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

Class AlignUtils

java.lang.Object

org.biojava.nbio.structure.align.helper.AlignUtils

public class AlignUtils
extends Object

Low level helper methods for CE and FATCAT algorithms.

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor	Description
AlignUtils()

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 from position pos, length fragmentLenght
static double[]	getDiagonalAtK(Atom[] atoms, int k)	Get distances along diagonal k from coordinate array coords.
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 Detail

AlignUtils

public AlignUtils()

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

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 from position pos, length fragmentLenght

Parameters:

ca -

pos -

fragmentLength -

Returns:

an Atom

getDiagonalAtK

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

Get distances along diagonal k from coordinate array coords.

Parameters:

atoms - set of atoms to be used

k - number of diagonal to be used

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