Classes
class	ABEGO_SS_Score

class	AdaptiveScoreHistogram

class	AmbigCSScore
	scores a fragment by the root mean square deviation of Phi and Psi angles. More...

class	AtomBasedConstraintsScore
	A base class for all scoring methods that need atom coordinates. More...

class	AtomPairConstraintsData
	Holds data about a single distance constraint in the form AtomPairConstraintsScore needs. More...

class	AtomPairConstraintsScore
	Scores a fragment with a set of AtomPair constraints. More...

class	BFactor
	BFactor score counts identical residues. More...

class	CachingScoringMethod

class	ConstScore
	ConstScore adds a constant to the total score for each position. More...

class	CSScore
	scores a fragment by the root mean square deviation of Phi and Psi angles. More...

class	DihedralConstraintsScore
	Scores a fragment with a set of Dihedral constraints. More...

class	DisulfideDistance
	scores a fragment by the root mean square deviation of Phi and Psi angles. More...

class	DisulfideIdentity
	DisulfideIdentity score counts identical residues. More...

class	FourAtomsConstraintData
	Holds data about a single four-body constraint in the form usefull for InterbondAngleScore and DihedralConstraintsScore classes. More...

class	FragmentAllAtomCrmsd
	scores a fragment by its crmsd to the given reference structure More...

class	FragmentChunkCrms
	scores a fragment by its tmscore to the given reference structure More...

class	FragmentCrmsd
	scores a fragment by its crmsd to the given reference structure More...

class	FragmentCrmsdResDepth
	scores a fragment by its crmsd to the given reference structure More...

class	FragmentDME
	scores a fragment by its DME to the given reference structure More...

class	FragmentScoreManager
	holds particular score components, weights and calculates the total score for a fragment candidate More...

class	FragmentScoreMap
	holds all small scores (score components) for a given fragment More...

class	FragmentScoringMethod
	a fragment candidate score More...

class	GunnCost

class	GunnCostScore
	scores a fragment by its crmsd to the given reference structure More...

struct	GunnTuple

class	HydrophobicityProfileSimilarity
	scores a fragment by its hydrophobicity similarity More...

class	HydrophobicitySimilarity
	scores a fragment by its hydrophobicity similarity More...

class	InterbondAngleScore
	Scores a fragment with a set of Dihedral constraints. More...

class	JCoupling
	scores a fragment by the JCouplings More...

class	LAMBEGO_Similarity
	scores a fragment by torsion bin similarity More...

class	MakeABEGO_SS_Score
	Maker class that produces a new ABEGO_SS_Score object. More...

class	MakeAmbigCSScore
	Maker class that produces a new AmbigCSScore object. More...

class	MakeAtomPairConstraintsScore
	Maker class that produces a new AtomPairConstraintsScore object. More...

class	MakeBFactor
	Maker class that produces a new BFactor object. More...

class	MakeConstScore
	Maker class that produces a new ConstScore object. More...

class	MakeCSScore
	Maker class that produces a new CSScore object. More...

class	MakeDihedralConstraintsScore
	Maker class that produces a new DihedralConstraintsScore object. More...

class	MakeDisulfideDistance
	Matker class that produces a new DisulfideDistance object. More...

class	MakeDisulfideIdentity
	Maker class that produces a new DisulfideIdentity object. More...

class	MakeFragmentAllAtomCrmsd
	Maker class that produces a new FragmentAllAtomCrmsd object. More...

class	MakeFragmentChunkCrms
	Maker class that produces a new FragmentChunkCrms object. More...

class	MakeFragmentCrmsd
	Maker class that produces a new FragmentCrmsd object. More...

class	MakeFragmentCrmsdResDepth
	Maker class that produces a new FragmentCrmsdResDepth object. More...

class	MakeFragmentDME
	Maker class that produces a new FragmentDME object. More...

class	MakeFragmentScoringMethod
	a fragment candidate More...

class	MakeGunnCostScore
	Maker class that produces a new GunnCostScore object. More...

class	MakeHydrophobicityProfileSimilarity
	Maker class that produces a new HydrophobicityProfileSimilarity object. More...

class	MakeHydrophobicitySimilarity
	Maker class that produces a new HydrophobicitySimilarity object. More...

class	MakeInterbondAngleScore
	Maker class that produces a new InterbondAngleScore object. More...

class	MakeJCoupling
	Matker class that produces a new JCoupling object. More...

class	MakeLAMBEGO_Similarity
	Maker class that produces a new TorsionBin object. More...

class	MakeMidPhiOut
	Matker class that produces a new MidPhiOut object. More...

class	MakeMidPsiOut
	Matker class that produces a new MidPsiOut object. More...

class	MakePartialSecondarySimilarity
	Maker class that produces a new PartialSecondarySimilarity object. More...

class	MakePCS_FragDistance
	Matker class that produces a new PCS_FragDistance object. More...

class	MakePhi
	Maker class that produces a new Phi object. More...

class	MakePhiPsiRmsd
	Matker class that produces a new PhiPsiRmsd object. More...

class	MakePhiPsiSquareWell
	Matker class that produces a new PhiPsiSquareWell object. More...

class	MakeProfileScore

class	MakeProfileScoreBlosum62

class	MakeProfileScoreDistWeight

class	MakeProfileScoreL1

class	MakeProfileScoreStructL1

class	MakeProfileScoreSubMatrix

class	MakeProlinePhiScore
	Maker class that produces a new ProlinePhiScore object. More...

class	MakePsi
	Maker class that produces a new Psi object. More...

class	MakeRamaScore
	Maker class that produces a new RamaScore object. More...

class	MakeRDCScore
	Maker class that produces a new RDCScore object. More...

class	MakeScoreEValuator

class	MakeSecondaryIdentity
	Maker class that produces a new SecondaryIdentity object. More...

class	MakeSecondarySimilarity
	Maker class that produces a new SecondarySimilarity object. More...

class	MakeSequenceIdentity
	Maker class that produces a new SequenceIdentity object. More...

class	MakeSolventAccessibility
	Maker class that produces a new SolventAccessibility object. More...

class	MakeTalosSSSimilarity
	Maker class that produces a new TalosSSSimilarity object. More...

class	MakeTorsionBinSimilarity
	Maker class that produces a new TorsionBin object. More...

class	MidPhiOut
	scores a fragment by the root mean square deviation of Phi and Psi angles. More...

class	MidPsiOut
	scores a fragment by the root mean square deviation of Psi and Psi angles. More...

class	PartialSecondarySimilarity
	scores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster. More...

class	PCS_FragDistance
	scores a fragment by the root mean square deviation of Phi and Psi angles. More...

class	Phi
	scores a fragment by its predicted phi similarity More...

class	PhiPsiRmsd
	scores a fragment by the root mean square deviation of Phi and Psi angles. More...

class	PhiPsiSquareWell
	scores a fragment by the root mean square deviation of Phi and Psi angles. More...

class	ProfileScore
	a fragment candidate More...

class	ProfileScoreBlosum62
	a fragment candidate More...

class	ProfileScoreDistWeight
	a fragment candidate More...

class	ProfileScoreL1
	a fragment candidate More...

class	ProfileScoreStructL1
	a fragment candidate More...

class	ProfileScoreSubMatrix
	a fragment candidate More...

class	ProlinePhiScore
	ProlinePhiScore score counts identical residues. More...

class	Psi
	scores a fragment by its predicted psi similarity More...

class	PValuedFragmentScoreManager
	holds particular score components, weights and calculates the total score for a fragment candidate More...

class	RamaScore
	RamaScore score counts identical residues. More...

class	RDCScore
	scores a fragment by its crmsd to the given reference structure More...

class	ScoreEValuator
	Computes E-Value for a Profile object. More...

class	SecondaryIdentity
	SequenceIdentity score counts how many residues share the same secondary structure. More...

class	SecondarySimilarity
	scores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster. More...

class	SequenceIdentity
	SequenceIdentity score counts identical residues. More...

class	SolventAccessibility
	scores a fragment by its predicted solvent accessibility More...

class	TalosSSSimilarity
	scores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster. More...

class	TorsionBinSimilarity
	scores a fragment by torsion bin similarity More...

Typedefs
typedef utility::vector1 < utility::vector1< core::Real > >	Matrix

typedef utility::pointer::shared_ptr < ABEGO_SS_Score >	ABEGO_SS_ScoreOP

typedef utility::pointer::shared_ptr < ABEGO_SS_Score const >	ABEGO_SS_ScoreCOP

typedef utility::pointer::shared_ptr < AdaptiveScoreHistogram >	AdaptiveScoreHistogramOP

typedef utility::pointer::shared_ptr < AdaptiveScoreHistogram const >	AdaptiveScoreHistogramCOP

typedef utility::pointer::shared_ptr < AtomBasedConstraintsScore >	AtomBasedConstraintsScoreOP

typedef utility::pointer::shared_ptr < AtomBasedConstraintsScore const >	AtomBasedConstraintsScoreCOP

typedef utility::pointer::shared_ptr < AtomPairConstraintsScore >	AtomPairConstraintsScoreOP

typedef utility::pointer::shared_ptr < AtomPairConstraintsScore const >	AtomPairConstraintsScoreCOP

typedef utility::pointer::shared_ptr < AtomPairConstraintsData >	AtomPairConstraintsDataOP

typedef utility::pointer::shared_ptr < AtomPairConstraintsData const >	AtomPairConstraintsDataCOP

typedef utility::pointer::shared_ptr < CachingScoringMethod >	CachingScoringMethodOP

typedef utility::pointer::shared_ptr < CachingScoringMethod const >	CachingScoringMethodCOP

typedef utility::pointer::shared_ptr < CSScore >	CSScoreOP

typedef utility::pointer::shared_ptr < CSScore const >	CSScoreCOP

typedef utility::pointer::shared_ptr < DihedralConstraintsScore >	DihedralConstraintsScoreOP

typedef utility::pointer::shared_ptr < DihedralConstraintsScore const >	DihedralConstraintsScoreCOP

typedef utility::pointer::shared_ptr < FourAtomsConstraintData >	FourAtomsConstraintDataOP

typedef utility::pointer::shared_ptr < FourAtomsConstraintData const >	FourAtomsConstraintDataCOP

typedef utility::pointer::shared_ptr < FragmentScoreManager >	FragmentScoreManagerOP

typedef utility::pointer::shared_ptr < FragmentScoreManager const >	FragmentScoreManagerCOP

typedef utility::pointer::shared_ptr < FragmentScoreMap >	FragmentScoreMapOP

typedef utility::pointer::shared_ptr < FragmentScoreMap const >	FragmentScoreMapCOP

typedef utility::pointer::shared_ptr < FragmentScoringMethod >	FragmentScoringMethodOP

typedef utility::pointer::shared_ptr < FragmentScoringMethod const >	FragmentScoringMethodCOP

typedef utility::pointer::shared_ptr < MakeFragmentScoringMethod >	MakeFragmentScoringMethodOP

typedef utility::pointer::shared_ptr < MakeFragmentScoringMethod const >	MakeFragmentScoringMethodCOP

typedef utility::pointer::shared_ptr < InterbondAngleScore >	InterbondAngleScoreOP

typedef utility::pointer::shared_ptr < InterbondAngleScore const >	InterbondAngleScoreCOP

typedef utility::pointer::shared_ptr < ProfileScore >	ProfileScoreOP

typedef utility::pointer::shared_ptr < ProfileScore const >	ProfileScoreCOP

typedef utility::pointer::shared_ptr < ProfileScoreL1 >	ProfileScoreL1OP

typedef utility::pointer::shared_ptr < ProfileScoreL1 const >	ProfileScoreL1COP

typedef utility::pointer::shared_ptr < RamaScore >	RamaScoreOP

typedef utility::pointer::shared_ptr < RamaScore const >	RamaScoreCOP

typedef utility::pointer::shared_ptr < SecondarySimilarity >	SecondarySimilarityOP

typedef utility::pointer::shared_ptr < SecondarySimilarity const >	SecondarySimilarityCOP

typedef utility::pointer::shared_ptr < TorsionBinSimilarity >	TorsionBinSimilarityOP

typedef utility::pointer::shared_ptr < TorsionBinSimilarity const >	TorsionBinSimilarityCOP

Functions
static basic::Tracer	trABEGO_SS_Score ("protocols.frag_picker.scores.ABEGO_SS_Score")

static basic::Tracer	trAdaptiveScoreHistogram ("fragment.picking.scores.AdaptiveScoreHistogram")

static basic::Tracer	trAmbigCSScore ("protocols.frag_picker.scores.AmbigCSScore")

static basic::Tracer	trAtomBasedConstraintsScore ("fragment.picking.scores.AtomBasedConstraintsScore")

static basic::Tracer	trAtomPairConstraintsScore ("fragment.picking.scores.AtomPairConstraintsScore")

static basic::Tracer	trCSScore ("protocols.frag_picker.scores.CSScore")

static basic::Tracer	trDihedralConstraintsScore ("fragment.picking.scores.DihedralConstraintsScore")

void	create_cache (utility::vector1< core::Size > &frag_sizes, core::Size query_len, core::Size longest_vall_chunk, utility::vector1< Matrix > &cache)

void	allocate_matrix (core::Size i_size, core::Size j_size, Matrix &dst)

void	do_one_line (core::Size start_i, core::Size start_j, Matrix &small_scores, core::Size frag_len, Matrix &frag_scores)

void	rolling_score (Matrix &small_scores, core::Size frag_len, Matrix &frag_scores)

static basic::Tracer	trRmsScore ("protocols.frag_picker.scores.FragmentAllAtomCrmsd")

static basic::Tracer	trTmScore ("protocols.frag_picker.scores.FragmentChunkCrms")

void	sequencealign (core::sequence::SequenceOP seq1, core::sequence::SequenceOP seq2, FArray1D_int &seqmapping)

static basic::Tracer	trRmsScore ("protocols.frag_picker.scores.FragmentCrmsd")

static basic::Tracer	trRmsScore ("protocols.frag_picker.scores.FragmentCrmsdResDepth")

static basic::Tracer	trDMEScore ("protocols.frag_picker.scores.FragmentDME")

bool	sort_scores (FragmentScoringMethodOP elem1, FragmentScoringMethodOP elem2)

static basic::Tracer	trGunnCost ("core.fragment.GunnCost")

static basic::Tracer	trGunnScore ("protocols.frag_picker.scores.GunnCostScore")

static basic::Tracer	trInterbondAngleScore ("fragment.picking.scores.InterbondAngleScore")

static basic::Tracer	trJCoupling ("protocols.frag_picker.scores.JCoupling")

static basic::Tracer	tr ("protocols.frag_picker.scores.LAMBEGO_Similarity")

static basic::Tracer	trPartialSecondarySimilarity ("protocols.frag_picker.scores.PartialSecondarySimilarity")

static basic::Tracer	trPhiPsiRmsd ("protocols.frag_picker.scores.PhiPsiRmsd")

static basic::Tracer	tr ("protocols.frag_picker.scores.PhiPsiSquareWell")

static basic::Tracer	trProfScore ("protocols.frag_picker.scores.ProfileScore")

static basic::Tracer	trProfScoreBlosum62 ("protocols.frag_picker.scores.ProfileScoreBlosum62")

static basic::Tracer	trProfScoreDistWeight ("protocols.frag_picker.scores.ProfileScoreDistWeight")

static basic::Tracer	trProfScoreL1 ("protocols.frag_picker.scores.ProfileScoreL1")

static basic::Tracer	trProfScoreL1 ("protocols.frag_picker.scores.ProfileScoreStructL1")

static basic::Tracer	trProfScoreSubMatrix ("protocols.frag_picker.scores.ProfileScoreSubMatrix")

static basic::Tracer	trRDCScore ("protocols.frag_picker.scores.RDCScore")

static basic::Tracer	trProfScore ("protocols.frag_picker.scores.ScoreEValuator")

static basic::Tracer	trSecondarySimilarity ("protocols.frag_picker.scores.SecondarySimilarity")

static basic::Tracer	trTalosSSSimilarity ("protocols.frag_picker.scores.TalosSSSimilarity")

static basic::Tracer	tr ("protocols.frag_picker.scores.TorsionBinSimilarity")

Typedef Documentation

typedef utility::pointer::shared_ptr< ABEGO_SS_Score const > protocols::frag_picker::scores::ABEGO_SS_ScoreCOP

typedef utility::pointer::shared_ptr< ABEGO_SS_Score > protocols::frag_picker::scores::ABEGO_SS_ScoreOP

typedef utility::pointer::shared_ptr<AdaptiveScoreHistogram const> protocols::frag_picker::scores::AdaptiveScoreHistogramCOP

typedef utility::pointer::shared_ptr<AdaptiveScoreHistogram> protocols::frag_picker::scores::AdaptiveScoreHistogramOP

typedef utility::pointer::shared_ptr<AtomBasedConstraintsScore const> protocols::frag_picker::scores::AtomBasedConstraintsScoreCOP

typedef utility::pointer::shared_ptr<AtomBasedConstraintsScore> protocols::frag_picker::scores::AtomBasedConstraintsScoreOP

typedef utility::pointer::shared_ptr<AtomPairConstraintsData const> protocols::frag_picker::scores::AtomPairConstraintsDataCOP

typedef utility::pointer::shared_ptr<AtomPairConstraintsData> protocols::frag_picker::scores::AtomPairConstraintsDataOP

typedef utility::pointer::shared_ptr<AtomPairConstraintsScore const> protocols::frag_picker::scores::AtomPairConstraintsScoreCOP

typedef utility::pointer::shared_ptr<AtomPairConstraintsScore> protocols::frag_picker::scores::AtomPairConstraintsScoreOP

typedef utility::pointer::shared_ptr< CachingScoringMethod const > protocols::frag_picker::scores::CachingScoringMethodCOP

typedef utility::pointer::shared_ptr< CachingScoringMethod > protocols::frag_picker::scores::CachingScoringMethodOP

typedef utility::pointer::shared_ptr< CSScore const > protocols::frag_picker::scores::CSScoreCOP

typedef utility::pointer::shared_ptr< CSScore > protocols::frag_picker::scores::CSScoreOP

typedef utility::pointer::shared_ptr<DihedralConstraintsScore const> protocols::frag_picker::scores::DihedralConstraintsScoreCOP

typedef utility::pointer::shared_ptr<DihedralConstraintsScore> protocols::frag_picker::scores::DihedralConstraintsScoreOP

typedef utility::pointer::shared_ptr<FourAtomsConstraintData const> protocols::frag_picker::scores::FourAtomsConstraintDataCOP

typedef utility::pointer::shared_ptr<FourAtomsConstraintData> protocols::frag_picker::scores::FourAtomsConstraintDataOP

typedef utility::pointer::shared_ptr<FragmentScoreManager const> protocols::frag_picker::scores::FragmentScoreManagerCOP

typedef utility::pointer::shared_ptr<FragmentScoreManager> protocols::frag_picker::scores::FragmentScoreManagerOP

typedef utility::pointer::shared_ptr<FragmentScoreMap const> protocols::frag_picker::scores::FragmentScoreMapCOP

typedef utility::pointer::shared_ptr<FragmentScoreMap> protocols::frag_picker::scores::FragmentScoreMapOP

typedef utility::pointer::shared_ptr<FragmentScoringMethod const> protocols::frag_picker::scores::FragmentScoringMethodCOP

typedef utility::pointer::shared_ptr<FragmentScoringMethod> protocols::frag_picker::scores::FragmentScoringMethodOP

typedef utility::pointer::shared_ptr<InterbondAngleScore const> protocols::frag_picker::scores::InterbondAngleScoreCOP

typedef utility::pointer::shared_ptr<InterbondAngleScore> protocols::frag_picker::scores::InterbondAngleScoreOP

typedef utility::pointer::shared_ptr<MakeFragmentScoringMethod const> protocols::frag_picker::scores::MakeFragmentScoringMethodCOP

typedef utility::pointer::shared_ptr<MakeFragmentScoringMethod> protocols::frag_picker::scores::MakeFragmentScoringMethodOP

typedef utility::vector1< utility::vector1< core::Real > > protocols::frag_picker::scores::Matrix

typedef utility::pointer::shared_ptr<ProfileScore const> protocols::frag_picker::scores::ProfileScoreCOP

typedef utility::pointer::shared_ptr< ProfileScoreL1 const > protocols::frag_picker::scores::ProfileScoreL1COP

typedef utility::pointer::shared_ptr< ProfileScoreL1 > protocols::frag_picker::scores::ProfileScoreL1OP

typedef utility::pointer::shared_ptr<ProfileScore> protocols::frag_picker::scores::ProfileScoreOP

typedef utility::pointer::shared_ptr< RamaScore const > protocols::frag_picker::scores::RamaScoreCOP

typedef utility::pointer::shared_ptr< RamaScore > protocols::frag_picker::scores::RamaScoreOP

typedef utility::pointer::shared_ptr< SecondarySimilarity const > protocols::frag_picker::scores::SecondarySimilarityCOP

typedef utility::pointer::shared_ptr< SecondarySimilarity > protocols::frag_picker::scores::SecondarySimilarityOP

typedef utility::pointer::shared_ptr< TorsionBinSimilarity const > protocols::frag_picker::scores::TorsionBinSimilarityCOP

typedef utility::pointer::shared_ptr< TorsionBinSimilarity > protocols::frag_picker::scores::TorsionBinSimilarityOP

Function Documentation

void protocols::frag_picker::scores::allocate_matrix	(	core::Size	i_size,
		core::Size	j_size,
		Matrix &	dst
	)

Referenced by create_cache().

void protocols::frag_picker::scores::create_cache	(	utility::vector1< core::Size > &	frag_sizes,
		core::Size	query_len,
		core::Size	longest_vall_chunk,
		utility::vector1< Matrix > &	cache
	)

References allocate_matrix().

Referenced by protocols::frag_picker::scores::ProfileScoreL1::ProfileScoreL1(), protocols::frag_picker::scores::ProfileScoreStructL1::ProfileScoreStructL1(), protocols::frag_picker::scores::SecondarySimilarity::SecondarySimilarity(), and protocols::frag_picker::scores::TalosSSSimilarity::TalosSSSimilarity().

void protocols::frag_picker::scores::do_one_line	(	core::Size	start_i,
		core::Size	start_j,
		Matrix &	small_scores,
		core::Size	frag_len,
		Matrix &	frag_scores
	)

References protocols::mean_field::min().

Referenced by rolling_score().

void protocols::frag_picker::scores::rolling_score	(	Matrix &	small_scores,
		core::Size	frag_len,
		Matrix &	frag_scores
	)

References do_one_line().

Referenced by protocols::frag_picker::scores::ProfileScoreStructL1::do_caching(), protocols::frag_picker::scores::ProfileScoreL1::do_caching(), protocols::frag_picker::scores::TalosSSSimilarity::do_caching(), and protocols::frag_picker::scores::SecondarySimilarity::do_caching().

void protocols::frag_picker::scores::sequencealign	(	core::sequence::SequenceOP	seq1,
		core::sequence::SequenceOP	seq2,
		FArray1D_int &	seqmapping
	)

References core::sequence::NWAligner::align(), protocols::mean_field::max(), protocols::mean_field::min(), and core::sequence::SequenceAlignment::sequence_mapping().

Referenced by protocols::frag_picker::scores::MakeFragmentChunkCrms::make().

bool protocols::frag_picker::scores::sort_scores	(	FragmentScoringMethodOP	elem1,
		FragmentScoringMethodOP	elem2
	)

Referenced by protocols::frag_picker::scores::FragmentScoreManager::add_scoring_method(), and core::scoring::constraints::KofNConstraint::score().

static basic::Tracer protocols::frag_picker::scores::tr ( "protocols.frag_picker.scores.TorsionBinSimilarity" )

static

static basic::Tracer protocols::frag_picker::scores::tr ( "protocols.frag_picker.scores.LAMBEGO_Similarity" )

static

Referenced by protocols::frag_picker::scores::FragmentScoreManager::describe_fragments(), protocols::frag_picker::scores::LAMBEGO_Similarity::do_caching(), protocols::frag_picker::scores::TorsionBinSimilarity::do_caching(), protocols::frag_picker::scores::MakePhiPsiSquareWell::make(), and protocols::frag_picker::scores::PhiPsiSquareWell::PhiPsiSquareWell().

static basic::Tracer protocols::frag_picker::scores::tr ( "protocols.frag_picker.scores.PhiPsiSquareWell" )

static

static basic::Tracer protocols::frag_picker::scores::trABEGO_SS_Score ( "protocols.frag_picker.scores.ABEGO_SS_Score" )

static

static basic::Tracer protocols::frag_picker::scores::trAdaptiveScoreHistogram ( "fragment.picking.scores.AdaptiveScoreHistogram" )

static

static basic::Tracer protocols::frag_picker::scores::trAmbigCSScore ( "protocols.frag_picker.scores.AmbigCSScore" )

static

Referenced by protocols::frag_picker::scores::AmbigCSScore::AmbigCSScore(), and protocols::frag_picker::scores::AmbigCSScore::do_caching().

static basic::Tracer protocols::frag_picker::scores::trAtomBasedConstraintsScore ( "fragment.picking.scores.AtomBasedConstraintsScore" )

static

Referenced by protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching().

static basic::Tracer protocols::frag_picker::scores::trAtomPairConstraintsScore ( "fragment.picking.scores.AtomPairConstraintsScore" )

static

Referenced by protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score(), protocols::frag_picker::scores::MakeAtomPairConstraintsScore::make(), and protocols::frag_picker::scores::AtomPairConstraintsScore::read_constraints().

static basic::Tracer protocols::frag_picker::scores::trCSScore ( "protocols.frag_picker.scores.CSScore" )

static

Referenced by protocols::frag_picker::scores::CSScore::CSScore(), and protocols::frag_picker::scores::CSScore::do_caching().

static basic::Tracer protocols::frag_picker::scores::trDihedralConstraintsScore ( "fragment.picking.scores.DihedralConstraintsScore" )

static

Referenced by protocols::frag_picker::scores::DihedralConstraintsScore::cached_score(), protocols::frag_picker::scores::MakeDihedralConstraintsScore::make(), and protocols::frag_picker::scores::DihedralConstraintsScore::read_constraints().

static basic::Tracer protocols::frag_picker::scores::trDMEScore ( "protocols.frag_picker.scores.FragmentDME" )

static

Referenced by protocols::frag_picker::scores::FragmentDME::fill_CA_coords(), protocols::frag_picker::scores::FragmentDME::FragmentDME(), and protocols::frag_picker::scores::MakeFragmentDME::make().

static basic::Tracer protocols::frag_picker::scores::trGunnCost ( "core.fragment.GunnCost" )

static

static basic::Tracer protocols::frag_picker::scores::trGunnScore ( "protocols.frag_picker.scores.GunnCostScore" )

static

Referenced by protocols::frag_picker::scores::GunnCostScore::cached_score(), protocols::frag_picker::scores::GunnCostScore::computeGunnTuples(), protocols::frag_picker::scores::GunnCostScore::do_caching(), protocols::frag_picker::scores::GunnCostScore::GunnCostScore(), and protocols::frag_picker::scores::MakeGunnCostScore::make().

static basic::Tracer protocols::frag_picker::scores::trInterbondAngleScore ( "fragment.picking.scores.InterbondAngleScore" )

static

Referenced by protocols::frag_picker::scores::InterbondAngleScore::cached_score(), protocols::frag_picker::scores::MakeInterbondAngleScore::make(), and protocols::frag_picker::scores::InterbondAngleScore::read_constraints().

static basic::Tracer protocols::frag_picker::scores::trJCoupling ( "protocols.frag_picker.scores.JCoupling" )

static

Referenced by protocols::frag_picker::scores::MakeJCoupling::make().

static basic::Tracer protocols::frag_picker::scores::trPartialSecondarySimilarity ( "protocols.frag_picker.scores.PartialSecondarySimilarity" )

static

Referenced by protocols::frag_picker::scores::PartialSecondarySimilarity::do_caching().

static basic::Tracer protocols::frag_picker::scores::trPhiPsiRmsd ( "protocols.frag_picker.scores.PhiPsiRmsd" )

static

Referenced by protocols::frag_picker::scores::MakePhiPsiRmsd::make(), and protocols::frag_picker::scores::PhiPsiRmsd::PhiPsiRmsd().

static basic::Tracer protocols::frag_picker::scores::trProfScore ( "protocols.frag_picker.scores.ProfileScore" )

static

Referenced by protocols::frag_picker::scores::ProfileScore::do_caching(), protocols::frag_picker::scores::MakeScoreEValuator::make(), and protocols::frag_picker::scores::MakeProfileScore::make().

static basic::Tracer protocols::frag_picker::scores::trProfScore ( "protocols.frag_picker.scores.ScoreEValuator" )

static

static basic::Tracer protocols::frag_picker::scores::trProfScoreBlosum62 ( "protocols.frag_picker.scores.ProfileScoreBlosum62" )

static

Referenced by protocols::frag_picker::scores::ProfileScoreBlosum62::do_caching(), and protocols::frag_picker::scores::MakeProfileScoreBlosum62::make().

static basic::Tracer protocols::frag_picker::scores::trProfScoreDistWeight ( "protocols.frag_picker.scores.ProfileScoreDistWeight" )

static

Referenced by protocols::frag_picker::scores::ProfileScoreDistWeight::do_caching(), and protocols::frag_picker::scores::MakeProfileScoreDistWeight::make().

static basic::Tracer protocols::frag_picker::scores::trProfScoreL1 ( "protocols.frag_picker.scores.ProfileScoreStructL1" )

static

static basic::Tracer protocols::frag_picker::scores::trProfScoreL1 ( "protocols.frag_picker.scores.ProfileScoreL1" )

static

static basic::Tracer protocols::frag_picker::scores::trProfScoreSubMatrix ( "protocols.frag_picker.scores.ProfileScoreSubMatrix" )

static

Referenced by protocols::frag_picker::scores::ProfileScoreSubMatrix::do_caching(), and protocols::frag_picker::scores::MakeProfileScoreSubMatrix::make().

static basic::Tracer protocols::frag_picker::scores::trRDCScore ( "protocols.frag_picker.scores.RDCScore" )

static

static basic::Tracer protocols::frag_picker::scores::trRmsScore ( "protocols.frag_picker.scores.FragmentCrmsdResDepth" )

static

static basic::Tracer protocols::frag_picker::scores::trRmsScore ( "protocols.frag_picker.scores.FragmentAllAtomCrmsd" )

static

static basic::Tracer protocols::frag_picker::scores::trRmsScore ( "protocols.frag_picker.scores.FragmentCrmsd" )

static

static basic::Tracer protocols::frag_picker::scores::trSecondarySimilarity ( "protocols.frag_picker.scores.SecondarySimilarity" )

static

Referenced by protocols::frag_picker::scores::SecondarySimilarity::do_caching(), and protocols::frag_picker::scores::SecondarySimilarity::do_caching_simple().

static basic::Tracer protocols::frag_picker::scores::trTalosSSSimilarity ( "protocols.frag_picker.scores.TalosSSSimilarity" )

static

Referenced by protocols::frag_picker::scores::TalosSSSimilarity::do_caching(), and protocols::frag_picker::scores::TalosSSSimilarity::do_caching_simple().

static basic::Tracer protocols::frag_picker::scores::trTmScore ( "protocols.frag_picker.scores.FragmentChunkCrms" )

static

Referenced by protocols::frag_picker::scores::MakeFragmentChunkCrms::make().

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