Package org.jmol.modelset
Class AtomIteratorWithinModel
java.lang.Object
org.jmol.modelset.AtomIteratorWithinModel
- All Implemented Interfaces:
AtomIndexIterator
- Direct Known Subclasses:
AtomIteratorWithinModelSet
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate int
private Atom[]
protected Bspf
private javajs.util.BS
private boolean
protected CubeIterator
private float
private boolean
private int
private boolean
private boolean
private boolean
protected int
private RadiusData
private boolean
private float
private Viewer
private int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addAtoms
(javajs.util.BS bsResult) turns this into a SPHERICAL iterator for "within Distance" measuresfloat
javajs.util.P3
boolean
hasNext()
protected boolean
hasNext2()
(package private) void
initialize
(Bspf bspf, javajs.util.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)
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Field Details
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cubeIterator
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bspf
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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
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vdw1
private float vdw1 -
isVdw
private boolean isVdw -
atoms
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vwr
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iNext
private int iNext
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Constructor Details
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AtomIteratorWithinModel
AtomIteratorWithinModel()
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Method Details
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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
- TODOthreadSafe
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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
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setCenter
public void setCenter(javajs.util.T3 center, float distance) - Specified by:
setCenter
in interfaceAtomIndexIterator
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setCenter2
protected void setCenter2(javajs.util.T3 center, float distance) -
hasNext
public boolean hasNext()- Specified by:
hasNext
in interfaceAtomIndexIterator
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hasNext2
protected boolean hasNext2() -
next
public int next()- Specified by:
next
in interfaceAtomIndexIterator
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foundDistance2
public float foundDistance2()- Specified by:
foundDistance2
in interfaceAtomIndexIterator
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addAtoms
public void addAtoms(javajs.util.BS bsResult) turns this into a SPHERICAL iterator for "within Distance" measures- Specified by:
addAtoms
in interfaceAtomIndexIterator
- Parameters:
bsResult
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release
public void release()- Specified by:
release
in interfaceAtomIndexIterator
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getPosition
public javajs.util.P3 getPosition()- Specified by:
getPosition
in interfaceAtomIndexIterator
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