Field Detail

• cubeIterator

  protected CubeIterator cubeIterator

• bspf

  protected Bspf bspf

• threadSafe

  private boolean threadSafe

• hemisphereOnly

  private boolean hemisphereOnly

• isZeroBased

  private boolean isZeroBased

• modelIndex

  protected int modelIndex

• atomIndex

  private int atomIndex

• zeroBase

  private int zeroBase

• distanceSquared

  private float distanceSquared

• bsSelected

  private BS bsSelected

• isGreaterOnly

  private boolean isGreaterOnly

• checkGreater

  private boolean checkGreater

• radiusData

  private RadiusData radiusData

• vdw1

  private float vdw1

• isVdw

  private boolean isVdw

• atoms

  private Atom[] atoms

• vwr

  private Viewer vwr

• iNext

  private int iNext

Constructor Detail

• AtomIteratorWithinModel

  AtomIteratorWithinModel()

Method Detail

• initialize

  void initialize​(Bspf bspf,
                  BS bsSelected,
                  boolean isGreaterOnly,
                  boolean isZeroBased,
                  boolean hemisphereOnly,
                  boolean threadSafe)

  ############## ITERATOR SHOULD BE RELEASED #################

  Parameters:

  bspf -

  bsSelected -

  isGreaterOnly -

  isZeroBased -

  hemisphereOnly - TODO

  threadSafe -

• setModel

  public void setModel​(ModelSet modelSet,
                       int modelIndex,
                       int firstModelAtom,
                       int atomIndex,
                       javajs.util.T3 center,
                       float distance,
                       RadiusData rd)

  Specified by:

  setModel in interface AtomIndexIterator

  firstModelAtom - an offset used in the AtomIteratorWithinSet only

• setCenter

  public void setCenter​(javajs.util.T3 center,
                        float distance)

  Specified by:

  setCenter in interface AtomIndexIterator

• setCenter2

  protected void setCenter2​(javajs.util.T3 center,
                            float distance)

• hasNext

  public boolean hasNext()

  Specified by:

  hasNext in interface AtomIndexIterator

• hasNext2

  protected boolean hasNext2()

• next

  public int next()

  Specified by:

  next in interface AtomIndexIterator

• foundDistance2

  public float foundDistance2()

  Specified by:

  foundDistance2 in interface AtomIndexIterator

• addAtoms

  public void addAtoms​(BS bsResult)

  turns this into a SPHERICAL iterator for "within Distance" measures

  Specified by:

  addAtoms in interface AtomIndexIterator

  Parameters:

  bsResult -

• release

  public void release()

  Specified by:

  release in interface AtomIndexIterator

• getPosition

  public javajs.util.P3 getPosition()

  Specified by:

  getPosition in interface AtomIndexIterator