Package org.biojava.nbio.structure.align.helper

Class AlignTools

java.lang.Object
org.biojava.nbio.structure.align.helper.AlignTools
public class AlignTools extends Object

  • Constructor Summary

    Constructors
    Constructor
    Description
    AlignTools()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static Atom
    getCenter(Atom[] ca, int pos, int fragmentLength)
    get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
    static double[]
    getDiagonalAtK(Atom[] atoms, int k)
     
    static Matrix
    getDistanceMatrix(Atom[] ca1, Atom[] ca2)
    Matrix of all distances between two sets of Atoms.
    static Atom[]
    getFragment(Atom[] caall, int pos, int fragmentLength)
    get a continue subset of Atoms based by the starting position and the length
    static Atom[]
    getFragmentFromIdxList(Atom[] caall, int[] idx)
    get a subset of Atoms based by their positions
    static Atom[]
    getFragmentNoClone(Atom[] caall, int pos, int fragmentLength)
    get a continue subset of Atoms based by the starting position and the length does not clone the original atoms.
    static double
    rms_dk_diag(double[] dk1, double[] dk2, int i, int j, int l, int k)
    Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • AlignTools

      public AlignTools()

  • Method Details

    • getFragmentFromIdxList

      public static Atom[] getFragmentFromIdxList(Atom[] caall, int[] idx)
      get a subset of Atoms based by their positions
      Parameters:
      caall -
      idx - an array where each element is a position of all the Atoms to return
      Returns:
      at Atom[] array

    • getFragment

      public static Atom[] getFragment(Atom[] caall, int pos, int fragmentLength)
      get a continue subset of Atoms based by the starting position and the length
      Parameters:
      caall -
      pos - ... the start position
      fragmentLength - .. the length of the subset to extract.
      Returns:
      an Atom[] array

    • getFragmentNoClone

      public static Atom[] getFragmentNoClone(Atom[] caall, int pos, int fragmentLength)
      get a continue subset of Atoms based by the starting position and the length does not clone the original atoms.
      Parameters:
      caall -
      pos - ... the start position
      fragmentLength - .. the length of the subset to extract.
      Returns:
      an Atom[] array

    • getCenter

      public static Atom getCenter(Atom[] ca, int pos, int fragmentLength)
      get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
      Parameters:
      ca -
      pos -
      fragmentLength -
      Returns:
      an Atom

    • getDiagonalAtK

      public static double[] getDiagonalAtK(Atom[] atoms, int k)

    • rms_dk_diag

      public static double rms_dk_diag(double[] dk1, double[] dk2, int i, int j, int l, int k)
      Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair. i,j is the fpair start in mol1 and mol2, l is the length of the fragment
      Parameters:
      dk1 - distances of structure 1
      dk2 - distance of structure 2
      i - position in structure 1
      j - position in structure 2
      l - length of the fragments
      k - diagonal used
      Returns:
      a double

    • getDistanceMatrix

      public static Matrix getDistanceMatrix(Atom[] ca1, Atom[] ca2)
      Matrix of all distances between two sets of Atoms. Does not superimpose or modify the Atoms.
      Parameters:
      ca1 -
      ca2 -
      Returns:
      a Matrix