org.strbio.mol.lib
Class ScoreUFSippl90

java.lang.Object
  org.strbio.mol.lib.ScoreUFSippl90

All Implemented Interfaces:

Description, AlignmentDependent, ScoreFunction, ScoreSetup2

public class ScoreUFSippl90
extends java.lang.Object
implements AlignmentDependent, ScoreFunction, ScoreSetup2, Description

A scoring function that uses Sippl's 90 parameters, without the frozen approximation.

  Version 1.1, 1/20/00 - added k restrictions
  Version 1.0, 1/11/00 - original version
  

Version:

1.1, 1/20/00

Author:

JMC

See Also:

Sippl90

Field Summary

java.lang.String	defaultFile the default potential was parameterized using the 681 proteins from Chandonia & Karplus, 1999.
int	kHigh Highest k value to restrict scoring to, or 0 for no restrictions.
int	kLow Lowest k value to restrict scoring to, or 0 for no restrictions.

Constructor Summary

ScoreUFSippl90()
initialize scoring system with default BackbonePotential.

ScoreUFSippl90(Sippl90 s90)
initialize scoring system from a pre-initialized potential.

ScoreUFSippl90(java.lang.String filename)
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 s, Polymer f) This function is called when you are done using the function on a pair.
void	restrictK(int low, int high) Restrict scoring to a range of k values.
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) Restrict scoring to a range of k values.
void	setAlignment(Alignment a) This function is called to provide the alignment.
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

Field Detail

kLow

public int kLow

Lowest k value to restrict scoring to, or 0 for no restrictions.

kHigh

public int kHigh

Highest k value to restrict scoring to, or 0 for no restrictions.

defaultFile

public final java.lang.String defaultFile

the default potential was parameterized using the 681 proteins from Chandonia & Karplus, 1999.

See Also:

Constant Field Values

Constructor Detail

ScoreUFSippl90

public ScoreUFSippl90(java.lang.String filename)

load potential in from a file.

Parameters:

filename - file name

ScoreUFSippl90

public ScoreUFSippl90(Sippl90 s90)

initialize scoring system from a pre-initialized potential.

ScoreUFSippl90

public ScoreUFSippl90()

initialize scoring system with default BackbonePotential.

Method Detail

restrictK

public void restrictK(int low,
                      int high)

Restrict scoring to a range of k values. Ends of the ranges are included. Set either value to 0 for no limits on that end.

setAlignment

public void setAlignment(Alignment a)

Description copied from interface: AlignmentDependent

This function is called to provide the alignment. Calls to the scoring function are evaluated on the basis of this alignment.

Specified by:

setAlignment in interface AlignmentDependent

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

score

public double score(Residue a,
                    Residue b)

Restrict scoring to a range of k values. Ends of the ranges are included. Set either value to 0 for no limits on that end.

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

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