org.strbio.mol.lib
Class ScoreAveragePSIBlast

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

All Implemented Interfaces:

Description, ScoreFunction, ScoreSetup, ScoreSetup2

public class ScoreAveragePSIBlast
extends java.lang.Object
implements ScoreFunction, ScoreSetup, ScoreSetup2, Description

A scoring function that uses PSI-BLAST matrices, averaging the score over all residues in the fold.

  Version 1.1, 3/10/00 - way faster
  Version 1.0, 9/29/99 - original version
  

Version:

1.1, 3/10/00

Author:

JMC

Constructor Summary

ScoreAveragePSIBlast()

Method Summary

void	describe(Printf outfile) This should print info about the object to an output file.
void	finished(Polymer p) This function is called when you are done using the function on a polymer.
void	finished(Polymer s, Polymer f) This function is called when you are done using the function on a pair.
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.
void	setup(Polymer s, Polymer f) This function is to set up the scoring function for use on a pair.

Methods inherited from class java.lang.Object

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

Constructor Detail

ScoreAveragePSIBlast

public ScoreAveragePSIBlast()

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

setup

public void setup(Polymer s,
                  Polymer f)

Description copied from interface: ScoreSetup2

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

Specified by:

setup in interface ScoreSetup2

finished

public void finished(Polymer s,
                     Polymer f)

Description copied from interface: ScoreSetup2

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

Specified by:

finished in interface ScoreSetup2

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

describe

public void describe(Printf outfile)

Description copied from interface: Description

This should print info about the object to an output file.

Specified by:

describe in interface Description