org.strbio.mol.lib
Class ScoreAlphaTau

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

All Implemented Interfaces:

ScoreFunction, ScoreSetup

public class ScoreAlphaTau
extends java.lang.Object
implements ScoreFunction, ScoreSetup

A scoring function that uses the 2ary prediction pseudopotential and alpha/tau angles of the fold. The table is scaled 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 1.4, 6/7/99 - moved to org.strbio.mol.lib
  Version 1.3, 8/3/98 - ref now an integer.
  Version 1.2, 7/9/98 - added separate, sigma
  Version 1.1, 4/3/98 - implements ScoreSetup, keeps track of potential object.
  Version 1.0, 4/1/98 - Original version
  

Version:

1.4, 6/7/99

Author:

JMC

Constructor Summary

ScoreAlphaTau(java.lang.String filename, int ref, boolean separate, double sigma)
load potential in from a file.

Method Summary

void	finished(Polymer p) This function is called when you are done using the function on a polymer.
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(ProfResPSI a, ProfResPSI b)
void	setup(Polymer p) This function is to set up the scoring function for use on a polymer.

Methods inherited from class java.lang.Object

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

Constructor Detail

ScoreAlphaTau

public ScoreAlphaTau(java.lang.String filename,
                     int ref,
                     boolean separate,
                     double sigma)

load potential in from a file.

Parameters:

filename - file name

ref - which reference state to use

Method Detail

score

public double score(ProfResPSI a,
                    ProfResPSI 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

setup

public void setup(Polymer p)

Description copied from interface: ScoreSetup

This function is to set up the scoring function for use on a polymer.

Specified by:

setup in interface ScoreSetup

finished

public void finished(Polymer p)

Description copied from interface: ScoreSetup

This function is called when you are done using the function on a polymer.

Specified by:

finished in interface ScoreSetup