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

a fragment candidate score More...

#include <FragmentScoringMethod.hh>

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

Collaboration diagram for protocols::frag_picker::scores::FragmentScoringMethod:

List of all members.

Public Member Functions
	FragmentScoringMethod (Size priority, 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.
Size	get_id ()
	Returns an integer index assigned to this scoring method by a scoring manager.
void	set_id (Size id)
	Sets a new integer index for this scoring method.
Size	get_priority ()
	Returns a priority of this scoring method.
Real	get_min_allowed_score ()
	Returns the lowest acceptable score value for this scoring method.
bool	get_use_lowest ()
	Returns the boolean choice on using the above lowest acceptable score value.
void	set_min_allowed_score (Real lowest_acceptable_value)
	Sets a new value of the lowest acceptable score.
Protected Attributes
Size	id_
Size	priority_
std::string	name_
Real	lowest_acceptable_value_
bool	use_lowest_

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Detailed Description

a fragment candidate score

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Constructor & Destructor Documentation

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

References make_table_of_pilot_apps::name.

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Member Function Documentation

Size protocols::frag_picker::scores::FragmentScoringMethod::get_id

(

)

[inline]

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

Referenced by protocols::frag_picker::FragmentPicker::set_up_quota_nnmake_style(), and protocols::frag_picker::FragmentPicker::set_up_ss_abego_quota().

Real protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score

(

)

[inline]

Returns the lowest acceptable score value for this scoring method.

Detailed: Fragments that are below the threshold will be discarded

Size protocols::frag_picker::scores::FragmentScoringMethod::get_priority

(

)

[inline]

Returns a priority of this scoring method.

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

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

(

)

[inline]

Returns a name of this scoring method.

bool protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest

(

)

[inline]

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

Detailed: False means there is no lowest acceptable score

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

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

void protocols::frag_picker::scores::FragmentScoringMethod::set_id

(

Size

id

)

[inline]

Sets a new integer index for this scoring method.

Detailed: the method should be called only by a scoring manager

void protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score

(

Real

lowest_acceptable_value

)

[inline]

Sets a new value of the lowest acceptable score.

Detailed: Fragments that are below the threshold will be discarded

---

Member Data Documentation

Size protocols::frag_picker::scores::FragmentScoringMethod::id_ [protected]

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

Real protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_ [protected]

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

std::string protocols::frag_picker::scores::FragmentScoringMethod::name_ [protected]

Size protocols::frag_picker::scores::FragmentScoringMethod::priority_ [protected]

bool protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_ [protected]

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

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

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