org.strbio.mol.lib
Class Score2ary

java.lang.Object
  org.strbio.mol.lib.Score2ary

All Implemented Interfaces:

ScoreFunction

public class Score2ary
extends java.lang.Object
implements ScoreFunction

A scoring function that checks if the real 2ary structure matches. 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, 4/1/98

Author:

JMC

Field Summary

static double	EQUAL
static double	NOTEQUAL

Constructor Summary

Score2ary()

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

Score2ary

public Score2ary()

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