org.strbio.mol.lib
Class ScorePredFreq

java.lang.Object
  extended by org.strbio.mol.lib.ScorePredFreq
All Implemented Interfaces:
ScoreFunction

public class ScorePredFreq
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 things by the predicted frequencies. 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
ScorePredFreq()
           
 
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

ScorePredFreq

public ScorePredFreq()
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