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

Class CECalculator

java.lang.Object
org.biojava.nbio.structure.align.ce.CECalculator
public class CECalculator 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:
Andreas Prlic

  • Field Details

    • isPrint

      protected static final boolean isPrint
      See Also:

    • 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:

    • nTraces

      protected int nTraces

    • params

      protected CeParameters params

    • nIter

      protected static final int nIter
      See Also:

  • Constructor Details

  • Method Details

    • 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

      @Deprecated public double calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform, boolean show) throws StructureException
      Deprecated.
      Use calc_rmsd(Atom[],Atom[],int,boolean) instead
      superimpose and get rmsd
      Parameters:
      pro1 -
      pro2 -
      strLen -
      storeTransform -
      show - Ignored. Formerly displayed the superposition with jmol.
      Returns:
      RMSD
      Throws:
      StructureException

    • calc_rmsd

      public double calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform) throws StructureException
      superimpose and get rmsd
      Parameters:
      pro1 -
      pro2 -
      strLen - Number of atoms from pro1 and pro2 to use
      storeTransform - Store rotation and shift matrices locally
      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)