Class AtomIteratorWithinModel

    • Field Detail

      • 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
      • vdw1

        private float vdw1
      • isVdw

        private boolean isVdw
      • atoms

        private Atom[] atoms
      • 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)
      • hasNext2

        protected boolean hasNext2()
      • addAtoms

        public void addAtoms​(BS bsResult)
        turns this into a SPHERICAL iterator for "within Distance" measures
        Specified by:
        addAtoms in interface AtomIndexIterator
        Parameters:
        bsResult -