Package org.biojava.nbio.structure.contact

Class Grid

java.lang.Object
org.biojava.nbio.structure.contact.Grid
public class Grid extends Object
A grid to be used for calculating atom contacts through geometric hashing algorithm. The grid is composed of cells of size of the cutoff so that the distances that need to be calculated are reduced to those within each cell and to the neighbouring cells.
Author:
duarte_j

  • Constructor Summary

    Constructors
    Constructor
    Description
    Grid(double cutoff)
    Creates a Grid, the cutoff is in Angstroms and can be specified to a precision of 0.01A

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addAtoms(Atom[] atoms)
    Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
    void
    addAtoms(Atom[] iAtoms, Atom[] jAtoms)
    Adds the i and j atoms and fills the grid.
    void
    addAtoms(Atom[] atoms, BoundingBox bounds)
    Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
    void
    addAtoms(Atom[] iAtoms, BoundingBox icoordbounds, Atom[] jAtoms, BoundingBox jcoordbounds)
    Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
    AtomContactSet
    getContacts()
    Returns all contacts, i.e.
    double
    getCutoff()
     
    boolean
    isNoOverlap()
    Tells whether (after having added atoms to grid) the i and j grids are not overlapping.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • Grid

      public Grid(double cutoff)
      Creates a Grid, the cutoff is in Angstroms and can be specified to a precision of 0.01A
      Parameters:
      cutoff -

  • Method Details

    • addAtoms

      public void addAtoms(Atom[] iAtoms, Atom[] jAtoms)
      Adds the i and j atoms and fills the grid. Their bounds will be computed.
      Parameters:
      iAtoms -
      jAtoms -

    • addAtoms

      public void addAtoms(Atom[] iAtoms, BoundingBox icoordbounds, Atom[] jAtoms, BoundingBox jcoordbounds)
      Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
      Parameters:
      iAtoms -
      icoordbounds -
      jAtoms -
      jcoordbounds -

    • addAtoms

      public void addAtoms(Atom[] atoms)
      Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts. The bounding box of the atoms will be computed based on input array
      Parameters:
      atoms -

    • addAtoms

      public void addAtoms(Atom[] atoms, BoundingBox bounds)
      Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts. The bounds calculated elsewhere can be passed, or if null they are computed.
      Parameters:
      atoms -
      bounds -

    • getContacts

      public AtomContactSet getContacts()
      Returns all contacts, i.e. all atoms that are within the cutoff distance. If both iAtoms and jAtoms are defined then contacts are between iAtoms and jAtoms, if jAtoms is null, then contacts are within the iAtoms.
      Returns:

    • getCutoff

      public double getCutoff()

    • isNoOverlap

      public boolean isNoOverlap()
      Tells whether (after having added atoms to grid) the i and j grids are not overlapping. Overlap is defined as enclosing bounds of the 2 grids being no more than one cell size apart.
      Returns:
      true if the 2 grids don't overlap, false if they do