org.strbio.mol.lib
Class ScoreFischer

java.lang.Object
  org.strbio.mol.lib.ScoreFischer

All Implemented Interfaces:

ScoreFunction

public class ScoreFischer
extends java.lang.Object
implements ScoreFunction

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. See Fischer & Eisenberg threading work. 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.

Version:

1.0, 7/22/98

Author:

JMC

Field Summary

static double	EQUAL
static double	NOTEQUAL

Constructor Summary

ScoreFischer()

Method Summary

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

EQUAL

public static final double EQUAL

See Also:

Constant Field Values

NOTEQUAL

public static final double NOTEQUAL

See Also:

Constant Field Values

Constructor Detail

ScoreFischer

public ScoreFischer()

Method Detail

score

public double score(Residue a,
                    Residue b)

score

public double score(Monomer a,
                    Monomer b)

Description copied from interface: ScoreFunction

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).

Specified by:

score in interface ScoreFunction