Rosetta Protocols  2014.35
Classes | Typedefs | Functions | Variables
protocols::frag_picker::scores Namespace Reference

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

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 
)
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 
)
void protocols::frag_picker::scores::sequencealign ( core::sequence::SequenceOP  seq1,
core::sequence::SequenceOP  seq2,
FArray1D_int &  seqmapping 
)
bool protocols::frag_picker::scores::sort_scores ( FragmentScoringMethodOP  elem1,
FragmentScoringMethodOP  elem2 
)

Variable Documentation

numeric::random::RandomGenerator protocols::frag_picker::scores::RG(10402)
static
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
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
basic::Tracer protocols::frag_picker::scores::trAtomBasedConstraintsScore("fragment.picking.scores.AtomBasedConstraintsScore")
static
basic::Tracer protocols::frag_picker::scores::trAtomPairConstraintsScore("fragment.picking.scores.AtomPairConstraintsScore")
static
basic::Tracer protocols::frag_picker::scores::trCSScore("protocols.frag_picker.scores.CSScore")
static
basic::Tracer protocols::frag_picker::scores::trDihedralConstraintsScore("fragment.picking.scores.DihedralConstraintsScore")
static
basic::Tracer protocols::frag_picker::scores::trDMEScore("protocols.frag_picker.scores.FragmentDME")
static
basic::Tracer protocols::frag_picker::scores::trGunnCost("core.fragment.GunnCost")
static
basic::Tracer protocols::frag_picker::scores::trGunnScore("protocols.frag_picker.scores.GunnCostScore")
static
basic::Tracer protocols::frag_picker::scores::trInterbondAngleScore("fragment.picking.scores.InterbondAngleScore")
static
basic::Tracer protocols::frag_picker::scores::trJCoupling("protocols.frag_picker.scores.JCoupling")
static
basic::Tracer protocols::frag_picker::scores::trPartialSecondarySimilarity("protocols.frag_picker.scores.PartialSecondarySimilarity")
static
basic::Tracer protocols::frag_picker::scores::trPhiPsiRmsd("protocols.frag_picker.scores.PhiPsiRmsd")
static
basic::Tracer protocols::frag_picker::scores::trProfScore("protocols.frag_picker.scores.ProfileScore")
static
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
basic::Tracer protocols::frag_picker::scores::trProfScoreDistWeight("protocols.frag_picker.scores.ProfileScoreDistWeight")
static
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
basic::Tracer protocols::frag_picker::scores::trRDCScore("protocols.frag_picker.scores.RDCScore")
static
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
basic::Tracer protocols::frag_picker::scores::trTalosSSSimilarity("protocols.frag_picker.scores.TalosSSSimilarity")
static
basic::Tracer protocols::frag_picker::scores::trTmScore("protocols.frag_picker.scores.FragmentChunkCrms")
static