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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)
 
 ~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 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 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_
 
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

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
filters::FilterOP protocols::simple_filters::ContactMolecularSurfaceFilter::clone ( ) const
overridevirtual
core::Real protocols::simple_filters::ContactMolecularSurfaceFilter::compute ( Pose const &  pose) const

calc contact molecular surface, returns results of the ContactMolecularSurfaceCalculator

Parameters
[in]posePose to be analyzed
Exceptions
EXCN_CalcInitFailedThrown if calculator couldn't be initialized
EXCN_ResultsInvalidThrown 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(), 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
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
void protocols::simple_filters::ContactMolecularSurfaceFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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]posePose to be analyzed
[out]sccInitialized, empty ContactMolecularSurfaceCalculator, to which pose residues are added

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), 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

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().

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