Rosetta: protocols::simple_filters::TotalSasaFilter Class Reference

Rosetta

#include <TotalSasaFilter.hh>

Inheritance diagram for protocols::simple_filters::TotalSasaFilter:

Inheritance graph

[legend]

Public Member Functions
	TotalSasaFilter ()

	TotalSasaFilter (core::Real const lower_threshold, bool const hydrophobic=false, bool const polar=false, core::Real const upper_threshold=100000000.0, bool report_per_residue_sasa=false)

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

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

void	task_factory (core::pack::task::TaskFactoryOP task_factory)
	Set the task factory to limit SASA calculation to packable residues. More...

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

	~TotalSasaFilter () 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...

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	lower_threshold_

core::Real	upper_threshold_

core::pack::task::TaskFactoryOP	taskfactory_

bool	hydrophobic_
	Residue subset definition. Only the surface area from packable residues. More...

bool	polar_

bool	report_per_residue_sasa_
	count only hydrophobics? polars? More...

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

Constructor & Destructor Documentation

◆ TotalSasaFilter() [1/2]

protocols::simple_filters::TotalSasaFilter::TotalSasaFilter ( )

◆ TotalSasaFilter() [2/2]

protocols::simple_filters::TotalSasaFilter::TotalSasaFilter	(	core::Real const	lower_threshold,
		bool const	hydrophobic = `false`,
		bool const	polar = `false`,
		core::Real const	upper_threshold = `100000000.0`,
		bool	report_per_residue_sasa = `false`
	)

◆ ~TotalSasaFilter()

protocols::simple_filters::TotalSasaFilter::~TotalSasaFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::simple_filters::TotalSasaFilter::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(), lower_threshold_, protocols::simple_filters::TR(), and upper_threshold_.

◆ class_name()

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

static

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

◆ clone()

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

overridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::simple_filters::TotalSasaFilter::compute ( core::pose::Pose const & pose ) const

References core::conformation::Residue::atom_type(), hydrophobic_, core::pose::metrics::CalculatorFactory::Instance(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::chemical::AtomType::is_polar_hydrogen(), core::pose::Pose::metric(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), polar_, report_per_residue_sasa_, core::pose::Pose::residue(), core::pose::Pose::size(), taskfactory_, and protocols::simple_filters::TR().

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

◆ fresh_instance()

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

overridevirtual

Implements protocols::filters::Filter.

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::simple_filters::TotalSasaFilter::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 hydrophobic_, lower_threshold_, core::pack::task::parse_task_operations(), polar_, report_per_residue_sasa_, task_factory(), protocols::simple_filters::TR(), and upper_threshold_.

◆ provide_xml_schema()

void protocols::simple_filters::TotalSasaFilter::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::TotalSasaFilterCreator::provide_xml_schema().

◆ report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), lower_threshold_, core::pose::Pose::metric(), core::conformation::Residue::name3(), core::conformation::membrane::out, core::pose::Pose::pdb_info(), report_per_residue_sasa_, core::pose::Pose::residue(), core::pose::Pose::size(), core::id::to_string(), and upper_threshold_.

◆ report_sm()

core::Real protocols::simple_filters::TotalSasaFilter::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().

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::simple_filters::TotalSasaFilter::task_factory ( )

References taskfactory_.

Referenced by parse_my_tag(), and task_factory().

◆ task_factory() [2/2]

void protocols::simple_filters::TotalSasaFilter::task_factory ( core::pack::task::TaskFactoryOP task_factory )

Set the task factory to limit SASA calculation to packable residues.

References task_factory(), and taskfactory_.

Member Data Documentation

◆ hydrophobic_

bool protocols::simple_filters::TotalSasaFilter::hydrophobic_

private

Residue subset definition. Only the surface area from packable residues.

Referenced by compute(), and parse_my_tag().

◆ lower_threshold_

core::Real protocols::simple_filters::TotalSasaFilter::lower_threshold_

private

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

◆ polar_

bool protocols::simple_filters::TotalSasaFilter::polar_

private

Referenced by compute(), and parse_my_tag().

◆ report_per_residue_sasa_

bool protocols::simple_filters::TotalSasaFilter::report_per_residue_sasa_

private

count only hydrophobics? polars?

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

◆ taskfactory_

core::pack::task::TaskFactoryOP protocols::simple_filters::TotalSasaFilter::taskfactory_

private

Referenced by compute(), and task_factory().

◆ upper_threshold_

core::Real protocols::simple_filters::TotalSasaFilter::upper_threshold_

private

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

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

src/protocols/simple_filters/TotalSasaFilter.hh
src/protocols/simple_filters/TotalSasaFilter.cc