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protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter Class Reference

#include <InterfaceHydrophobicResidueContactsFilter.hh>

Inheritance diagram for protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter:
Inheritance graph
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Public Member Functions

 InterfaceHydrophobicResidueContactsFilter (core::Size const hydrophobic_residue_contacts_threshold=DEFAULT_THRESHOLD, core::select::residue_selector::ResidueSelectorCOP target_selector=nullptr, core::select::residue_selector::ResidueSelectorCOP binder_selector=nullptr, core::scoring::ScoreFunctionCOP scorefxn=nullptr, core::Real score_cut=DEFAULT_SCORE_CUT, std::string const &apolar_res=DEFAULT_APOLAR_RES)
 
bool apply (core::pose::Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
InterfaceHydrophobicResidueContactsFilteroperator= (InterfaceHydrophobicResidueContactsFilter const &ot)
 
 InterfaceHydrophobicResidueContactsFilter (InterfaceHydrophobicResidueContactsFilter const &init)
 
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::Size compute (core::pose::Pose const &pose) const
 
 ~InterfaceHydrophobicResidueContactsFilter () 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 (Filter 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 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)
 

Static Public Attributes

static const core::Size DEFAULT_THRESHOLD = 5
 
static const std::string DEFAULT_APOLAR_RES = "ALA,CYS,CYD,PHE,ILE,LEU,MET,PRO,THR,VAL,TRP,TYR"
 
static const core::Real DEFAULT_SCORE_CUT = -0.5
 
static const std::set
< core::scoring::ScoreType
SCORE_TERMS
 

Private Member Functions

void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_apolar_res (std::string const &apolar_res)
 
void sanity_check () const
 

Private Attributes

core::Size hydrophobic_residue_contacts_threshold_
 
core::select::residue_selector::ResidueSelectorCOP target_selector_
 
core::select::residue_selector::ResidueSelectorCOP binder_selector_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Real score_cut_
 
std::set< std::string > apolar_res_set_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Constructor & Destructor Documentation

protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::InterfaceHydrophobicResidueContactsFilter ( core::Size const  hydrophobic_residue_contacts_threshold = DEFAULT_THRESHOLD,
core::select::residue_selector::ResidueSelectorCOP  target_selector = nullptr,
core::select::residue_selector::ResidueSelectorCOP  binder_selector = nullptr,
core::scoring::ScoreFunctionCOP  scorefxn = nullptr,
core::Real  score_cut = DEFAULT_SCORE_CUT,
std::string const &  apolar_res = DEFAULT_APOLAR_RES 
)
inline

References set_apolar_res(), and set_scorefxn().

protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::InterfaceHydrophobicResidueContactsFilter ( InterfaceHydrophobicResidueContactsFilter const &  init)
inline

References core::init::init().

protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::~InterfaceHydrophobicResidueContactsFilter ( )
overridedefault

Member Function Documentation

bool protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::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(), and hydrophobic_residue_contacts_threshold_.

std::string protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::class_name ( )
static
filters::FilterOP protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::clone ( ) const
inlineoverridevirtual
core::Size protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::compute ( core::pose::Pose const &  pose) const
filters::FilterOP protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::fresh_instance ( ) const
inlineoverridevirtual
std::string protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

InterfaceHydrophobicResidueContactsFilter& protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::operator= ( InterfaceHydrophobicResidueContactsFilter const &  ot)
inline
void protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

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

void protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::sanity_check ( ) const
private
void protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::set_apolar_res ( std::string const &  apolar_res)
private
void protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)
private

Member Data Documentation

std::set<std::string> protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::apolar_res_set_
private
core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::binder_selector_
private
const std::string protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::DEFAULT_APOLAR_RES = "ALA,CYS,CYD,PHE,ILE,LEU,MET,PRO,THR,VAL,TRP,TYR"
static

Referenced by provide_xml_schema().

const core::Real protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::DEFAULT_SCORE_CUT = -0.5
static

Referenced by provide_xml_schema().

const core::Size protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::DEFAULT_THRESHOLD = 5
static

Referenced by provide_xml_schema().

core::Size protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::hydrophobic_residue_contacts_threshold_
private

Referenced by apply(), operator=(), and parse_my_tag().

core::Real protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::score_cut_
private
const std::set< core::scoring::ScoreType > protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::SCORE_TERMS
static
Initial value:

Referenced by set_scorefxn().

core::scoring::ScoreFunctionOP protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::scorefxn_
private
core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::target_selector_
private

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