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Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::simple_filters::ContactMolecularSurfaceFilter Class Reference

#include <ContactMolecularSurfaceFilter.hh>

Inheritance diagram for protocols::simple_filters::ContactMolecularSurfaceFilter:
Inheritance graph
[legend]

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

◆ DataMap

◆ Filter

◆ FilterOP

◆ Pose

◆ Real

◆ Super

◆ 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

◆ clone()

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

◆ compute()

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

◆ 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)

◆ 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

◆ 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)

◆ parse_my_tag()

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

◆ provide_xml_schema()

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

◆ 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]posePose to be analyzed
[out]sccInitialized, 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)

◆ 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

◆ distance_weight_

Real protocols::simple_filters::ContactMolecularSurfaceFilter::distance_weight_
private

◆ 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

◆ 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

◆ selector2_

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

◆ use_rosetta_radii_

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

◆ 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: