org.strbio.mol.lib
Interface ScoreFunction

All Known Implementing Classes:

Score2ary, ScoreAlphaTau, ScoreAveragePSIBlast, ScoreAverageReversePSIBlast, ScoreBlosum62, ScoreDefay, ScoreFischer, ScoreID, ScoreJDB10, ScorePairwiseDistance, ScorePhiPsi, ScorePred2ary, ScorePredFreq, ScorePSIBlast, ScoreReversePSIBlast, ScoreScaledDefay, ScoreScaledID, ScoreSippl90, ScoreUFSippl90

public interface ScoreFunction

Interface for scoring functions. A scoring function returns the score for aligning two monomers of a polymer. The first monomer is from the sequence, the second from the fold (for functions where that matters).

Version:

1.0, 3/31/98

Author:

JMC

See Also:

ScoreList

Method Summary

double

score(Monomer seqMon, Monomer foldMon) This function should return a score for aligning two monomers of a polymer, preferably with low = good, high = bad.

Method Detail

score

double score(Monomer seqMon,
             Monomer foldMon)

This function should return a score for aligning two monomers of a polymer, preferably with low = good, high = bad. If this is not the case, be sure to comment it as such! If monomer order matters to your scoring function, the first monomer should be from the sequence (unknown structure), and the second monomer should be from the fold (known structure).