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Description
Interface Summary  

AlignmentDependent  Interface for scoring functions that are dependent on the rest of the alignment. 
Blast  Interface for common Blastrelated routines. 
GapModel  Interface for gap penalties for alignment. 
PSIBlast  Interface for common PSIblast related routines. 
ScoreFunction  Interface for scoring functions. 
ScoreSetup  Interface for scoring functions that need to be set up before being used on a given polymer. 
ScoreSetup2  Interface for scoring functions that need to be set up before being used on a given seq/fold pair. 
SSPredictor  Interface for common secondary structure prediction routines. 
ThreadMethod  A method that does threading. 
Class Summary  

AlignmentParameters  Alignment parameters. 
AlignmentParametersEA  Parameters, with some statistical functions to tell you how accurate they are at alignment and/or fold recognition. 
BackbonePotential  methods for handling the 2ary prediction dependent backbone pseudopotential. 
BlastAdapter  Adapter class to implement the routines in Blast. 
BlastConstants  Some constants used in BLAST 2.0.6. 
DayhoffMatrices  Dayhoff matrices (various) Dayhoff, MO 1978 Atlas of Protein Sequence and Structure volume 5, #3 p. 353  358. 
FoldLibrary  A standard fold library for threading; i.e. the TOM fold library, or the Fischer fold library. 
FRParameters  Fold recognition parameters. 
FRParametersNode  Fold recognition parameters. 
GapAffine  Affine gap penalties. 
GapConstant  Constant gap penalties. 
GapDistanceDependent  Distance dependent gap penalties. 
GapModelAdapter  Default implementation of GapModel. 
JMCThreadMethod  JMC's global threading method. 
JMCThreadMethod2  JMC's global threading method, based on a combination of methods. 
MinareaResults  Class containing results of minarea. 
OptimalAAParameters  The optimal alignment parameters for maximizing alignment accuracy. 
OptimalAAParametersFR  The optimal fold recognition parameters. 
OptimalFRParameters  The optimal fold recognition parameters. 
Pred2ary  Predicts secondary structure using JMC's Pred2ary program. 
ProteinFilter  A file filter for returning likely protein formats. 
PSIBlastMatrices  Matrix used in PSIBlast comparisons. 
Score2ary  A scoring function that checks if the real 2ary structure matches. 
ScoreAlphaTau  A scoring function that uses the 2ary prediction pseudopotential and alpha/tau angles of the fold. 
ScoreAveragePSIBlast  A scoring function that uses PSIBLAST matrices, averaging the score over all residues in the fold. 
ScoreAverageReversePSIBlast  A scoring function that uses PSIBLAST matrices. 
ScoreBlosum62  A scoring function that uses the default Blosum62 matrix Version 1.0, 1/28/99  original version 
ScoreDefay  A scoring function from Tom Defay's algorithm. 
ScoreFischer  A scoring function that checks if the predicted 2ary structure in the sequence matches the real secondary structure in the fold, while weighting a match by the predicted frequency. 
ScoreID  A scoring function that returns a nonscaled identity matrix. 
ScoreJDB10  A scoring function that uses JDB's 10% ID matrix. 
ScoreList  A scoring function return a identity matrix; this is set up so that a sampling of all calls to score() over a large set of sequences and folds will average 0.0 with a standard deviation of 1.0. 
ScorePairwiseDistance  A scoring function based on the CA distance between 2 residues. 
ScorePhiPsi  A scoring function that uses the 2ary prediction pseudopotential and phi/psi angles of the fold. 
ScorePred2ary  A scoring function that checks if the predicted 2ary structure in the sequence matches the real secondary structure in the fold. 
ScorePredFreq  A scoring function that checks if the predicted 2ary structure in the sequence matches the real secondary structure in the fold, while weighting things by the predicted frequencies. 
ScorePSIBlast  A scoring function that uses PSIBLAST matrices. 
ScoreReversePSIBlast  A scoring function that uses PSIBLAST matrices. 
ScoreScaledDefay  A scoring function from Tom Defay's algorithm, but rescaled. 
ScoreScaledID  A scoring function that returns a scaled identity matrix. 
ScoreSippl90  A scoring function that uses Sippl's 90 parameters, with the frozen approximation. 
ScoreUFSippl90  A scoring function that uses Sippl's 90 parameters, without the frozen approximation. 
Sippl90  Sippl scoring method, from JMB 90 papers. 
ThreadResults  Threading results on one protein. 
TOMFoldLibrary  The TOM fold library. 
UserFoldLibrary  A standard fold library for threading, loaded in by the user. 
These classes represent conceptual objects used in structural biology algorithms.


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