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 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 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 More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_ptr < RDCScore >	RDCScoreOP

typedef utility::pointer::owning_ptr < RDCScore const >	RDCScoreCOP

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

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

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

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

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

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

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

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

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

bool	sort_scores (FragmentScoringMethodOP elem1, FragmentScoringMethodOP elem2)

Variables
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")

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

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

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")

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	trRDCScore ("fragment.picking.scores.RDCScore")

static numeric::random::RandomGenerator	RG (10402)

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::owning_ptr< ABEGO_SS_Score const > protocols::frag_picker::scores::ABEGO_SS_ScoreCOP

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_ptr<RDCScore const> protocols::frag_picker::scores::RDCScoreCOP

typedef utility::pointer::owning_ptr<RDCScore> protocols::frag_picker::scores::RDCScoreOP

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

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

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

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

Function Documentation

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

Referenced by create_cache().

void protocols::frag_picker::scores::create_cache	(	utility::vector1< Size > &	frag_sizes,
		Size	query_len,
		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	(	Size	start_i,
		Size	start_j,
		Matrix &	small_scores,
		Size	frag_len,
		Matrix &	frag_scores
	)

References size().

Referenced by rolling_score().

void protocols::frag_picker::scores::rolling_score	(	Matrix &	small_scores,
		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(), core::sequence::SequenceAlignment::sequence_mapping(), and ss.

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().

Variable Documentation

numeric::random::RandomGenerator protocols::frag_picker::scores::RG(10402)

static

Referenced by protocols::frag_picker::scores::ScoreEValuator::score().

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

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().

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

static

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

static

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

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().

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

static

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

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().

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().

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().

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().

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

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().

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().

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

static

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

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

static

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

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().

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().

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

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().

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().

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

static

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

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().

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

static

Referenced by protocols::frag_picker::scores::RDCScore::read_RDC_file().

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

static

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

static

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

static

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

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().

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().

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

static

Referenced by protocols::frag_picker::scores::FragmentChunkCrms::fill_bb_coords(), and protocols::frag_picker::scores::MakeFragmentChunkCrms::make().

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