protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter Class Reference

#include <InterfaceHydrophobicResidueContactsFilter.hh>

Inheritance diagram for protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter:

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
InterfaceHydrophobicResidueContactsFilter &	operator= (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 () 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 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)

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

InterfaceHydrophobicResidueContactsFilter() [1/2]

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().

InterfaceHydrophobicResidueContactsFilter() [2/2]

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

inline

References core::init::init().

~InterfaceHydrophobicResidueContactsFilter()

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

overridedefault

Member Function Documentation

apply()

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_.

class_name()

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

static

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

clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Size protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::compute

(

core::pose::Pose const &

pose

)

const

References apolar_res_set_, binder_selector_, core::pose::Pose::energies(), core::conformation::Residue::name3(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energy(), protocols::toolbox::pose_manipulation::rigid_body_move(), sanity_check(), score_cut_, core::pose::Pose::size(), target_selector_, and protocols::simple_filters::TR().

Referenced by apply(), report(), and report_sm().

fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

operator=()

InterfaceHydrophobicResidueContactsFilter& protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::operator= ( InterfaceHydrophobicResidueContactsFilter const &  ot )

inline

References apolar_res_set_, binder_selector_, hydrophobic_residue_contacts_threshold_, score_cut_, scorefxn_, and target_selector_.

parse_my_tag()

void protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::parse_my_tag ( utility::tag::TagCOP  , basic::datacache::DataMap &    )

overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References apolar_res_set_, binder_selector_, hydrophobic_residue_contacts_threshold_, core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), sanity_check(), score_cut_, set_apolar_res(), set_scorefxn(), target_selector_, and protocols::simple_filters::TR().

provide_xml_schema()

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

static

References core::select::residue_selector::attributes_for_parse_residue_selector_when_required(), core::scoring::attributes_for_parse_score_function_w_description_when_required(), class_name(), DEFAULT_APOLAR_RES, DEFAULT_SCORE_CUT, DEFAULT_THRESHOLD, core::id::to_string(), and protocols::filters::xsd_type_definition_w_attributes().

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

report()

void protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and core::conformation::membrane::out.

report_sm()

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().

sanity_check()

void protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::sanity_check ( ) const

private

References apolar_res_set_, binder_selector_, score_cut_, scorefxn_, target_selector_, and protocols::simple_filters::TR().

Referenced by compute(), and parse_my_tag().

set_apolar_res()

void protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::set_apolar_res ( std::string const &  apolar_res )

private

References apolar_res_set_, and protocols::sparta::split().

Referenced by InterfaceHydrophobicResidueContactsFilter(), and parse_my_tag().

set_scorefxn()

void protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn )

private

References core::scoring::name_from_score_type(), SCORE_TERMS, scorefxn_, and protocols::simple_filters::TR().

Referenced by InterfaceHydrophobicResidueContactsFilter(), and parse_my_tag().

Member Data Documentation

apolar_res_set_

std::set<std::string> protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::apolar_res_set_

private

Referenced by compute(), operator=(), parse_my_tag(), sanity_check(), and set_apolar_res().

binder_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::binder_selector_

private

Referenced by compute(), operator=(), parse_my_tag(), and sanity_check().

DEFAULT_APOLAR_RES

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().

DEFAULT_SCORE_CUT

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

static

Referenced by provide_xml_schema().

DEFAULT_THRESHOLD

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

static

Referenced by provide_xml_schema().

hydrophobic_residue_contacts_threshold_

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

private

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

score_cut_

core::Real protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::score_cut_

private

Referenced by compute(), operator=(), parse_my_tag(), and sanity_check().

SCORE_TERMS

const std::set< core::scoring::ScoreType > protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::SCORE_TERMS

static

Initial value:

= std::set<core::scoring::ScoreType> {
core::scoring::ScoreType::fa_rep,
core::scoring::ScoreType::fa_atr,
core::scoring::ScoreType::fa_sol
}

Referenced by set_scorefxn().

scorefxn_

core::scoring::ScoreFunctionOP protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::scorefxn_

private

Referenced by operator=(), sanity_check(), and set_scorefxn().

target_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::target_selector_

private

Referenced by compute(), operator=(), parse_my_tag(), and sanity_check().

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

• src/protocols/simple_filters/InterfaceHydrophobicResidueContactsFilter.hh
• src/protocols/simple_filters/InterfaceHydrophobicResidueContactsFilter.cc