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 java.lang.Object implements AtomIndexIterator
-
-
Field Summary
Fields Modifier and Type Field Description private int
atomIndex
private Atom[]
atoms
protected Bspf
bspf
private BS
bsSelected
private boolean
checkGreater
protected CubeIterator
cubeIterator
private float
distanceSquared
private boolean
hemisphereOnly
private int
iNext
private boolean
isGreaterOnly
private boolean
isVdw
private boolean
isZeroBased
protected int
modelIndex
private RadiusData
radiusData
private boolean
threadSafe
private float
vdw1
private Viewer
vwr
private int
zeroBase
-
Constructor Summary
Constructors Constructor Description AtomIteratorWithinModel()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addAtoms(BS bsResult)
turns this into a SPHERICAL iterator for "within Distance" measuresfloat
foundDistance2()
javajs.util.P3
getPosition()
boolean
hasNext()
protected boolean
hasNext2()
(package private) void
initialize(Bspf bspf, BS bsSelected, boolean isGreaterOnly, boolean isZeroBased, boolean hemisphereOnly, boolean threadSafe)
############## ITERATOR SHOULD BE RELEASED #################int
next()
void
release()
void
setCenter(javajs.util.T3 center, float distance)
protected void
setCenter2(javajs.util.T3 center, float distance)
void
setModel(ModelSet modelSet, int modelIndex, int firstModelAtom, int atomIndex, javajs.util.T3 center, float distance, RadiusData rd)
-
-
-
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
-
-
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
- TODOthreadSafe
-
-
setModel
public void setModel(ModelSet modelSet, int modelIndex, int firstModelAtom, int atomIndex, javajs.util.T3 center, float distance, RadiusData rd)
- Specified by:
setModel
in interfaceAtomIndexIterator
firstModelAtom
- an offset used in the AtomIteratorWithinSet only
-
setCenter
public void setCenter(javajs.util.T3 center, float distance)
- Specified by:
setCenter
in interfaceAtomIndexIterator
-
setCenter2
protected void setCenter2(javajs.util.T3 center, float distance)
-
hasNext
public boolean hasNext()
- Specified by:
hasNext
in interfaceAtomIndexIterator
-
hasNext2
protected boolean hasNext2()
-
next
public int next()
- Specified by:
next
in interfaceAtomIndexIterator
-
foundDistance2
public float foundDistance2()
- Specified by:
foundDistance2
in interfaceAtomIndexIterator
-
addAtoms
public void addAtoms(BS bsResult)
turns this into a SPHERICAL iterator for "within Distance" measures- Specified by:
addAtoms
in interfaceAtomIndexIterator
- Parameters:
bsResult
-
-
release
public void release()
- Specified by:
release
in interfaceAtomIndexIterator
-
getPosition
public javajs.util.P3 getPosition()
- Specified by:
getPosition
in interfaceAtomIndexIterator
-
-