protocols::simple_filters::NMerPSSMEnergyFilter Class Reference

#include <NMerPSSMEnergyFilter.hh>

Inheritance diagram for protocols::simple_filters::NMerPSSMEnergyFilter:

Public Member Functions
	NMerPSSMEnergyFilter ()
	NMerPSSMEnergyFilter (core::Real const score_type_threshold, std::string string_resnums)
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
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::Real	compute_residue (core::pose::Pose const &pose, core::Size const seqpos) const
core::Real	compute (core::pose::Pose const &pose) const
	~NMerPSSMEnergyFilter () 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)

Private Attributes
core::Real	score_type_threshold_
std::string	string_resnums_
core::scoring::methods::NMerPSSMEnergy	energy_method_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Constructor & Destructor Documentation

NMerPSSMEnergyFilter() [1/2]

protocols::simple_filters::NMerPSSMEnergyFilter::NMerPSSMEnergyFilter

(

)

NMerPSSMEnergyFilter() [2/2]

protocols::simple_filters::NMerPSSMEnergyFilter::NMerPSSMEnergyFilter	(	core::Real const	score_type_threshold,
		std::string	string_resnums
	)

References score_type_threshold_, and string_resnums_.

~NMerPSSMEnergyFilter()

protocols::simple_filters::NMerPSSMEnergyFilter::~NMerPSSMEnergyFilter ( )

overridedefault

Member Function Documentation

apply()

bool protocols::simple_filters::NMerPSSMEnergyFilter::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(), protocols::filters::Filter::score(), score_type_threshold_, and protocols::simple_filters::TR().

class_name()

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

static

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

clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::simple_filters::NMerPSSMEnergyFilter::compute

(

core::pose::Pose const &

pose

)

const

References compute_residue(), core::pose::get_resnum_list_ordered(), protocols::filters::Filter::score(), core::pose::Pose::size(), and string_resnums_.

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

compute_residue()

core::Real protocols::simple_filters::NMerPSSMEnergyFilter::compute_residue	(	core::pose::Pose const &	pose,
		core::Size const	seqpos
	)		const

References energy_method_, core::scoring::nmer_pssm, core::pose::Pose::residue(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), and core::pose::Pose::size().

Referenced by compute().

fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

void protocols::simple_filters::NMerPSSMEnergyFilter::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 energy_method_, core::scoring::methods::NMerPSSMEnergy::gate_pssm_scores(), core::scoring::methods::NMerPSSMEnergy::nmer_length(), core::scoring::methods::NMerPSSMEnergy::nmer_pssm_scorecut(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_list(), score_type_threshold_, and string_resnums_.

provide_xml_schema()

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

static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

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

report()

void protocols::simple_filters::NMerPSSMEnergyFilter::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::NMerPSSMEnergyFilter::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().

Member Data Documentation

energy_method_

core::scoring::methods::NMerPSSMEnergy protocols::simple_filters::NMerPSSMEnergyFilter::energy_method_

private

Referenced by compute_residue(), and parse_my_tag().

score_type_threshold_

core::Real protocols::simple_filters::NMerPSSMEnergyFilter::score_type_threshold_

private

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

string_resnums_

std::string protocols::simple_filters::NMerPSSMEnergyFilter::string_resnums_

private

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

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

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