protocols::sewing::scoring::TopNMotifScorer Class Reference

#include <TopNMotifScorer.hh>

Inheritance diagram for protocols::sewing::scoring::TopNMotifScorer:

Public Member Functions
	TopNMotifScorer ()
	default construct More...
	~TopNMotifScorer () override=default
	TopNMotifScorer (TopNMotifScorer const &)
core::Real	score (data_storage::SmartAssemblyCOP assembly) override
core::Real	norm_motif_score (data_storage::SmartAssemblyCOP assembly)
core::Real	full_motif_score (data_storage::SmartAssemblyCOP assembly)
std::string	get_name () const override
core::Real	get_weight () const override
void	set_weight (core::Real) override
virtual core::Size	get_scores_to_keep () const
virtual void	set_scores_to_keep (core::Size)
void	set_options_from_tag (utility::tag::TagCOP scorer_tag, basic::datacache::DataMap &datamap) override
Public Member Functions inherited from protocols::sewing::scoring::MotifScorer
	MotifScorer ()
	default construct More...
	~MotifScorer () override=default
	MotifScorer (MotifScorer const &)
core::Real	norm_motif_score (data_storage::SmartAssemblyCOP assembly)
core::Real	full_motif_score (data_storage::SmartAssemblyCOP assembly)
numeric::xyzTransform< core::Real >	get_stub (data_storage::SmartSewingResidueCOP residue) const
core::Real	get_score (numeric::xyzTransform< core::Real > stub1, char ss1, char aa1, numeric::xyzTransform< core::Real > stub2, char ss2, char aa2) const
core::Real	get_last_score () const override
void	set_last_score (core::Real score) override
core::Real	get_old_last_score () const override
void	set_old_last_score (core::Real score) override
Public Member Functions inherited from protocols::sewing::scoring::AssemblyScorer
virtual	~AssemblyScorer ()=default
	Destructor. More...
	AssemblyScorer ()=default
	Prevent direct instantiation: No other constructors allowed. More...
	AssemblyScorer (AssemblyScorer const &)=default

Static Public Member Functions
static std::string	type_name ()
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &)
Static Public Member Functions inherited from protocols::sewing::scoring::MotifScorer
static std::string	type_name ()
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &)

Private Attributes
core::Real	weight_ =1.0
utility::vector1< core::Real >	scores_
core::Size	scores_to_keep_ =1.0

Additional Inherited Members
Protected Attributes inherited from protocols::sewing::scoring::MotifScorer
core::scoring::motif::MotifHashManager &	mman_
core::chemical::ResidueTypeSetCOP	res_type_set_
core::Real	last_score_ =1000
core::Real	old_last_score_ =1000

Constructor & Destructor Documentation

TopNMotifScorer() [1/2]

protocols::sewing::scoring::TopNMotifScorer::TopNMotifScorer

(

)

default construct

References scores_.

~TopNMotifScorer()

protocols::sewing::scoring::TopNMotifScorer::~TopNMotifScorer ( )

overridedefault

TopNMotifScorer() [2/2]

protocols::sewing::scoring::TopNMotifScorer::TopNMotifScorer

(

TopNMotifScorer const &

src

)

Member Function Documentation

full_motif_score()

core::Real protocols::sewing::scoring::TopNMotifScorer::full_motif_score

(

data_storage::SmartAssemblyCOP

assembly

)

use Will's Motif score to calculate the motif score for the entire Assembly

References core::sequence::end, protocols::sewing::scoring::MotifScorer::get_score(), protocols::sewing::scoring::MotifScorer::get_stub(), protocols::sewing::scoring::MotifScorer::res_type_set_, score(), scores_, scores_to_keep_, and protocols::sewing::scoring::TR().

Referenced by norm_motif_score().

get_name()

std::string protocols::sewing::scoring::TopNMotifScorer::get_name ( ) const

overridevirtual

Reimplemented from protocols::sewing::scoring::MotifScorer.

get_scores_to_keep()

core::Size protocols::sewing::scoring::TopNMotifScorer::get_scores_to_keep ( ) const

virtual

References scores_to_keep_.

get_weight()

core::Real protocols::sewing::scoring::TopNMotifScorer::get_weight ( ) const

overridevirtual

Reimplemented from protocols::sewing::scoring::MotifScorer.

References weight_.

norm_motif_score()

core::Real protocols::sewing::scoring::TopNMotifScorer::norm_motif_score

(

data_storage::SmartAssemblyCOP

assembly

)

Motif score of the entire Assembly divided by total residue

References full_motif_score().

Referenced by score().

provide_xml_schema()

void protocols::sewing::scoring::TopNMotifScorer::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References protocols::sewing::scoring::AssemblyScorerFactory::assembly_scorer_ct_namer(), and type_name().

Referenced by protocols::sewing::scoring::TopNMotifScorerCreator::provide_xml_schema().

score()

core::Real protocols::sewing::scoring::TopNMotifScorer::score ( data_storage::SmartAssemblyCOP  assembly )

overridevirtual

Use the negative normalized motif score

Reimplemented from protocols::sewing::scoring::MotifScorer.

References protocols::sewing::scoring::MotifScorer::get_last_score(), norm_motif_score(), protocols::sewing::scoring::MotifScorer::set_last_score(), protocols::sewing::scoring::MotifScorer::set_old_last_score(), and protocols::sewing::scoring::TR().

Referenced by full_motif_score().

set_options_from_tag()

void protocols::sewing::scoring::TopNMotifScorer::set_options_from_tag ( utility::tag::TagCOP  scorer_tag, basic::datacache::DataMap &  datamap  )

overridevirtual

Reimplemented from protocols::sewing::scoring::MotifScorer.

References scores_to_keep_, protocols::sewing::scoring::TR(), and weight_.

set_scores_to_keep()

void protocols::sewing::scoring::TopNMotifScorer::set_scores_to_keep ( core::Size  new_scores )

virtual

References scores_to_keep_.

set_weight()

void protocols::sewing::scoring::TopNMotifScorer::set_weight ( core::Real  weight )

overridevirtual

Reimplemented from protocols::sewing::scoring::MotifScorer.

References weight_.

type_name()

std::string protocols::sewing::scoring::TopNMotifScorer::type_name ( )

static

Referenced by protocols::sewing::scoring::TopNMotifScorerCreator::keyname(), and provide_xml_schema().

Member Data Documentation

scores_

utility::vector1<core::Real> protocols::sewing::scoring::TopNMotifScorer::scores_

private

Referenced by full_motif_score(), and TopNMotifScorer().

scores_to_keep_

core::Size protocols::sewing::scoring::TopNMotifScorer::scores_to_keep_ =1.0

private

Referenced by full_motif_score(), get_scores_to_keep(), set_options_from_tag(), and set_scores_to_keep().

weight_

core::Real protocols::sewing::scoring::TopNMotifScorer::weight_ =1.0

private

Referenced by get_weight(), set_options_from_tag(), and set_weight().

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

• src/protocols/sewing/scoring/TopNMotifScorer.hh
• src/protocols/sewing/scoring/TopNMotifScorer.cc