Constructor Detail

• 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 Detail

• 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