protocols::sewing::scoring::MotifScorer Class Reference

#include <MotifScorer.hh>

Inheritance diagram for protocols::sewing::scoring::MotifScorer:

Public Member Functions
	MotifScorer ()
	default construct More...
	~MotifScorer () override=default
	MotifScorer (MotifScorer 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)
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
std::string	get_name () const override
core::Real	get_weight () const override
void	set_weight (core::Real) override
void	set_options_from_tag (utility::tag::TagCOP scorer_tag, basic::datacache::DataMap &datamap) override
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 &)

Protected Attributes
core::scoring::motif::MotifHashManager &	mman_
core::chemical::ResidueTypeSetCOP	res_type_set_
core::Real	last_score_ =1000
core::Real	old_last_score_ =1000

Private Attributes
core::Real	weight_ =1

Constructor & Destructor Documentation

protocols::sewing::scoring::MotifScorer::MotifScorer

(

)

default construct

References weight_.

protocols::sewing::scoring::MotifScorer::~MotifScorer ( )

overridedefault

protocols::sewing::scoring::MotifScorer::MotifScorer

(

MotifScorer const &

src

)

Member Function Documentation

core::Real protocols::sewing::scoring::MotifScorer::full_motif_score

(

data_storage::SmartAssemblyCOP

assembly

)

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

References get_score(), get_stub(), res_type_set_, and score().

Referenced by norm_motif_score().

core::Real protocols::sewing::scoring::MotifScorer::get_last_score ( ) const

overridevirtual

Implements protocols::sewing::scoring::AssemblyScorer.

References last_score_.

Referenced by protocols::sewing::scoring::SegmentContactOrderScorer::score(), protocols::sewing::scoring::TopNMotifScorer::score(), protocols::sewing::scoring::InterModelMotifScorer::score(), protocols::sewing::scoring::StartingNodeMotifScorer::score(), protocols::sewing::scoring::TerminusMotifScorer::score(), protocols::sewing::scoring::IntraDesignTerminusMotifScorer::score(), protocols::sewing::scoring::PartnerMotifScorer::score(), protocols::sewing::scoring::SubsetPartnerMotifScorer::score(), and score().

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

overridevirtual

Implements protocols::sewing::scoring::AssemblyScorer.

Reimplemented in protocols::sewing::scoring::TerminusMotifScorer, protocols::sewing::scoring::SubsetPartnerMotifScorer, protocols::sewing::scoring::StartingNodeMotifScorer, protocols::sewing::scoring::PartnerMotifScorer, protocols::sewing::scoring::SegmentContactOrderScorer, and protocols::sewing::scoring::TopNMotifScorer.

core::Real protocols::sewing::scoring::MotifScorer::get_old_last_score ( ) const

overridevirtual

Implements protocols::sewing::scoring::AssemblyScorer.

References old_last_score_.

core::Real protocols::sewing::scoring::MotifScorer::get_score	(	numeric::xyzTransform< core::Real >	stub1,
		char	ss1,
		char	aa1,
		numeric::xyzTransform< core::Real >	stub2,
		char	ss2,
		char	aa2
	)		const

References core::scoring::motif::MotifHashManager::get_xform_score_BB_BB(), mman_, and score().

Referenced by protocols::sewing::scoring::SegmentContactOrderScorer::contact_order_score(), protocols::sewing::scoring::InterModelMotifScorer::full_motif_score(), protocols::sewing::scoring::TopNMotifScorer::full_motif_score(), protocols::sewing::scoring::StartingNodeMotifScorer::full_motif_score(), full_motif_score(), protocols::sewing::scoring::SubsetPartnerMotifScorer::interface_motif_score(), and protocols::sewing::scoring::PartnerMotifScorer::interface_motif_score().

numeric::xyzTransform< core::Real > protocols::sewing::scoring::MotifScorer::get_stub

(

data_storage::SmartSewingResidueCOP

residue

)

const

References core::pose::motif::get_backbone_reference_frame(), and protocols::kinmatch::xyz().

Referenced by protocols::sewing::scoring::SegmentContactOrderScorer::contact_order_score(), protocols::sewing::scoring::InterModelMotifScorer::full_motif_score(), protocols::sewing::scoring::TopNMotifScorer::full_motif_score(), protocols::sewing::scoring::StartingNodeMotifScorer::full_motif_score(), full_motif_score(), protocols::sewing::scoring::SubsetPartnerMotifScorer::interface_motif_score(), and protocols::sewing::scoring::PartnerMotifScorer::interface_motif_score().

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

overridevirtual

Implements protocols::sewing::scoring::AssemblyScorer.

Reimplemented in protocols::sewing::scoring::TopNMotifScorer, protocols::sewing::scoring::PartnerMotifScorer, protocols::sewing::scoring::SubsetPartnerMotifScorer, protocols::sewing::scoring::TerminusMotifScorer, protocols::sewing::scoring::SegmentContactOrderScorer, and protocols::sewing::scoring::StartingNodeMotifScorer.

References weight_.

core::Real protocols::sewing::scoring::MotifScorer::norm_motif_score

(

data_storage::SmartAssemblyCOP

assembly

)

Motif score of the entire Assembly divided by total residue

References full_motif_score().

Referenced by score().

void protocols::sewing::scoring::MotifScorer::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::MotifScorerCreator::provide_xml_schema().

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

overridevirtual

Use the negative normalized motif score

Implements protocols::sewing::scoring::AssemblyScorer.

Reimplemented in protocols::sewing::scoring::PartnerMotifScorer, protocols::sewing::scoring::SubsetPartnerMotifScorer, protocols::sewing::scoring::TerminusMotifScorer, protocols::sewing::scoring::StartingNodeMotifScorer, protocols::sewing::scoring::SegmentContactOrderScorer, and protocols::sewing::scoring::TopNMotifScorer.

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

Referenced by full_motif_score(), get_score(), set_last_score(), and set_old_last_score().

void protocols::sewing::scoring::MotifScorer::set_last_score ( core::Real  score )

overridevirtual

Implements protocols::sewing::scoring::AssemblyScorer.

References last_score_, and score().

Referenced by protocols::sewing::scoring::SegmentContactOrderScorer::score(), protocols::sewing::scoring::TopNMotifScorer::score(), protocols::sewing::scoring::InterModelMotifScorer::score(), protocols::sewing::scoring::StartingNodeMotifScorer::score(), protocols::sewing::scoring::TerminusMotifScorer::score(), protocols::sewing::scoring::IntraDesignTerminusMotifScorer::score(), protocols::sewing::scoring::PartnerMotifScorer::score(), protocols::sewing::scoring::SubsetPartnerMotifScorer::score(), and score().

void protocols::sewing::scoring::MotifScorer::set_old_last_score ( core::Real  score )

overridevirtual

Implements protocols::sewing::scoring::AssemblyScorer.

References old_last_score_, and score().

Referenced by protocols::sewing::scoring::SegmentContactOrderScorer::score(), protocols::sewing::scoring::TopNMotifScorer::score(), protocols::sewing::scoring::InterModelMotifScorer::score(), protocols::sewing::scoring::StartingNodeMotifScorer::score(), protocols::sewing::scoring::TerminusMotifScorer::score(), protocols::sewing::scoring::IntraDesignTerminusMotifScorer::score(), protocols::sewing::scoring::PartnerMotifScorer::score(), protocols::sewing::scoring::SubsetPartnerMotifScorer::score(), and score().

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

overridevirtual

Implements protocols::sewing::scoring::AssemblyScorer.

Reimplemented in protocols::sewing::scoring::TerminusMotifScorer, protocols::sewing::scoring::SubsetPartnerMotifScorer, protocols::sewing::scoring::TopNMotifScorer, protocols::sewing::scoring::PartnerMotifScorer, protocols::sewing::scoring::StartingNodeMotifScorer, and protocols::sewing::scoring::SegmentContactOrderScorer.

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

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

overridevirtual

Implements protocols::sewing::scoring::AssemblyScorer.

Reimplemented in protocols::sewing::scoring::TopNMotifScorer, protocols::sewing::scoring::PartnerMotifScorer, protocols::sewing::scoring::SubsetPartnerMotifScorer, protocols::sewing::scoring::TerminusMotifScorer, protocols::sewing::scoring::SegmentContactOrderScorer, and protocols::sewing::scoring::StartingNodeMotifScorer.

References weight_.

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

static

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

Member Data Documentation

core::Real protocols::sewing::scoring::MotifScorer::last_score_ =1000

protected

Referenced by get_last_score(), and set_last_score().

core::scoring::motif::MotifHashManager& protocols::sewing::scoring::MotifScorer::mman_

protected

Referenced by get_score().

core::Real protocols::sewing::scoring::MotifScorer::old_last_score_ =1000

protected

Referenced by get_old_last_score(), and set_old_last_score().

core::chemical::ResidueTypeSetCOP protocols::sewing::scoring::MotifScorer::res_type_set_

protected

Referenced by protocols::sewing::scoring::SegmentContactOrderScorer::contact_order_score(), protocols::sewing::scoring::InterModelMotifScorer::full_motif_score(), protocols::sewing::scoring::TopNMotifScorer::full_motif_score(), protocols::sewing::scoring::StartingNodeMotifScorer::full_motif_score(), full_motif_score(), protocols::sewing::scoring::SubsetPartnerMotifScorer::interface_motif_score(), and protocols::sewing::scoring::PartnerMotifScorer::interface_motif_score().

core::Real protocols::sewing::scoring::MotifScorer::weight_ =1

private

Referenced by get_weight(), MotifScorer(), 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/MotifScorer.hh
• src/protocols/sewing/scoring/MotifScorer.cc