org.strbio.mol.lib
Class ScoreDefay

java.lang.Object
  extended by org.strbio.mol.lib.ScoreDefay
All Implemented Interfaces:
ScoreFunction
Direct Known Subclasses:
ScoreScaledDefay

public class ScoreDefay
extends java.lang.Object
implements ScoreFunction

A scoring function from Tom Defay's algorithm. Defay & Cohen, JMB 262: 314-323. 1996.

 Version 1.01, 7/20/98 - changed to reflect re-coding of environment
  value in VAR files from the [-4:-1] range to the [-5:-2] range.
 Version 1.0, 4/1/98 - original version
 

Version:
1.01, 7/20/98
Author:
JMC

Field Summary
 java.lang.String defaultTable
          the default table comes from Tom Defay's "easy table"
 
Constructor Summary
ScoreDefay()
          If no filename is specified, use the default table.
ScoreDefay(java.lang.String filename)
           
 
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

defaultTable

public final java.lang.String defaultTable
the default table comes from Tom Defay's "easy table"

See Also:
Constant Field Values
Constructor Detail

ScoreDefay

public ScoreDefay(java.lang.String filename)
           throws java.io.IOException
Throws:
java.io.IOException

ScoreDefay

public ScoreDefay()
If no filename is specified, use the default table. Can't call the other constructor due to stupid Java syntax.

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