#include <ContactMolecularSurfaceFilter.hh>

Inheritance diagram for protocols::simple_filters::ContactMolecularSurfaceFilter:

Public Types
typedef protocols::filters::Filter	Super

typedef protocols::filters::Filter	Filter

typedef protocols::filters::FilterOP	FilterOP

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

typedef core::scoring::sc::ContactMolecularSurfaceCalculator	ContactMolecularSurfaceCalculator

Public Member Functions
	ContactMolecularSurfaceFilter ()

	ContactMolecularSurfaceFilter (Real const &filtered_area, Real const &distance_weight, bool const quick, bool const verbose)

	~ContactMolecularSurfaceFilter () override=default

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

void	quick (bool const quick)

void	verbose (bool const verbose)

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	parse xml More...

bool	apply (Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...

Real	report_sm (Pose const &pose) const override
	used to report filter internals through a score or silent file More...

core::Real	compute (Pose const &pose) const
	calc contact molecular surface, returns results of the ContactMolecularSurfaceCalculator More...

std::string	name () const override

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	Filter (Filter const &)

	~Filter () override

virtual void	report (std::ostream &, core::pose::Pose const &) const

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 Member Functions
void	setup_from_selectors (Pose const &pose, ContactMolecularSurfaceCalculator &scc) const
	Uses residue selectors to set up the ContactMolecularSurfaceCalculator. More...

Private Attributes
Real	filtered_area_

Real	distance_weight_

Real	near_squared_size_

bool	apolar_target_

bool	quick_ = false

bool	verbose_ = false

core::select::residue_selector::ResidueSelectorCOP	selector1_

core::select::residue_selector::ResidueSelectorCOP	selector2_

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

Member Typedef Documentation

typedef core::scoring::sc::ContactMolecularSurfaceCalculator protocols::simple_filters::ContactMolecularSurfaceFilter::ContactMolecularSurfaceCalculator

typedef basic::datacache::DataMap protocols::simple_filters::ContactMolecularSurfaceFilter::DataMap

typedef protocols::filters::Filter protocols::simple_filters::ContactMolecularSurfaceFilter::Filter

typedef protocols::filters::FilterOP protocols::simple_filters::ContactMolecularSurfaceFilter::FilterOP

typedef core::pose::Pose protocols::simple_filters::ContactMolecularSurfaceFilter::Pose

typedef core::Real protocols::simple_filters::ContactMolecularSurfaceFilter::Real

typedef protocols::filters::Filter protocols::simple_filters::ContactMolecularSurfaceFilter::Super

typedef utility::tag::TagCOP protocols::simple_filters::ContactMolecularSurfaceFilter::TagCOP

Constructor & Destructor Documentation

protocols::simple_filters::ContactMolecularSurfaceFilter::ContactMolecularSurfaceFilter ( )

protocols::simple_filters::ContactMolecularSurfaceFilter::ContactMolecularSurfaceFilter	(	Real const &	filtered_area,
		Real const &	distance_weight,
		bool const	quick,
		bool const	verbose
	)

protocols::simple_filters::ContactMolecularSurfaceFilter::~ContactMolecularSurfaceFilter ( )

overridedefault

Member Function Documentation

bool protocols::simple_filters::ContactMolecularSurfaceFilter::apply ( Pose const & pose ) const

overridevirtual

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

Implements protocols::filters::Filter.

References compute(), filtered_area_, and protocols::simple_filters::tr().

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

static

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

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

overridevirtual

Implements protocols::filters::Filter.

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

calc contact molecular surface, returns results of the ContactMolecularSurfaceCalculator

Parameters

[in] pose Pose to be analyzed

Exceptions

EXCN_CalcInitFailed	Thrown if calculator couldn't be initialized
EXCN_ResultsInvalid	Thrown if computed results are invalid

Returns: ContactMolecularSurfaceCalculator::RESULTS object

References core::scoring::sc::ContactMolecularSurfaceCalculator::CalcContactArea(), core::scoring::sc::MolecularSurfaceCalculator::density, distance_weight_, core::scoring::sc::MolecularSurfaceCalculator::Init(), core::scoring::sc::MolecularSurfaceCalculator::near_squared_size, near_squared_size_, quick_, core::scoring::sc::MolecularSurfaceCalculator::Reset(), selector1_, selector2_, core::scoring::sc::MolecularSurfaceCalculator::settings, setup_from_selectors(), protocols::simple_filters::tr(), verbose_, and core::scoring::sc::MolecularSurfaceCalculator::weight.

Referenced by apply(), and report_sm().

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

overridevirtual

Implements protocols::filters::Filter.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_filters::ContactMolecularSurfaceFilter::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References apolar_target_, distance_weight_, filtered_area_, core::select::residue_selector::get_residue_selector(), near_squared_size_, quick_, selector1_, selector2_, protocols::simple_filters::tr(), and verbose_.

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

static

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

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

void protocols::simple_filters::ContactMolecularSurfaceFilter::quick ( bool const quick )

References quick_.

core::Real protocols::simple_filters::ContactMolecularSurfaceFilter::report_sm ( Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute(), and protocols::simple_filters::tr().

void protocols::simple_filters::ContactMolecularSurfaceFilter::setup_from_selectors	(	Pose const &	pose,
		ContactMolecularSurfaceCalculator &	scc
	)		const

private

Uses residue selectors to set up the ContactMolecularSurfaceCalculator.

Parameters

[in]	pose	Pose to be analyzed
[out]	scc	Initialized, empty ContactMolecularSurfaceCalculator, to which pose residues are added

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), apolar_target_, core::pose::Pose::residue(), selector1_, selector2_, and protocols::simple_filters::tr().

Referenced by compute().

void protocols::simple_filters::ContactMolecularSurfaceFilter::verbose ( bool const verbose )

References verbose_.

Member Data Documentation

bool protocols::simple_filters::ContactMolecularSurfaceFilter::apolar_target_

private

Referenced by parse_my_tag(), and setup_from_selectors().

Real protocols::simple_filters::ContactMolecularSurfaceFilter::distance_weight_

private

Referenced by compute(), and parse_my_tag().

Real protocols::simple_filters::ContactMolecularSurfaceFilter::filtered_area_

private

Referenced by apply(), and parse_my_tag().

Real protocols::simple_filters::ContactMolecularSurfaceFilter::near_squared_size_

private

Referenced by compute(), and parse_my_tag().

bool protocols::simple_filters::ContactMolecularSurfaceFilter::quick_ = false

private

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

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ContactMolecularSurfaceFilter::selector1_

private

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

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ContactMolecularSurfaceFilter::selector2_

private

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

bool protocols::simple_filters::ContactMolecularSurfaceFilter::verbose_ = false

private

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

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

src/protocols/simple_filters/ContactMolecularSurfaceFilter.hh
src/protocols/simple_filters/ContactMolecularSurfaceFilter.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation