Rosetta 3.4
Classes | Typedefs | Functions | Variables
protocols::frag_picker::scores Namespace Reference

Classes

class  ABEGO_SS_Score
class  MakeABEGO_SS_Score
 Maker class that produces a new ABEGO_SS_Score object. More...
class  AdaptiveScoreHistogram
class  AmbigCSScore
 scores a fragment by the root mean square deviation of Phi and Psi angles. More...
class  MakeAmbigCSScore
 Maker class that produces a new AmbigCSScore object. More...
class  AtomBasedConstraintsScore
 A base class for all scoring methods that need atom coordinates. More...
class  AtomPairConstraintsScore
 Scores a fragment with a set of AtomPair constraints. More...
class  AtomPairConstraintsData
 Holds data about a single distance constraint in the form AtomPairConstraintsScore needs. More...
class  MakeAtomPairConstraintsScore
 Maker class that produces a new AtomPairConstraintsScore object. More...
class  BFactor
 BFactor score counts identical residues. More...
class  MakeBFactor
 Maker class that produces a new BFactor object. More...
class  CachingScoringMethod
class  ConstScore
 ConstScore adds a constant to the total score for each position. More...
class  MakeConstScore
 Maker class that produces a new ConstScore object. More...
class  CSScore
 scores a fragment by the root mean square deviation of Phi and Psi angles. More...
class  MakeCSScore
 Maker class that produces a new CSScore object. More...
class  DihedralConstraintsScore
 Scores a fragment with a set of Dihedral constraints. More...
class  MakeDihedralConstraintsScore
 Maker class that produces a new DihedralConstraintsScore object. More...
class  DisulfideDistance
 scores a fragment by the root mean square deviation of Phi and Psi angles. More...
class  MakeDisulfideDistance
 Matker class that produces a new DisulfideDistance object. More...
class  DisulfideIdentity
 DisulfideIdentity score counts identical residues. More...
class  MakeDisulfideIdentity
 Maker class that produces a new DisulfideIdentity object. 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  MakeFragmentAllAtomCrmsd
 Maker class that produces a new FragmentAllAtomCrmsd object. More...
class  FragmentCrmsd
 scores a fragment by its crmsd to the given reference structure More...
class  MakeFragmentCrmsd
 Maker class that produces a new FragmentCrmsd object. More...
class  FragmentCrmsdResDepth
 scores a fragment by its crmsd to the given reference structure More...
class  MakeFragmentCrmsdResDepth
 Maker class that produces a new FragmentCrmsdResDepth object. More...
class  FragmentDME
 scores a fragment by its DME to the given reference structure More...
class  MakeFragmentDME
 Maker class that produces a new FragmentDME object. 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  MakeFragmentScoringMethod
 a fragment candidate More...
struct  GunnTuple
class  GunnCost
class  GunnCostScore
 scores a fragment by its crmsd to the given reference structure More...
class  MakeGunnCostScore
 Maker class that produces a new GunnCostScore object. More...
class  HydrophobicityProfileSimilarity
 scores a fragment by its hydrophobicity similarity More...
class  MakeHydrophobicityProfileSimilarity
 Maker class that produces a new HydrophobicityProfileSimilarity object. More...
class  HydrophobicitySimilarity
 scores a fragment by its hydrophobicity similarity More...
class  MakeHydrophobicitySimilarity
 Maker class that produces a new HydrophobicitySimilarity object. More...
class  InterbondAngleScore
 Scores a fragment with a set of Dihedral constraints. More...
class  MakeInterbondAngleScore
 Maker class that produces a new InterbondAngleScore object. More...
class  JCoupling
 scores a fragment by the JCouplings More...
class  MakeJCoupling
 Matker class that produces a new JCoupling object. More...
class  LAMBEGO_Similarity
 scores a fragment by torsion bin similarity More...
class  MakeLAMBEGO_Similarity
 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  MakeMidPhiOut
 Matker class that produces a new MidPhiOut object. More...
class  MidPsiOut
 scores a fragment by the root mean square deviation of Psi and Psi angles. More...
class  MakeMidPsiOut
 Matker class that produces a new MidPsiOut object. 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  MakePartialSecondarySimilarity
 Maker class that produces a new PartialSecondarySimilarity object. More...
class  PCS_FragDistance
 scores a fragment by the root mean square deviation of Phi and Psi angles. More...
class  MakePCS_FragDistance
 Matker class that produces a new PCS_FragDistance object. More...
class  Phi
 scores a fragment by its predicted phi similarity More...
class  MakePhi
 Maker class that produces a new Phi object. More...
class  PhiPsiRmsd
 scores a fragment by the root mean square deviation of Phi and Psi angles. More...
class  MakePhiPsiRmsd
 Matker class that produces a new PhiPsiRmsd object. More...
class  PhiPsiSquareWell
 scores a fragment by the root mean square deviation of Phi and Psi angles. More...
class  MakePhiPsiSquareWell
 Matker class that produces a new PhiPsiSquareWell object. More...
class  ProfileScore
 a fragment candidate More...
class  MakeProfileScore
class  ProfileScoreBlosum62
 a fragment candidate More...
class  MakeProfileScoreBlosum62
class  ProfileScoreDistWeight
 a fragment candidate More...
class  MakeProfileScoreDistWeight
class  ProfileScoreL1
 a fragment candidate More...
class  MakeProfileScoreL1
class  ProfileScoreStructL1
 a fragment candidate More...
class  MakeProfileScoreStructL1
class  ProfileScoreSubMatrix
 a fragment candidate More...
class  MakeProfileScoreSubMatrix
class  ProlinePhiScore
 ProlinePhiScore score counts identical residues. More...
class  MakeProlinePhiScore
 Maker class that produces a new ProlinePhiScore object. More...
class  Psi
 scores a fragment by its predicted psi similarity More...
class  MakePsi
 Maker class that produces a new Psi object. 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  MakeRamaScore
 Maker class that produces a new RamaScore object. More...
class  RDCScore
 scores a fragment by its crmsd to the given reference structure More...
class  MakeRDCScore
 Maker class that produces a new RDCScore object. More...
class  ScoreEValuator
 Computes E-Value for a Profile object. More...
class  MakeScoreEValuator
class  SecondaryIdentity
 SequenceIdentity score counts how many residues share the same secondary structure. More...
class  MakeSecondaryIdentity
 Maker class that produces a new SecondaryIdentity object. 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  MakeSecondarySimilarity
 Maker class that produces a new SecondarySimilarity object. More...
class  SequenceIdentity
 SequenceIdentity score counts identical residues. More...
class  MakeSequenceIdentity
 Maker class that produces a new SequenceIdentity object. More...
class  SolventAccessibility
 scores a fragment by its predicted solvent accessibility More...
class  MakeSolventAccessibility
 Maker class that produces a new SolventAccessibility object. 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  MakeTalosSSSimilarity
 Maker class that produces a new TalosSSSimilarity object. More...
class  TorsionBinSimilarity
 scores a fragment by torsion bin similarity More...
class  MakeTorsionBinSimilarity
 Maker class that produces a new TorsionBin object. More...

Typedefs

typedef utility::vector1
< utility::vector1< Real > > 
Matrix
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
< 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
< RDCScore
RDCScoreOP
typedef
utility::pointer::owning_ptr
< RDCScore const > 
RDCScoreCOP

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

Variables

static const core::Real PHI_MIN_CONF = 0.5
static const core::Real PSI_MIN_CONF = 0.5

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 
)

Referenced by rolling_score().

void protocols::frag_picker::scores::rolling_score ( Matrix small_scores,
Size  frag_len,
Matrix frag_scores 
)
bool protocols::frag_picker::scores::sort_scores ( FragmentScoringMethodOP  elem1,
FragmentScoringMethodOP  elem2 
)
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]
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]
static basic::Tracer protocols::frag_picker::scores::trAtomBasedConstraintsScore ( "fragment.picking.scores.AtomBasedConstraintsScore"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trAtomPairConstraintsScore ( "fragment.picking.scores.AtomPairConstraintsScore"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trCSScore ( "protocols.frag_picker.scores.CSScore"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trDihedralConstraintsScore ( "fragment.picking.scores.DihedralConstraintsScore"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trDMEScore ( "protocols.frag_picker.scores.FragmentDME"  ) [static]
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]
static basic::Tracer protocols::frag_picker::scores::trInterbondAngleScore ( "fragment.picking.scores.InterbondAngleScore"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trJCoupling ( "protocols.frag_picker.scores.JCoupling"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trPartialSecondarySimilarity ( "protocols.frag_picker.scores.PartialSecondarySimilarity"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trPhiPsiRmsd ( "protocols.frag_picker.scores.PhiPsiRmsd"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trPhiPsiSquareWell ( "protocols.frag_picker.scores.PhiPsiSquareWell"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trProfScore ( "protocols.frag_picker.scores.ScoreEValuator"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trProfScore ( "protocols.frag_picker.scores.ProfileScore"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trProfScoreBlosum62 ( "protocols.frag_picker.scores.ProfileScoreBlosum62"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trProfScoreDistWeight ( "protocols.frag_picker.scores.ProfileScoreDistWeight"  ) [static]
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]
static basic::Tracer protocols::frag_picker::scores::trRDCScore ( "protocols.frag_picker.scores.RDCScore"  ) [static]
static basic::Tracer protocols::frag_picker::scores::trRDCScore ( "fragment.picking.scores.RDCScore"  ) [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.FragmentCrmsdResDepth"  ) [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]
static basic::Tracer protocols::frag_picker::scores::trTalosSSSimilarity ( "protocols.frag_picker.scores.TalosSSSimilarity"  ) [static]

Variable Documentation

 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines