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Packages that use Description | |
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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 |
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Classes in org.strbio.mol.lib that implement Description | |
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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 |
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Classes in org.strbio.raf that implement Description | |
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class |
GapRAF
Gap penalties for RAF. |
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