org.biojava.bio.structure.align.helper
Class AlignTools

java.lang.Object
  extended by org.biojava.bio.structure.align.helper.AlignTools

public class AlignTools
extends Object


Constructor Summary
AlignTools()
           
 
Method Summary
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 3d coords"
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 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 Detail

AlignTools

public AlignTools()
Method Detail

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

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 3d coords"

Parameters:
ca1 -
ca2 -
Returns:
a Matrixd