protocols::frag_picker::scores::FragmentScoringMethod Class Reference

a fragment candidate score More...

#include <FragmentScoringMethod.hh>

Inheritance diagram for protocols::frag_picker::scores::FragmentScoringMethod:

Public Member Functions
	FragmentScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)
virtual bool	score (FragmentCandidateOP, FragmentScoreMapOP)=0
std::string &	get_score_name ()
	Returns a name of this scoring method. More...
core::Size	get_id ()
	Returns an integer index assigned to this scoring method by a scoring manager. More...
void	set_id (core::Size id)
	Sets a new integer index for this scoring method. More...
core::Size	get_priority ()
	Returns a priority of this scoring method. More...
core::Real	get_min_allowed_score ()
	Returns the lowest acceptable score value for this scoring method. More...
bool	get_use_lowest ()
	Returns the boolean choice on using the above lowest acceptable score value. More...
void	set_min_allowed_score (core::Real lowest_acceptable_value)
	Sets a new value of the lowest acceptable score. More...

Protected Attributes
core::Size	id_
core::Size	priority_
std::string	name_
core::Real	lowest_acceptable_value_
bool	use_lowest_

Detailed Description

a fragment candidate score

Constructor & Destructor Documentation

protocols::frag_picker::scores::FragmentScoringMethod::FragmentScoringMethod ( core::Size  priority, core::Real  lowest_acceptable_value, bool  use_lowest, std::string  name  )

inline

Member Function Documentation

core::Size protocols::frag_picker::scores::FragmentScoringMethod::get_id ( )

inline

Returns an integer index assigned to this scoring method by a scoring manager.

References id_.

core::Real protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score ( )

inline

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

References lowest_acceptable_value_.

core::Size protocols::frag_picker::scores::FragmentScoringMethod::get_priority ( )

inline

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

References priority_.

std::string& protocols::frag_picker::scores::FragmentScoringMethod::get_score_name ( )

inline

Returns a name of this scoring method.

References name_.

bool protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest ( )

inline

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

References use_lowest_.

virtual bool protocols::frag_picker::scores::FragmentScoringMethod::score ( FragmentCandidateOP  , FragmentScoreMapOP    )

pure virtual

Implemented in protocols::frag_picker::scores::HydrophobicityProfileSimilarity, protocols::frag_picker::scores::HydrophobicitySimilarity, protocols::frag_picker::scores::ABEGO_SS_Score, protocols::frag_picker::scores::SecondarySimilarity, protocols::frag_picker::scores::SolventAccessibility, protocols::frag_picker::scores::FragmentChunkCrms, protocols::frag_picker::scores::PartialSecondarySimilarity, protocols::frag_picker::scores::Psi, protocols::frag_picker::scores::CachingScoringMethod, protocols::frag_picker::scores::FragmentCrmsd, protocols::frag_picker::scores::Phi, protocols::frag_picker::scores::TalosSSSimilarity, protocols::frag_picker::scores::FragmentCrmsdResDepth, protocols::frag_picker::scores::FragmentAllAtomCrmsd, protocols::frag_picker::scores::FragmentDME, protocols::frag_picker::scores::CSScore, protocols::frag_picker::scores::RamaScore, protocols::frag_picker::scores::GunnCostScore, protocols::frag_picker::scores::SecondaryIdentity, protocols::frag_picker::scores::AmbigCSScore, protocols::frag_picker::scores::ConstScore, protocols::frag_picker::scores::PhiPsiSquareWell, protocols::frag_picker::scores::ProfileScoreL1, protocols::frag_picker::scores::PhiPsiRmsd, protocols::frag_picker::scores::ProlinePhiScore, protocols::frag_picker::scores::SequenceIdentity, protocols::frag_picker::scores::MidPhiOut, protocols::frag_picker::scores::MidPsiOut, protocols::frag_picker::scores::PCS_FragDistance, protocols::frag_picker::scores::ProfileScoreBlosum62, protocols::frag_picker::scores::ScoreEValuator, protocols::frag_picker::scores::DisulfideDistance, protocols::frag_picker::scores::JCoupling, protocols::frag_picker::scores::BFactor, protocols::frag_picker::scores::ProfileScoreStructL1, protocols::frag_picker::scores::DisulfideIdentity, protocols::frag_picker::scores::ProfileScoreSubMatrix, and protocols::frag_picker::scores::RDCScore.

void protocols::frag_picker::scores::FragmentScoringMethod::set_id ( core::Size  id )

inline

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

References id_.

void protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score ( core::Real  lowest_acceptable_value )

inline

Sets a new value of the lowest acceptable score.

Fragments that are below the threshold will be discarded

References lowest_acceptable_value_.

Member Data Documentation

core::Size protocols::frag_picker::scores::FragmentScoringMethod::id_

protected

Referenced by protocols::frag_picker::scores::ProfileScoreSubMatrix::cached_score(), protocols::frag_picker::scores::ProfileScoreStructL1::cached_score(), protocols::frag_picker::scores::DisulfideDistance::cached_score(), protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score(), protocols::frag_picker::scores::ProfileScoreBlosum62::cached_score(), protocols::frag_picker::scores::MidPhiOut::cached_score(), protocols::frag_picker::scores::MidPsiOut::cached_score(), protocols::frag_picker::scores::PCS_FragDistance::cached_score(), protocols::frag_picker::scores::PhiPsiRmsd::cached_score(), protocols::frag_picker::scores::AmbigCSScore::cached_score(), protocols::frag_picker::scores::ProfileScoreL1::cached_score(), protocols::frag_picker::scores::GunnCostScore::cached_score(), protocols::frag_picker::scores::InterbondAngleScore::cached_score(), protocols::frag_picker::scores::RamaScore::cached_score(), protocols::frag_picker::scores::CSScore::cached_score(), protocols::frag_picker::scores::FragmentDME::cached_score(), protocols::frag_picker::scores::DihedralConstraintsScore::cached_score(), protocols::frag_picker::scores::ProfileScoreDistWeight::cached_score(), protocols::frag_picker::scores::SecondarySimilarity::cached_score(), protocols::frag_picker::scores::FragmentCrmsdResDepth::cached_score(), protocols::frag_picker::scores::FragmentCrmsd::cached_score(), protocols::frag_picker::scores::LAMBEGO_Similarity::cached_score(), protocols::frag_picker::scores::TorsionBinSimilarity::cached_score(), protocols::frag_picker::scores::ABEGO_SS_Score::cached_score(), protocols::frag_picker::scores::PhiPsiRmsd::describe_score(), get_id(), protocols::frag_picker::scores::RDCScore::score(), protocols::frag_picker::scores::ProfileScoreStructL1::score(), protocols::frag_picker::scores::JCoupling::score(), protocols::frag_picker::scores::PhiPsiSquareWell::score(), protocols::frag_picker::scores::ProfileScoreL1::score(), protocols::frag_picker::scores::ConstScore::score(), protocols::frag_picker::scores::GunnCostScore::score(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::score(), protocols::frag_picker::scores::FragmentDME::score(), protocols::frag_picker::scores::FragmentCrmsdResDepth::score(), protocols::frag_picker::scores::Phi::score(), protocols::frag_picker::scores::FragmentCrmsd::score(), protocols::frag_picker::scores::FragmentChunkCrms::score(), protocols::frag_picker::scores::PartialSecondarySimilarity::score(), protocols::frag_picker::scores::Psi::score(), protocols::frag_picker::scores::SolventAccessibility::score(), protocols::frag_picker::scores::SecondarySimilarity::score(), protocols::frag_picker::scores::ABEGO_SS_Score::score(), protocols::frag_picker::scores::HydrophobicitySimilarity::score(), protocols::frag_picker::scores::HydrophobicityProfileSimilarity::score(), and set_id().

core::Real protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_

protected

Referenced by protocols::frag_picker::scores::ProfileScoreSubMatrix::cached_score(), protocols::frag_picker::scores::ProfileScoreStructL1::cached_score(), protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score(), protocols::frag_picker::scores::DisulfideDistance::cached_score(), protocols::frag_picker::scores::PCS_FragDistance::cached_score(), protocols::frag_picker::scores::ProfileScoreBlosum62::cached_score(), protocols::frag_picker::scores::PhiPsiRmsd::cached_score(), protocols::frag_picker::scores::ProfileScoreL1::cached_score(), protocols::frag_picker::scores::AmbigCSScore::cached_score(), protocols::frag_picker::scores::GunnCostScore::cached_score(), protocols::frag_picker::scores::InterbondAngleScore::cached_score(), protocols::frag_picker::scores::RamaScore::cached_score(), protocols::frag_picker::scores::CSScore::cached_score(), protocols::frag_picker::scores::DihedralConstraintsScore::cached_score(), protocols::frag_picker::scores::FragmentDME::cached_score(), protocols::frag_picker::scores::ProfileScoreDistWeight::cached_score(), protocols::frag_picker::scores::SecondarySimilarity::cached_score(), protocols::frag_picker::scores::FragmentCrmsdResDepth::cached_score(), protocols::frag_picker::scores::FragmentCrmsd::cached_score(), protocols::frag_picker::scores::LAMBEGO_Similarity::cached_score(), protocols::frag_picker::scores::TorsionBinSimilarity::cached_score(), protocols::frag_picker::scores::ABEGO_SS_Score::cached_score(), protocols::frag_picker::scores::PhiPsiRmsd::describe_score(), get_min_allowed_score(), protocols::frag_picker::scores::RDCScore::score(), protocols::frag_picker::scores::ProfileScoreStructL1::score(), protocols::frag_picker::scores::JCoupling::score(), protocols::frag_picker::scores::ProfileScoreL1::score(), protocols::frag_picker::scores::PhiPsiSquareWell::score(), protocols::frag_picker::scores::GunnCostScore::score(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::score(), protocols::frag_picker::scores::FragmentDME::score(), protocols::frag_picker::scores::FragmentCrmsdResDepth::score(), protocols::frag_picker::scores::FragmentCrmsd::score(), protocols::frag_picker::scores::Phi::score(), protocols::frag_picker::scores::Psi::score(), protocols::frag_picker::scores::FragmentChunkCrms::score(), protocols::frag_picker::scores::PartialSecondarySimilarity::score(), protocols::frag_picker::scores::SolventAccessibility::score(), protocols::frag_picker::scores::SecondarySimilarity::score(), protocols::frag_picker::scores::ABEGO_SS_Score::score(), protocols::frag_picker::scores::HydrophobicitySimilarity::score(), protocols::frag_picker::scores::HydrophobicityProfileSimilarity::score(), and set_min_allowed_score().

std::string protocols::frag_picker::scores::FragmentScoringMethod::name_

protected

Referenced by get_score_name().

core::Size protocols::frag_picker::scores::FragmentScoringMethod::priority_

protected

Referenced by get_priority().

bool protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_

protected

Referenced by protocols::frag_picker::scores::ProfileScoreSubMatrix::cached_score(), protocols::frag_picker::scores::ProfileScoreStructL1::cached_score(), protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score(), protocols::frag_picker::scores::DisulfideDistance::cached_score(), protocols::frag_picker::scores::PCS_FragDistance::cached_score(), protocols::frag_picker::scores::ProfileScoreBlosum62::cached_score(), protocols::frag_picker::scores::PhiPsiRmsd::cached_score(), protocols::frag_picker::scores::ProfileScoreL1::cached_score(), protocols::frag_picker::scores::AmbigCSScore::cached_score(), protocols::frag_picker::scores::GunnCostScore::cached_score(), protocols::frag_picker::scores::InterbondAngleScore::cached_score(), protocols::frag_picker::scores::RamaScore::cached_score(), protocols::frag_picker::scores::CSScore::cached_score(), protocols::frag_picker::scores::DihedralConstraintsScore::cached_score(), protocols::frag_picker::scores::FragmentDME::cached_score(), protocols::frag_picker::scores::ProfileScoreDistWeight::cached_score(), protocols::frag_picker::scores::SecondarySimilarity::cached_score(), protocols::frag_picker::scores::FragmentCrmsdResDepth::cached_score(), protocols::frag_picker::scores::FragmentCrmsd::cached_score(), protocols::frag_picker::scores::LAMBEGO_Similarity::cached_score(), protocols::frag_picker::scores::TorsionBinSimilarity::cached_score(), protocols::frag_picker::scores::ABEGO_SS_Score::cached_score(), protocols::frag_picker::scores::PhiPsiRmsd::describe_score(), get_use_lowest(), protocols::frag_picker::scores::RDCScore::score(), protocols::frag_picker::scores::ProfileScoreStructL1::score(), protocols::frag_picker::scores::JCoupling::score(), protocols::frag_picker::scores::ProfileScoreL1::score(), protocols::frag_picker::scores::PhiPsiSquareWell::score(), protocols::frag_picker::scores::GunnCostScore::score(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::score(), protocols::frag_picker::scores::FragmentDME::score(), protocols::frag_picker::scores::FragmentCrmsdResDepth::score(), protocols::frag_picker::scores::FragmentCrmsd::score(), protocols::frag_picker::scores::Phi::score(), protocols::frag_picker::scores::FragmentChunkCrms::score(), protocols::frag_picker::scores::Psi::score(), protocols::frag_picker::scores::PartialSecondarySimilarity::score(), protocols::frag_picker::scores::SolventAccessibility::score(), protocols::frag_picker::scores::SecondarySimilarity::score(), protocols::frag_picker::scores::ABEGO_SS_Score::score(), protocols::frag_picker::scores::HydrophobicitySimilarity::score(), and protocols::frag_picker::scores::HydrophobicityProfileSimilarity::score().

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

• src/protocols/frag_picker/scores/FragmentScoringMethod.hh