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
      Parameters:
      modelSet -
      modelIndex -
      firstModelAtom - an offset used in the AtomIteratorWithinSet only
      atomIndex -
      center -
      distance -
      rd -
    • 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