protocols::sewing::scoring::TerminusMotifScorer Class Reference

#include <TerminusMotifScorer.hh>

Inheritance diagram for protocols::sewing::scoring::TerminusMotifScorer:

Public Member Functions
	TerminusMotifScorer ()
	default construct More...
	~TerminusMotifScorer () override=default
	TerminusMotifScorer (TerminusMotifScorer const &)
core::Real	score (data_storage::SmartAssemblyCOP assembly) override
core::Real	terminus_motif_score (data_storage::SmartAssemblyCOP assembly)
core::Real	get_weight () const override
void	set_weight (core::Real) override
core::Size	get_partner_residue () const
core::Real	get_optimum_distance () const
core::Real	get_maximum_unpenalized_variance () const
char	get_terminus () const
void	set_partner_residue (core::Size)
void	set_optimum_distance (core::Real)
void	set_maximum_unpenalized_variance (core::Real)
void	set_terminus (char)
std::string	get_name () const override
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_ =0
core::Size	partner_residue_ =1
core::Real	optimum_distance_ =0
core::Real	maximum_unpenalized_variance_ =0
char	terminus_ ='X'

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

protocols::sewing::scoring::TerminusMotifScorer::TerminusMotifScorer

(

)

default construct

protocols::sewing::scoring::TerminusMotifScorer::~TerminusMotifScorer ( )

overridedefault

protocols::sewing::scoring::TerminusMotifScorer::TerminusMotifScorer

(

TerminusMotifScorer const &

src

)

Member Function Documentation

core::Real protocols::sewing::scoring::TerminusMotifScorer::get_maximum_unpenalized_variance

(

)

const

References maximum_unpenalized_variance_.

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

inlineoverridevirtual

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

core::Real protocols::sewing::scoring::TerminusMotifScorer::get_optimum_distance

(

)

const

References optimum_distance_.

core::Size protocols::sewing::scoring::TerminusMotifScorer::get_partner_residue

(

)

const

References partner_residue_.

char protocols::sewing::scoring::TerminusMotifScorer::get_terminus

(

)

const

References terminus_.

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

overridevirtual

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

References weight_.

void protocols::sewing::scoring::TerminusMotifScorer::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::TerminusMotifScorerCreator::provide_xml_schema().

core::Real protocols::sewing::scoring::TerminusMotifScorer::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(), protocols::sewing::scoring::MotifScorer::set_last_score(), protocols::sewing::scoring::MotifScorer::set_old_last_score(), and terminus_motif_score().

void protocols::sewing::scoring::TerminusMotifScorer::set_maximum_unpenalized_variance

(

core::Real

setting

)

References maximum_unpenalized_variance_.

void protocols::sewing::scoring::TerminusMotifScorer::set_optimum_distance

(

core::Real

setting

)

References optimum_distance_.

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

overridevirtual

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

References maximum_unpenalized_variance_, optimum_distance_, partner_residue_, terminus_, protocols::sewing::scoring::TR(), and weight_.

void protocols::sewing::scoring::TerminusMotifScorer::set_partner_residue

(

core::Size

setting

)

References partner_residue_.

void protocols::sewing::scoring::TerminusMotifScorer::set_terminus

(

char

setting

)

References terminus_.

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

overridevirtual

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

References weight_.

core::Real protocols::sewing::scoring::TerminusMotifScorer::terminus_motif_score

(

data_storage::SmartAssemblyCOP

assembly

)

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

References core::kinematics::distance(), maximum_unpenalized_variance_, optimum_distance_, partner_residue_, terminus_, and protocols::sewing::scoring::TR().

Referenced by score().

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

static

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

Member Data Documentation

core::Real protocols::sewing::scoring::TerminusMotifScorer::maximum_unpenalized_variance_ =0

private

Referenced by get_maximum_unpenalized_variance(), set_maximum_unpenalized_variance(), set_options_from_tag(), and terminus_motif_score().

core::Real protocols::sewing::scoring::TerminusMotifScorer::optimum_distance_ =0

private

Referenced by get_optimum_distance(), set_optimum_distance(), set_options_from_tag(), and terminus_motif_score().

core::Size protocols::sewing::scoring::TerminusMotifScorer::partner_residue_ =1

private

Referenced by get_partner_residue(), set_options_from_tag(), set_partner_residue(), and terminus_motif_score().

char protocols::sewing::scoring::TerminusMotifScorer::terminus_ ='X'

private

Referenced by get_terminus(), set_options_from_tag(), set_terminus(), and terminus_motif_score().

core::Real protocols::sewing::scoring::TerminusMotifScorer::weight_ =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/TerminusMotifScorer.hh
• src/protocols/sewing/scoring/TerminusMotifScorer.cc