Uses of Interface
org.strbio.io.Description

Packages that use Description
org.strbio.mol.lib These classes represent conceptual objects used in structural biology algorithms. 
org.strbio.raf These classes are related to the RAF file format used by the ASTRAL database
 

Uses of Description in org.strbio.mol.lib
 

Classes in org.strbio.mol.lib that implement Description
 class AlignmentParameters
          Alignment parameters.
 class AlignmentParametersEA
          Parameters, with some statistical functions to tell you how accurate they are at alignment and/or fold recognition.
 class FoldLibrary
          A standard fold library for threading; i.e. the TOM fold library, or the Fischer fold library.
 class FRParameters
          Fold recognition parameters.
 class FRParametersNode
          Fold recognition parameters.
 class GapAffine
          Affine gap penalties.
 class GapConstant
          Constant gap penalties.
 class GapDistanceDependent
          Distance dependent gap penalties.
 class GapModelAdapter
          Default implementation of GapModel.
 class OptimalAAParameters
          The optimal alignment parameters for maximizing alignment accuracy.
 class OptimalAAParametersFR
          The optimal fold recognition parameters.
 class OptimalFRParameters
          The optimal fold recognition parameters.
 class ScoreAveragePSIBlast
          A scoring function that uses PSI-BLAST matrices, averaging the score over all residues in the fold.
 class ScoreAverageReversePSIBlast
          A scoring function that uses PSI-BLAST matrices.
 class 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.
 class ScorePhiPsi
          A scoring function that uses the 2ary prediction pseudopotential and phi/psi angles of the fold.
 class ScorePSIBlast
          A scoring function that uses PSI-BLAST matrices.
 class ScoreReversePSIBlast
          A scoring function that uses PSI-BLAST matrices.
 class ScoreSippl90
          A scoring function that uses Sippl's 90 parameters, with the frozen approximation.
 class ScoreUFSippl90
          A scoring function that uses Sippl's 90 parameters, without the frozen approximation.
 class TOMFoldLibrary
          The TOM fold library.
 class UserFoldLibrary
          A standard fold library for threading, loaded in by the user.
 

Uses of Description in org.strbio.raf
 

Classes in org.strbio.raf that implement Description
 class GapRAF
          Gap penalties for RAF.