Uses of Interface
org.strbio.mol.lib.ScoreFunction

Packages that use ScoreFunction

org.strbio.mol.lib

These classes represent conceptual objects used in structural biology algorithms.

Uses of ScoreFunction in org.strbio.mol.lib

Classes in org.strbio.mol.lib that implement ScoreFunction

class	Score2ary A scoring function that checks if the real 2ary structure matches.
class	ScoreAlphaTau A scoring function that uses the 2ary prediction pseudopotential and alpha/tau angles of the fold.
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	ScoreBlosum62 A scoring function that uses the default Blosum62 matrix Version 1.0, 1/28/99 - original version
class	ScoreDefay A scoring function from Tom Defay's algorithm.
class	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.
class	ScoreID A scoring function that returns a non-scaled identity matrix.
class	ScoreJDB10 A scoring function that uses JDB's 10% ID matrix.
class	ScorePairwiseDistance A scoring function based on the CA distance between 2 residues.
class	ScorePhiPsi A scoring function that uses the 2ary prediction pseudopotential and phi/psi angles of the fold.
class	ScorePred2ary A scoring function that checks if the predicted 2ary structure in the sequence matches the real secondary structure in the fold.
class	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.
class	ScorePSIBlast A scoring function that uses PSI-BLAST matrices.
class	ScoreReversePSIBlast A scoring function that uses PSI-BLAST matrices.
class	ScoreScaledDefay A scoring function from Tom Defay's algorithm, but rescaled.
class	ScoreScaledID A scoring function that returns a scaled identity matrix.
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.

Fields in org.strbio.mol.lib declared as ScoreFunction

ScoreFunction

ScoreList.func This encapsulates an object that implements ScoreFunction.

Methods in org.strbio.mol.lib with parameters of type ScoreFunction

void	AlignmentParameters.addScoreFunction(ScoreFunction s) Add new scoring function with default weight.
void	AlignmentParameters.addScoreFunction(ScoreFunction s, double weight) Add new scoring function with specified weight.

Constructors in org.strbio.mol.lib with parameters of type ScoreFunction

ScoreList(ScoreFunction sf)
make a ScoreList node with a ScoreFunction.

ScoreList(ScoreFunction sf, double w)
make a ScoreList node with a ScoreFunction and a weight.