org.strbio.mol.lib
Class ScorePhiPsi

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

All Implemented Interfaces:

Description, ScoreFunction, ScoreSetup

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

A scoring function that uses the 2ary prediction pseudopotential and phi/psi 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

Field Summary

java.lang.String

defaultFile the default potential was parameterized using the 681 proteins from Chandonia & Karplus, 1999, with separate GPN residues.

Constructor Summary

ScorePhiPsi()
initialize scoring system with default BackbonePotential.

ScorePhiPsi(BackbonePotential bb)
initialize scoring system from a pre-initialized BackbonePotential

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

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.
BackbonePotential	getPotential() Return the current potential.
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	setPotential(BackbonePotential bb) Use a pre-initialized BackbonePotential.
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

Field Detail

defaultFile

public final java.lang.String defaultFile

the default potential was parameterized using the 681 proteins from Chandonia & Karplus, 1999, with separate GPN residues.

See Also:

Constant Field Values

Constructor Detail

ScorePhiPsi

public ScorePhiPsi(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

ScorePhiPsi

public ScorePhiPsi(BackbonePotential bb)

initialize scoring system from a pre-initialized BackbonePotential

ScorePhiPsi

public ScorePhiPsi()

initialize scoring system with default BackbonePotential.

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

setPotential

public void setPotential(BackbonePotential bb)

Use a pre-initialized BackbonePotential.

getPotential

public BackbonePotential getPotential()

Return the current potential. This is a pointer to the actual one being used, not a copy, so changes apply.

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

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