Package org.biojava.nbio.structure.align.ce

Class CeCalculatorEnhanced

java.lang.Object

org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

public class CeCalculatorEnhanced
extends Object

This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I. Shindyalov and P.Bourne (1998). The original CE paper is available from here: http://peds.oxfordjournals.org/cgi/content/short/11/9/739. This class is a pretty much exact 1:1 port from C, where I cared about exact reproduce of the CE results and not about Java style.

Author:

Spencer Bliven, Andreas Prlic

Field Summary

Fields

Modifier and Type	Field	Description
protected int[]	bestTrace1
protected int[]	bestTrace2
protected int[][]	bestTraces1
protected int[][]	bestTraces2
protected double	bestTraceScore
protected int[]	bestTracesN
protected double[]	bestTracesScores
static boolean	GLOBAL_ALIGN1
static boolean	GLOBAL_ALIGN2
protected static boolean	isPrint
protected double[][]	mat
protected int	nBestTrace
protected int	nBestTraces
protected static int	nIter
protected int	nTrace
protected int	nTraces
protected CeParameters	params
protected int[]	trace1
protected int[]	trace2
protected static double	zThr

Constructor Summary

Constructors

Constructor	Description
CeCalculatorEnhanced(CeParameters params)

Method Summary

Modifier and Type	Method	Description
void	addMatrixListener(MatrixListener li)
double	calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform, boolean show)	superimpose and get rmsd
void	convertAfpChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2)	copy data from this class into AFPChain container object.
protected int	doIter0(int newBestTrace, double traceTotalScore, double bestTracesMax)
AFPChain	extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
int[]	getAlign_se1()
int[]	getAlign_se2()
double[][]	getDist1()
double[][]	getDist2()
int	getLcmp()
double[][]	getMatMatrix()	Caution: this matrix is overwriten with very different data at several points in the alignment algorithm.
int	getnAtom()
Matrix	getRotationMatrix()	Gets the rotation matrix from the last call to calc_rmsd.
protected double	getScore2(int jse1, int jse2, double[][] traceScore, int traceIndex_, int[] traceIndex, int winSizeComb1, int winSizeComb2, double score0, double score1)
protected double	getScoreFromDistanceMatrices(int mse1, int mse2, int winSize)
Atom	getShift()	Gets the shift from the last call to calc_rmsd.
double[][]	initSumOfDistances(int nse1, int nse2, int winSize, int winSizeComb1, Atom[] ca1, Atom[] ca2)
void	nextStep(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void	setAlign_se1(int[] alignSe1)
void	setAlign_se2(int[] alignSe2)
void	setDist1(double[][] dist1)
void	setDist2(double[][] dist2)
void	setLcmp(int lcmp)
void	setMatMatrix(double[][] matrix)
void	setnAtom(int nAtom)
void	traceFragmentMatrix(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static double[][]	updateMatrixWithSequenceConservation(double[][] max, Atom[] ca1, Atom[] ca2, CeParameters params)	Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.
protected double	zStrAlign(int winSize, int nTrace, double score, int nGaps)

Methods inherited from class java.lang.Object

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

Field Detail

isPrint

protected static final boolean isPrint

See Also:

Constant Field Values

mat

protected double[][] mat

bestTrace1

protected int[] bestTrace1

bestTrace2

protected int[] bestTrace2

bestTraces1

protected int[][] bestTraces1

bestTraces2

protected int[][] bestTraces2

nBestTrace

protected int nBestTrace

nBestTraces

protected int nBestTraces

bestTracesN

protected int[] bestTracesN

bestTraceScore

protected double bestTraceScore

nTrace

protected int nTrace

bestTracesScores

protected double[] bestTracesScores

trace1

protected int[] trace1

trace2

protected int[] trace2

zThr

protected static final double zThr

See Also:

Constant Field Values

nTraces

protected int nTraces

params

protected CeParameters params

nIter

protected static final int nIter

See Also:

Constant Field Values

GLOBAL_ALIGN1

public static final boolean GLOBAL_ALIGN1

See Also:

Constant Field Values

GLOBAL_ALIGN2

public static final boolean GLOBAL_ALIGN2

See Also:

Constant Field Values

Constructor Detail

CeCalculatorEnhanced

public CeCalculatorEnhanced(CeParameters params)

Method Detail

extractFragments

public AFPChain extractFragments(AFPChain afpChain,
                                 Atom[] ca1,
                                 Atom[] ca2)
                          throws StructureException

Parameters:

afpChain - A new AFPChain, which will be filled in by this function

ca1 -

ca2 -

Returns:

afpChain

Throws:

StructureException

initSumOfDistances

public double[][] initSumOfDistances(int nse1,
                                     int nse2,
                                     int winSize,
                                     int winSizeComb1,
                                     Atom[] ca1,
                                     Atom[] ca2)

traceFragmentMatrix

public void traceFragmentMatrix(AFPChain afpChain,
                                Atom[] ca1,
                                Atom[] ca2)

getScore2

protected double getScore2(int jse1,
                           int jse2,
                           double[][] traceScore,
                           int traceIndex_,
                           int[] traceIndex,
                           int winSizeComb1,
                           int winSizeComb2,
                           double score0,
                           double score1)

doIter0

protected int doIter0(int newBestTrace,
                      double traceTotalScore,
                      double bestTracesMax)

getScoreFromDistanceMatrices

protected double getScoreFromDistanceMatrices(int mse1,
                                              int mse2,
                                              int winSize)

nextStep

public void nextStep(AFPChain afpChain,
                     Atom[] ca1,
                     Atom[] ca2)
              throws StructureException

Throws:

StructureException

updateMatrixWithSequenceConservation

public static double[][] updateMatrixWithSequenceConservation(double[][] max,
                                                              Atom[] ca1,
                                                              Atom[] ca2,
                                                              CeParameters params)

Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.

Parameters:

max - alignment matrix

ca1 - Atoms for protein 1

ca2 - Atoms for Protein 2

params - alignment parameters

Returns:

modified alignment matrix

addMatrixListener

public void addMatrixListener(MatrixListener li)

calc_rmsd

public double calc_rmsd(Atom[] pro1,
                        Atom[] pro2,
                        int strLen,
                        boolean storeTransform,
                        boolean show)
                 throws StructureException

superimpose and get rmsd

Parameters:

pro1 -

pro2 -

strLen -

storeTransform -

show -

Returns:

RMSD

Throws:

StructureException

zStrAlign

protected double zStrAlign(int winSize,
                           int nTrace,
                           double score,
                           int nGaps)

convertAfpChain

public void convertAfpChain(AFPChain afpChain,
                            Atom[] ca1,
                            Atom[] ca2)

copy data from this class into AFPChain container object.

Parameters:

afpChain -

ca1 -

ca2 -

getnAtom

public int getnAtom()

setnAtom

public void setnAtom(int nAtom)

getLcmp

public int getLcmp()

setLcmp

public void setLcmp(int lcmp)

getAlign_se1

public int[] getAlign_se1()

setAlign_se1

public void setAlign_se1(int[] alignSe1)

getAlign_se2

public int[] getAlign_se2()

setAlign_se2

public void setAlign_se2(int[] alignSe2)

getMatMatrix

public double[][] getMatMatrix()

Caution: this matrix is overwriten with very different data at several points in the alignment algorithm. After initSumOfDistances is run, this will hold the distance matrix between AFPs.

Returns:

mat

setMatMatrix

public void setMatMatrix(double[][] matrix)

getRotationMatrix

public Matrix getRotationMatrix()

Gets the rotation matrix from the last call to calc_rmsd.

Returns:

The rotatiokn matrix

getShift

public Atom getShift()

Gets the shift from the last call to calc_rmsd.

Returns:

The shift

getDist1

public double[][] getDist1()

setDist1

public void setDist1(double[][] dist1)

getDist2

public double[][] getDist2()

setDist2

public void setDist2(double[][] dist2)