Package org.jmol.modelset

Class AtomIteratorWithinModel

java.lang.Object
org.jmol.modelset.AtomIteratorWithinModel
All Implemented Interfaces:
AtomIndexIterator
Direct Known Subclasses:
AtomIteratorWithinModelSet
public class AtomIteratorWithinModel extends Object implements AtomIndexIterator

  • Field Details

    • 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 javajs.util.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 Details

    • AtomIteratorWithinModel

      AtomIteratorWithinModel()

  • Method Details

    • initialize

      void initialize(Bspf bspf, javajs.util.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(javajs.util.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