protocols::simple_filters::ContactMolecularSurfaceFilter Class Reference

#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, bool const use_rosetta_radii=false)
	ContactMolecularSurfaceFilter (Real const &filtered_area, Real const &distance_weight, bool const quick, bool const verbose, core::select::residue_selector::ResidueSelectorCOP const selector1, core::select::residue_selector::ResidueSelectorCOP const selector2, bool const use_rosetta_radii=false)
	~ContactMolecularSurfaceFilter () override=default
filters::FilterOP	clone () const override
filters::FilterOP	fresh_instance () const override
bool	quick () const
bool	verbose () const
bool	use_rosetta_radii () const
bool	apolar_target () const
Real	filtered_area () const
Real	distance_weight () const
Real	near_squared_size () const
core::select::residue_selector::ResidueSelectorCOP	selector1 () const
core::select::residue_selector::ResidueSelectorCOP	selector2 () const
void	quick (bool const quick)
void	verbose (bool const verbose)
void	use_rosetta_radii (bool const use_rosetta_radii)
void	apolar_target (bool const apolar_target)
void	filtered_area (Real const filtered_area)
void	distance_weight (Real const distance_weight)
void	near_squared_size (Real const near_squared_size)
void	selector1 (core::select::residue_selector::ResidueSelectorCOP const selector)
void	selector2 (core::select::residue_selector::ResidueSelectorCOP const selector)
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 () 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
bool	use_rosetta_radii_ = 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

ContactMolecularSurfaceCalculator

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

DataMap

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

Filter

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

FilterOP

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

Pose

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

Real

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

Super

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

TagCOP

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

Constructor & Destructor Documentation

ContactMolecularSurfaceFilter() [1/3]

protocols::simple_filters::ContactMolecularSurfaceFilter::ContactMolecularSurfaceFilter

(

)

ContactMolecularSurfaceFilter() [2/3]

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

ContactMolecularSurfaceFilter() [3/3]

protocols::simple_filters::ContactMolecularSurfaceFilter::ContactMolecularSurfaceFilter	(	Real const &	filtered_area,
		Real const &	distance_weight,
		bool const	quick,
		bool const	verbose,
		core::select::residue_selector::ResidueSelectorCOP const	selector1,
		core::select::residue_selector::ResidueSelectorCOP const	selector2,
		bool const	use_rosetta_radii = false
	)

~ContactMolecularSurfaceFilter()

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

overridedefault

Member Function Documentation

apolar_target() [1/2]

bool protocols::simple_filters::ContactMolecularSurfaceFilter::apolar_target

(

)

const

References apolar_target_.

Referenced by apolar_target().

apolar_target() [2/2]

void protocols::simple_filters::ContactMolecularSurfaceFilter::apolar_target

(

bool const

apolar_target

)

References apolar_target(), and apolar_target_.

apply()

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().

class_name()

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

static

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

clone()

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

overridevirtual

Implements protocols::filters::Filter.

compute()

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(), core::scoring::sc::MolecularSurfaceCalculator::use_rosetta_radii, use_rosetta_radii_, verbose_, and core::scoring::sc::MolecularSurfaceCalculator::weight.

Referenced by apply(), and report_sm().

distance_weight() [1/2]

core::Real protocols::simple_filters::ContactMolecularSurfaceFilter::distance_weight

(

)

const

References distance_weight_.

Referenced by distance_weight().

distance_weight() [2/2]

void protocols::simple_filters::ContactMolecularSurfaceFilter::distance_weight

(

core::Real const

distance_weight

)

References distance_weight(), and distance_weight_.

filtered_area() [1/2]

core::Real protocols::simple_filters::ContactMolecularSurfaceFilter::filtered_area

(

)

const

References filtered_area_.

Referenced by filtered_area().

filtered_area() [2/2]

void protocols::simple_filters::ContactMolecularSurfaceFilter::filtered_area

(

core::Real const

filtered_area

)

References filtered_area(), and filtered_area_.

fresh_instance()

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

overridevirtual

Implements protocols::filters::Filter.

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

near_squared_size() [1/2]

core::Real protocols::simple_filters::ContactMolecularSurfaceFilter::near_squared_size

(

)

const

References near_squared_size_.

Referenced by near_squared_size().

near_squared_size() [2/2]

void protocols::simple_filters::ContactMolecularSurfaceFilter::near_squared_size

(

core::Real const

near_squared_size

)

References near_squared_size(), and near_squared_size_.

parse_my_tag()

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(), use_rosetta_radii_, and verbose_.

provide_xml_schema()

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().

quick() [1/2]

bool protocols::simple_filters::ContactMolecularSurfaceFilter::quick

(

)

const

References quick_.

Referenced by quick().

quick() [2/2]

void protocols::simple_filters::ContactMolecularSurfaceFilter::quick

(

bool const

quick

)

References quick(), and quick_.

report_sm()

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().

selector1() [1/2]

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ContactMolecularSurfaceFilter::selector1

(

)

const

References selector1_.

selector1() [2/2]

void protocols::simple_filters::ContactMolecularSurfaceFilter::selector1

(

core::select::residue_selector::ResidueSelectorCOP const

selector

)

References selector1_.

selector2() [1/2]

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ContactMolecularSurfaceFilter::selector2

(

)

const

References selector2_.

selector2() [2/2]

void protocols::simple_filters::ContactMolecularSurfaceFilter::selector2

(

core::select::residue_selector::ResidueSelectorCOP const

selector

)

References selector2_.

setup_from_selectors()

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().

use_rosetta_radii() [1/2]

bool protocols::simple_filters::ContactMolecularSurfaceFilter::use_rosetta_radii

(

)

const

References use_rosetta_radii_.

Referenced by use_rosetta_radii().

use_rosetta_radii() [2/2]

void protocols::simple_filters::ContactMolecularSurfaceFilter::use_rosetta_radii

(

bool const

use_rosetta_radii

)

References use_rosetta_radii(), and use_rosetta_radii_.

verbose() [1/2]

bool protocols::simple_filters::ContactMolecularSurfaceFilter::verbose

(

)

const

References verbose_.

Referenced by verbose().

verbose() [2/2]

void protocols::simple_filters::ContactMolecularSurfaceFilter::verbose

(

bool const

verbose

)

References verbose(), and verbose_.

Member Data Documentation

apolar_target_

bool protocols::simple_filters::ContactMolecularSurfaceFilter::apolar_target_

private

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

distance_weight_

Real protocols::simple_filters::ContactMolecularSurfaceFilter::distance_weight_

private

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

filtered_area_

Real protocols::simple_filters::ContactMolecularSurfaceFilter::filtered_area_

private

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

near_squared_size_

Real protocols::simple_filters::ContactMolecularSurfaceFilter::near_squared_size_

private

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

quick_

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

private

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

selector1_

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

private

Referenced by compute(), parse_my_tag(), selector1(), and setup_from_selectors().

selector2_

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

private

Referenced by compute(), parse_my_tag(), selector2(), and setup_from_selectors().

use_rosetta_radii_

bool protocols::simple_filters::ContactMolecularSurfaceFilter::use_rosetta_radii_ = false

private

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

verbose_

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