Uses of Package
org.strbio.mol.lib

Packages that use org.strbio.mol.lib

org.strbio.app	These classes are stand-alone applications.
org.strbio.local	These classes are for running or exchanging data with local programs (other programs installed on your computer).
org.strbio.mol	These classes represent objects or concepts useful to structural biologists.
org.strbio.mol.lib	These classes represent conceptual objects used in structural biology algorithms.
org.strbio.net	These classes are for running or exchanging data with non-local programs (i.e., programs that you run by submitting data to a web page).
org.strbio.raf	These classes are related to the RAF file format used by the ASTRAL database.

Classes in org.strbio.mol.lib used by org.strbio.app

AlignmentParametersEA
Parameters, with some statistical functions to tell you how accurate they are at alignment and/or fold recognition.

ThreadMethod
A method that does threading.

Classes in org.strbio.mol.lib used by org.strbio.local

Blast
Interface for common Blast-related routines.

MinareaResults
Class containing results of minarea.

PSIBlast
Interface for common PSI-blast related routines.

PSIBlastMatrices
Matrix used in PSIBlast comparisons.

Classes in org.strbio.mol.lib used by org.strbio.mol

AlignmentParameters
Alignment parameters.

BackbonePotential
methods for handling the 2ary prediction dependent backbone pseudopotential.

Blast
Interface for common Blast-related routines.

GapModel
Interface for gap penalties for alignment.

MinareaResults
Class containing results of minarea.

PSIBlastMatrices
Matrix used in PSIBlast comparisons.

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.

SSPredictor
Interface for common secondary structure prediction routines.

ThreadMethod
A method that does threading.

ThreadResults
Threading results on one protein.

Classes in org.strbio.mol.lib used by org.strbio.mol.lib

AlignmentDependent
Interface for scoring functions that are dependent on the rest of the alignment.

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.

Blast
Interface for common Blast-related routines.

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.

GapModel
Interface for gap penalties for alignment.

GapModelAdapter
Default implementation of GapModel.

PSIBlast
Interface for common PSI-blast related routines.

PSIBlastMatrices
Matrix used in PSIBlast comparisons.

ScoreDefay
A scoring function from Tom Defay's algorithm.

ScoreFunction
Interface for scoring functions.

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.

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.

Sippl90
Sippl scoring method, from JMB 90 papers.

SSPredictor
Interface for common secondary structure prediction routines.

ThreadMethod
A method that does threading.

ThreadResults
Threading results on one protein.

Classes in org.strbio.mol.lib used by org.strbio.net

Blast
Interface for common Blast-related routines.

BlastAdapter
Adapter class to implement the routines in Blast.

PSIBlast
Interface for common PSI-blast related routines.

PSIBlastMatrices
Matrix used in PSIBlast comparisons.

Classes in org.strbio.mol.lib used by org.strbio.raf

AlignmentParameters
Alignment parameters.

GapModel
Interface for gap penalties for alignment.

GapModelAdapter
Default implementation of GapModel.