protocols::simple_filters::NMerSVMEnergyFilter Class Reference

#include <NMerSVMEnergyFilter.hh>

Inheritance diagram for protocols::simple_filters::NMerSVMEnergyFilter:

Public Member Functions
	NMerSVMEnergyFilter ()
	NMerSVMEnergyFilter (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 (core::pose::Pose const &pose) const
	~NMerSVMEnergyFilter () 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_
bool	dump_table_
std::string	string_resnums_
core::scoring::methods::EnergyMethodOptions	opts_
core::scoring::methods::NMerSVMEnergy	energy_method_ = core::scoring::methods::NMerSVMEnergy( opts_ )
bool	count_eps_
bool	rank_as_score_
core::Real	ep_cutoff_

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

Constructor & Destructor Documentation

NMerSVMEnergyFilter() [1/2]

protocols::simple_filters::NMerSVMEnergyFilter::NMerSVMEnergyFilter

(

)

NMerSVMEnergyFilter() [2/2]

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

References score_type_threshold_, and string_resnums_.

~NMerSVMEnergyFilter()

protocols::simple_filters::NMerSVMEnergyFilter::~NMerSVMEnergyFilter ( )

overridedefault

Member Function Documentation

apply()

bool protocols::simple_filters::NMerSVMEnergyFilter::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::NMerSVMEnergyFilter::class_name ( )

static

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

clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::simple_filters::NMerSVMEnergyFilter::compute

(

core::pose::Pose const &

pose

)

const

References count_eps_, dump_table_, protocols::simple_filters::nmer_svm_res_data::energy, energy_method_, ep_cutoff_, core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(), core::pose::get_resnum_list_ordered(), core::scoring::methods::NMerSVMEnergy::n_svms(), core::scoring::methods::NMerSVMEnergy::nmer_length(), protocols::simple_filters::nmer_svm_res_data::nmer_seq, core::pose::Pose::pdb_info(), protocols::simple_filters::nmer_svm_res_data::pdb_seqpos, protocols::simple_filters::print_nmer_svm_energy_data(), rank_as_score_, protocols::filters::Filter::score(), protocols::simple_filters::nmer_svm_res_data::seqpos, core::pose::Pose::sequence(), core::pose::Pose::size(), string_resnums_, protocols::simple_filters::nmer_svm_res_data::svm_energies, protocols::simple_filters::nmer_svm_res_data::svm_rank_avg, protocols::simple_filters::nmer_svm_res_data::svm_ranks, and core::id::to_string().

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

fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

void protocols::simple_filters::NMerSVMEnergyFilter::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 count_eps_, dump_table_, energy_method_, ep_cutoff_, core::scoring::methods::NMerSVMEnergy::gate_svm_scores(), core::scoring::methods::NMerSVMEnergy::nmer_length(), core::scoring::methods::NMerSVMEnergy::nmer_svm_scorecut(), rank_as_score_, core::scoring::methods::NMerSVMEnergy::read_nmer_svm(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_list(), score_type_threshold_, and string_resnums_.

provide_xml_schema()

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

static

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

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

report()

void protocols::simple_filters::NMerSVMEnergyFilter::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::NMerSVMEnergyFilter::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

count_eps_

bool protocols::simple_filters::NMerSVMEnergyFilter::count_eps_

private

Referenced by compute(), and parse_my_tag().

dump_table_

bool protocols::simple_filters::NMerSVMEnergyFilter::dump_table_

private

Referenced by compute(), and parse_my_tag().

energy_method_

core::scoring::methods::NMerSVMEnergy protocols::simple_filters::NMerSVMEnergyFilter::energy_method_ = core::scoring::methods::NMerSVMEnergy( opts_ )

private

Referenced by compute(), and parse_my_tag().

ep_cutoff_

core::Real protocols::simple_filters::NMerSVMEnergyFilter::ep_cutoff_

private

Referenced by compute(), and parse_my_tag().

opts_

core::scoring::methods::EnergyMethodOptions protocols::simple_filters::NMerSVMEnergyFilter::opts_

private

rank_as_score_

bool protocols::simple_filters::NMerSVMEnergyFilter::rank_as_score_

private

Referenced by compute(), and parse_my_tag().

score_type_threshold_

core::Real protocols::simple_filters::NMerSVMEnergyFilter::score_type_threshold_

private

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

string_resnums_

std::string protocols::simple_filters::NMerSVMEnergyFilter::string_resnums_

private

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

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

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