inline

References residue_.

Referenced by apply(), compute(), parse_my_tag(), and report().

void protocols::simple_filters::ResidueBurialFilter::residue ( std::string const & s )

inline

References residue_.

core::Real protocols::simple_filters::ResidueBurialFilter::residue_fraction_buried ( ) const

inline

References residue_fraction_buried_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::ResidueBurialFilter::residue_fraction_buried ( core::Real const r )

inline

References residue_fraction_buried_.

core::pack::task::TaskFactoryOP protocols::simple_filters::ResidueBurialFilter::task_factory ( ) const

References task_factory_.

Referenced by apply(), parse_my_tag(), report(), and report_sm().

void protocols::simple_filters::ResidueBurialFilter::task_factory ( core::pack::task::TaskFactoryOP tf )

References task_factory_.

Member Data Documentation

core::Real protocols::simple_filters::ResidueBurialFilter::distance_threshold_

private

Referenced by compute(), distance_threshold(), and parse_my_tag().

core::Size protocols::simple_filters::ResidueBurialFilter::neighbors_

private

Referenced by apply(), neighbors(), and parse_my_tag().

std::string protocols::simple_filters::ResidueBurialFilter::residue_

private

Referenced by residue().

core::Real protocols::simple_filters::ResidueBurialFilter::residue_fraction_buried_

private

used to determine which residues to check for burial dynamically. All designable residues will be checked, and if any of them is buried, returns true

Referenced by residue_fraction_buried().

core::pack::task::TaskFactoryOP protocols::simple_filters::ResidueBurialFilter::task_factory_

private

Referenced by task_factory().

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

src/protocols/simple_filters/ResidueBurialFilter.hh
src/protocols/simple_filters/ResidueBurialFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation