org.jmol.adapter.smarter
Class AtomSetCollection

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollection

public class AtomSetCollection
extends java.lang.Object


Field Summary
(package private)  boolean applySymmetryToBonds
           
(package private)  int atomCount
           
(package private)  Atom[] atoms
           
(package private)  int[] atomSetAtomCounts
           
(package private)  java.util.Hashtable[] atomSetAuxiliaryInfo
           
(package private)  int[] atomSetBondCounts
           
(package private)  java.util.Hashtable atomSetCollectionAuxiliaryInfo
           
(package private)  java.util.Properties atomSetCollectionProperties
           
(package private)  int atomSetCount
           
(package private)  java.lang.String[] atomSetNames
           
(package private)  int[] atomSetNumbers
           
(package private)  java.util.Properties[] atomSetProperties
           
(package private)  java.util.Hashtable atomSymbolicMap
           
(package private)  int bondCount
           
(package private)  int bondCount0
           
(package private)  int bondIndex0
           
(package private)  Bond[] bonds
           
(package private)  javax.vecmath.Point3f[] cartesians
           
(package private)  boolean checkSpecial
           
(package private)  java.lang.String collectionName
           
(package private)  int[] connectLast
           
(package private)  int connectNextAtomIndex
           
(package private)  int connectNextAtomSet
           
(package private)  boolean coordinatesAreFractional
           
(package private)  int currentAtomSetIndex
           
(package private)  boolean doNormalize
           
(package private)  boolean doPackUnitCell
           
 java.lang.String errorMessage
           
(package private)  java.lang.String fileTypeName
           
(package private) static int GLOBAL_FRACTCOORD
           
(package private) static int GLOBAL_latticeCells
           
(package private) static int GLOBAL_SYMMETRY
           
(package private) static java.lang.String[] globalBooleans
           
(package private)  boolean haveMappedSerials
           
(package private)  boolean isLatticeRange
           
private  boolean isTrajectory
           
(package private)  int[] latticeCells
           
private  int maxX
           
private  int maxY
           
private  int maxZ
           
private  int minX
           
private  int minY
           
private  int minZ
           
private  boolean noAutoBond
           
(package private)  float[] notionalUnitCell
           
static java.lang.String[] notionalUnitcellTags
           
private  javax.vecmath.Point3f ptOffset
           
private  javax.vecmath.Point3f ptTemp
           
private  javax.vecmath.Point3f ptTemp1
           
private  javax.vecmath.Point3f ptTemp2
           
private  float rmaxx
           
private  float rmaxy
           
private  float rmaxz
           
private  float rminx
           
private  float rminy
           
private  float rminz
           
(package private)  int structureCount
           
(package private)  Structure[] structures
           
(package private)  SymmetryInterface symmetry
           
(package private)  float symmetryRange
           
(package private)  javax.vecmath.Point3f[] trajectoryStep
           
(package private)  int trajectoryStepCount
           
(package private)  java.util.Vector trajectorySteps
           
(package private)  java.util.Vector vConnect
           
(package private)  VolumeDataInterface vd
           
 
Constructor Summary
AtomSetCollection(AtomSetCollection[] array)
          Creates an AtomSetCollection based on an array of AtomSetCollection
AtomSetCollection(java.lang.String fileTypeName)
           
AtomSetCollection(java.util.Vector list)
          Creates an AtomSetCollection based on a Vector of AtomSetCollection or Vector (from zipped zip files)
 
Method Summary
 void addAtom(Atom atom)
           
 void addAtomWithMappedName(Atom atom)
           
 void addAtomWithMappedSerialNumber(Atom atom)
           
 void addBond(Bond bond)
           
 void addConnection(int[] is)
           
 Atom addNewAtom()
           
 Bond addNewBond(int atomIndex1, int atomIndex2)
           
 Bond addNewBond(int atomIndex1, int atomIndex2, int order)
           
(package private)  Bond addNewBond(java.lang.String atomName1, java.lang.String atomName2)
           
 Bond addNewBond(java.lang.String atomName1, java.lang.String atomName2, int order)
           
 Bond addNewBondWithMappedSerialNumbers(int atomSerial1, int atomSerial2, int order)
           
(package private)  boolean addSpaceGroupOperation(java.lang.String xyz)
           
 void addStructure(Structure structure)
           
private  void addTrajectoryStep()
           
protected  void appendAtomSetCollection(int collectionIndex, AtomSetCollection collection)
          Appends an AtomSetCollection
private  void appendAtomSetCollection(java.util.Vector list)
           
private  void applyAllSymmetry(int maxX, int maxY, int maxZ)
           
(package private)  void applySymmetry()
           
(package private)  void applySymmetry(int maxX, int maxY, int maxZ)
           
(package private)  void applySymmetry(SymmetryInterface symmetry)
           
 void applySymmetry(java.util.Vector biomts, boolean applySymmetryToBonds, java.lang.String filter)
           
 void clearSymbolicMap()
           
(package private)  void cloneAtomSetProperties(int index)
          Clones the properties of an atom set and associated it with the current atom set.
 void cloneFirstAtomSet()
           
 void cloneFirstAtomSetWithBonds(int nBonds)
           
 void cloneLastAtomSet()
           
 void cloneLastAtomSetProperties()
          Clones the properties of the last atom set and associates it with the current atom set.
 void connectAll(int maxSerial)
           
 void createAtomSerialMap()
           
 void discardPreviousAtoms()
           
private  void finalizeTrajectory(boolean addStep)
           
(package private)  void finalizeTrajectory(java.util.Vector trajectorySteps)
           
(package private)  void finish()
           
(package private)  void freeze()
           
(package private)  void getAltLocLists()
           
 Atom getAtom(int i)
           
 int getAtomCount()
           
 int getAtomNameIndex(java.lang.String atomName)
           
 Atom[] getAtoms()
           
 int getAtomSerialNumberIndex(int serialNumber)
           
(package private)  java.util.Hashtable getAtomSetAuxiliaryInfo(int atomSetIndex)
           
(package private)  java.lang.Object getAtomSetAuxiliaryInfo(int index, java.lang.String key)
           
 java.lang.Object getAtomSetCollectionAuxiliaryInfo(java.lang.String key)
           
(package private)  java.lang.String getAtomSetCollectionProperty(java.lang.String key)
           
 int getAtomSetCount()
           
(package private)  java.lang.String getAtomSetName(int atomSetIndex)
           
(package private)  int getAtomSetNumber(int atomSetIndex)
           
(package private)  java.util.Properties getAtomSetProperties(int atomSetIndex)
           
 Bond getBond(int i)
           
 int getBondCount()
           
 Bond[] getBonds()
           
 int getCurrentAtomSetIndex()
           
 int getFirstAtomSetAtomCount()
           
(package private)  void getInsertionLists()
           
 int getLastAtomSetAtomCount()
           
 int getLastAtomSetAtomIndex()
           
private  SymmetryInterface getSymmetry()
           
 java.lang.Object getVolumeData()
           
(package private)  boolean hasAlternateLocations()
           
(package private)  boolean hasInsertions()
           
private  boolean isInSymmetryRange(javax.vecmath.Point3f c)
           
 boolean isTrajectory()
           
private static boolean isWithinCell(javax.vecmath.Point3f pt, int minX, int maxX, int minY, int maxY, int minZ, int maxZ)
           
(package private)  void mapAtomName(java.lang.String atomName, int atomIndex)
           
(package private)  void mapMostRecentAtomName()
           
(package private)  void mapMostRecentAtomSerialNumber()
           
 void mapPartialCharge(java.lang.String atomName, float charge)
           
 void newAtomSet()
           
(package private)  Atom newCloneAtom(Atom atom)
           
 void newVolumeData()
           
 void removeAtomSet()
           
 java.util.Properties setAtomNames(java.util.Properties atomIdNames)
           
 void setAtomSetAuxiliaryInfo(java.lang.String key, java.lang.Object value)
          Sets auxiliary information for the AtomSet
(package private)  void setAtomSetAuxiliaryInfo(java.lang.String key, java.lang.Object value, int atomSetIndex)
          Sets auxiliary information for the an AtomSet
 void setAtomSetCollectionAuxiliaryInfo(java.lang.String key, java.lang.Object value)
           
 boolean setAtomSetCollectionPartialCharges(java.lang.String auxKey)
          Sets the partial atomic charges based on atomSetCollection auxiliary info
 void setAtomSetCollectionProperty(java.lang.String key, java.lang.String value)
          Sets a property for the AtomSetCollection
 void setAtomSetName(java.lang.String atomSetName)
          Sets the name for the current AtomSet
 void setAtomSetName(java.lang.String atomSetName, int atomSetIndex)
          Sets the name for an AtomSet
 void setAtomSetNames(java.lang.String atomSetName, int n)
          Sets the atom set names of the last n atomSets
 void setAtomSetNumber(int atomSetNumber)
          Sets the number for the current AtomSet
(package private)  boolean setAtomSetPartialCharges(java.lang.String auxKey)
          Sets the partial atomic charges based on atomSet auxiliary info
 void setAtomSetProperties(java.lang.String key, java.lang.String value, int n)
          Sets the same properties for the last n atomSets.
 void setAtomSetProperty(java.lang.String key, java.lang.String value)
          Sets a property for the AtomSet
 void setAtomSetProperty(java.lang.String key, java.lang.String value, int atomSetIndex)
          Sets the a property for the an AtomSet
(package private)  void setAtomSetSpaceGroupName(java.lang.String spaceGroupName)
           
 void setCheckSpecial(boolean TF)
           
 void setCollectionName(java.lang.String collectionName)
           
(package private)  void setCoordinatesAreFractional(boolean coordinatesAreFractional)
           
 void setFileTypeName(java.lang.String type)
          Just sets the overall file type after the fact.
(package private)  void setGlobalBoolean(int globalIndex)
           
(package private)  void setLatticeCells(int[] latticeCells, boolean applySymmetryToBonds, boolean doPackUnitCell)
           
 void setLatticeParameter(int latt)
           
(package private)  void setNoAutoBond()
           
(package private)  boolean setNotionalUnitCell(float[] info)
           
private  void setSymmetryMinMax(javax.vecmath.Point3f c)
           
(package private)  void setSymmetryRange(float factor)
           
 boolean setTrajectory()
           
 void setVolumetricOrigin(float x, float y, float z)
           
 void setVolumetricVector(int i, float x, float y, float z)
           
 void setVoxelCounts(int nPointsX, int nPointsY, int nPointsZ)
           
 void setVoxelData(float[][][] voxelData)
           
private  int symmetryAddAtoms(int iAtomFirst, int noSymmetryCount, int transX, int transY, int transZ, int baseCount, int pt, int iCellOpPt)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

fileTypeName

java.lang.String fileTypeName

collectionName

java.lang.String collectionName

atomSetCollectionProperties

java.util.Properties atomSetCollectionProperties

atomSetCollectionAuxiliaryInfo

java.util.Hashtable atomSetCollectionAuxiliaryInfo

globalBooleans

static final java.lang.String[] globalBooleans

GLOBAL_FRACTCOORD

static final int GLOBAL_FRACTCOORD
See Also:
Constant Field Values

GLOBAL_SYMMETRY

static final int GLOBAL_SYMMETRY
See Also:
Constant Field Values

GLOBAL_latticeCells

static final int GLOBAL_latticeCells
See Also:
Constant Field Values

notionalUnitcellTags

public static final java.lang.String[] notionalUnitcellTags

atomCount

int atomCount

atoms

Atom[] atoms

bondCount

int bondCount

bonds

Bond[] bonds

structureCount

int structureCount

structures

Structure[] structures

atomSetCount

int atomSetCount

currentAtomSetIndex

int currentAtomSetIndex

atomSetNumbers

int[] atomSetNumbers

atomSetNames

java.lang.String[] atomSetNames

atomSetAtomCounts

int[] atomSetAtomCounts

atomSetBondCounts

int[] atomSetBondCounts

atomSetProperties

java.util.Properties[] atomSetProperties

atomSetAuxiliaryInfo

java.util.Hashtable[] atomSetAuxiliaryInfo

latticeCells

int[] latticeCells

errorMessage

public java.lang.String errorMessage

coordinatesAreFractional

boolean coordinatesAreFractional

isTrajectory

private boolean isTrajectory

trajectoryStepCount

int trajectoryStepCount

trajectoryStep

javax.vecmath.Point3f[] trajectoryStep

trajectorySteps

java.util.Vector trajectorySteps

notionalUnitCell

float[] notionalUnitCell

noAutoBond

private boolean noAutoBond

vConnect

java.util.Vector vConnect

connectNextAtomIndex

int connectNextAtomIndex

connectNextAtomSet

int connectNextAtomSet

connectLast

int[] connectLast

symmetryRange

float symmetryRange

symmetry

SymmetryInterface symmetry

doNormalize

boolean doNormalize

doPackUnitCell

boolean doPackUnitCell

isLatticeRange

boolean isLatticeRange

rminx

private float rminx

rminy

private float rminy

rminz

private float rminz

rmaxx

private float rmaxx

rmaxy

private float rmaxy

rmaxz

private float rmaxz

ptOffset

private final javax.vecmath.Point3f ptOffset

minX

private int minX

maxX

private int maxX

minY

private int minY

maxY

private int maxY

minZ

private int minZ

maxZ

private int maxZ

cartesians

javax.vecmath.Point3f[] cartesians

bondCount0

int bondCount0

bondIndex0

int bondIndex0

applySymmetryToBonds

boolean applySymmetryToBonds

checkSpecial

boolean checkSpecial

ptTemp

private final javax.vecmath.Point3f ptTemp

ptTemp1

private final javax.vecmath.Point3f ptTemp1

ptTemp2

private final javax.vecmath.Point3f ptTemp2

atomSymbolicMap

java.util.Hashtable atomSymbolicMap

haveMappedSerials

boolean haveMappedSerials

vd

VolumeDataInterface vd
Constructor Detail

AtomSetCollection

public AtomSetCollection(java.lang.String fileTypeName)

AtomSetCollection

public AtomSetCollection(AtomSetCollection[] array)
Creates an AtomSetCollection based on an array of AtomSetCollection

Parameters:
array - Array of AtomSetCollection

AtomSetCollection

public AtomSetCollection(java.util.Vector list)
Creates an AtomSetCollection based on a Vector of AtomSetCollection or Vector (from zipped zip files)

Parameters:
list - Vector of AtomSetCollection
Method Detail

getAtomCount

public int getAtomCount()

getAtoms

public Atom[] getAtoms()

getAtom

public Atom getAtom(int i)

getBondCount

public int getBondCount()

getBonds

public Bond[] getBonds()

getBond

public Bond getBond(int i)

getAtomSetCount

public int getAtomSetCount()

getCurrentAtomSetIndex

public int getCurrentAtomSetIndex()

isTrajectory

public boolean isTrajectory()

appendAtomSetCollection

private void appendAtomSetCollection(java.util.Vector list)

setFileTypeName

public void setFileTypeName(java.lang.String type)
Just sets the overall file type after the fact.

Parameters:
type -

setTrajectory

public boolean setTrajectory()

appendAtomSetCollection

protected void appendAtomSetCollection(int collectionIndex,
                                       AtomSetCollection collection)
Appends an AtomSetCollection

Parameters:
collectionIndex - collection index for new model number
collection - AtomSetCollection to append

setNoAutoBond

void setNoAutoBond()

finish

void finish()

freeze

void freeze()

discardPreviousAtoms

public void discardPreviousAtoms()

removeAtomSet

public void removeAtomSet()

newCloneAtom

Atom newCloneAtom(Atom atom)
            throws java.lang.Exception
Throws:
java.lang.Exception

cloneFirstAtomSet

public void cloneFirstAtomSet()
                       throws java.lang.Exception
Throws:
java.lang.Exception

cloneFirstAtomSetWithBonds

public void cloneFirstAtomSetWithBonds(int nBonds)
                                throws java.lang.Exception
Throws:
java.lang.Exception

cloneLastAtomSet

public void cloneLastAtomSet()
                      throws java.lang.Exception
Throws:
java.lang.Exception

getFirstAtomSetAtomCount

public int getFirstAtomSetAtomCount()

getLastAtomSetAtomCount

public int getLastAtomSetAtomCount()

getLastAtomSetAtomIndex

public int getLastAtomSetAtomIndex()

addNewAtom

public Atom addNewAtom()

addAtom

public void addAtom(Atom atom)

addAtomWithMappedName

public void addAtomWithMappedName(Atom atom)

addAtomWithMappedSerialNumber

public void addAtomWithMappedSerialNumber(Atom atom)

addNewBond

public Bond addNewBond(int atomIndex1,
                       int atomIndex2)

addNewBond

Bond addNewBond(java.lang.String atomName1,
                java.lang.String atomName2)

addNewBond

public Bond addNewBond(int atomIndex1,
                       int atomIndex2,
                       int order)

addNewBond

public Bond addNewBond(java.lang.String atomName1,
                       java.lang.String atomName2,
                       int order)

addNewBondWithMappedSerialNumbers

public Bond addNewBondWithMappedSerialNumbers(int atomSerial1,
                                              int atomSerial2,
                                              int order)

addConnection

public void addConnection(int[] is)

connectAll

public void connectAll(int maxSerial)

addBond

public void addBond(Bond bond)

addStructure

public void addStructure(Structure structure)

setAtomSetSpaceGroupName

void setAtomSetSpaceGroupName(java.lang.String spaceGroupName)

setCoordinatesAreFractional

void setCoordinatesAreFractional(boolean coordinatesAreFractional)

setSymmetryRange

void setSymmetryRange(float factor)

setLatticeCells

void setLatticeCells(int[] latticeCells,
                     boolean applySymmetryToBonds,
                     boolean doPackUnitCell)

getSymmetry

private SymmetryInterface getSymmetry()

setNotionalUnitCell

boolean setNotionalUnitCell(float[] info)

setGlobalBoolean

void setGlobalBoolean(int globalIndex)

addSpaceGroupOperation

boolean addSpaceGroupOperation(java.lang.String xyz)

setLatticeParameter

public void setLatticeParameter(int latt)

applySymmetry

void applySymmetry()
             throws java.lang.Exception
Throws:
java.lang.Exception

applySymmetry

void applySymmetry(SymmetryInterface symmetry)
             throws java.lang.Exception
Throws:
java.lang.Exception

applySymmetry

void applySymmetry(int maxX,
                   int maxY,
                   int maxZ)
             throws java.lang.Exception
Throws:
java.lang.Exception

setSymmetryMinMax

private void setSymmetryMinMax(javax.vecmath.Point3f c)

isInSymmetryRange

private boolean isInSymmetryRange(javax.vecmath.Point3f c)

isWithinCell

private static boolean isWithinCell(javax.vecmath.Point3f pt,
                                    int minX,
                                    int maxX,
                                    int minY,
                                    int maxY,
                                    int minZ,
                                    int maxZ)

applyAllSymmetry

private void applyAllSymmetry(int maxX,
                              int maxY,
                              int maxZ)
                       throws java.lang.Exception
Throws:
java.lang.Exception

setCheckSpecial

public void setCheckSpecial(boolean TF)

symmetryAddAtoms

private int symmetryAddAtoms(int iAtomFirst,
                             int noSymmetryCount,
                             int transX,
                             int transY,
                             int transZ,
                             int baseCount,
                             int pt,
                             int iCellOpPt)
                      throws java.lang.Exception
Throws:
java.lang.Exception

applySymmetry

public void applySymmetry(java.util.Vector biomts,
                          boolean applySymmetryToBonds,
                          java.lang.String filter)

setCollectionName

public void setCollectionName(java.lang.String collectionName)

mapMostRecentAtomName

void mapMostRecentAtomName()

clearSymbolicMap

public void clearSymbolicMap()

mapMostRecentAtomSerialNumber

void mapMostRecentAtomSerialNumber()

createAtomSerialMap

public void createAtomSerialMap()

mapAtomName

void mapAtomName(java.lang.String atomName,
                 int atomIndex)

getAtomNameIndex

public int getAtomNameIndex(java.lang.String atomName)

getAtomSerialNumberIndex

public int getAtomSerialNumberIndex(int serialNumber)

setAtomSetCollectionProperty

public void setAtomSetCollectionProperty(java.lang.String key,
                                         java.lang.String value)
Sets a property for the AtomSetCollection

Parameters:
key - The poperty key.
value - The property value.

getAtomSetCollectionProperty

java.lang.String getAtomSetCollectionProperty(java.lang.String key)

setAtomSetCollectionAuxiliaryInfo

public void setAtomSetCollectionAuxiliaryInfo(java.lang.String key,
                                              java.lang.Object value)

setAtomSetCollectionPartialCharges

public boolean setAtomSetCollectionPartialCharges(java.lang.String auxKey)
Sets the partial atomic charges based on atomSetCollection auxiliary info

Parameters:
auxKey - The auxiliary key name that contains the charges
Returns:
true if the data exist; false if not

mapPartialCharge

public void mapPartialCharge(java.lang.String atomName,
                             float charge)

getAtomSetCollectionAuxiliaryInfo

public java.lang.Object getAtomSetCollectionAuxiliaryInfo(java.lang.String key)

addTrajectoryStep

private void addTrajectoryStep()

finalizeTrajectory

void finalizeTrajectory(java.util.Vector trajectorySteps)

finalizeTrajectory

private void finalizeTrajectory(boolean addStep)

newAtomSet

public void newAtomSet()

setAtomSetName

public void setAtomSetName(java.lang.String atomSetName)
Sets the name for the current AtomSet

Parameters:
atomSetName - The name to be associated with the current AtomSet

setAtomSetName

public void setAtomSetName(java.lang.String atomSetName,
                           int atomSetIndex)
Sets the name for an AtomSet

Parameters:
atomSetName - The number to be associated with the AtomSet
atomSetIndex - The index of the AtomSet that needs the association

setAtomSetNames

public void setAtomSetNames(java.lang.String atomSetName,
                            int n)
Sets the atom set names of the last n atomSets

Parameters:
atomSetName - The name
n - The number of last AtomSets that need these set

setAtomSetNumber

public void setAtomSetNumber(int atomSetNumber)
Sets the number for the current AtomSet

Parameters:
atomSetNumber - The number for the current AtomSet.

setAtomSetProperty

public void setAtomSetProperty(java.lang.String key,
                               java.lang.String value)
Sets a property for the AtomSet

Parameters:
key - The key for the property
value - The value to be associated with the key

setAtomSetAuxiliaryInfo

public void setAtomSetAuxiliaryInfo(java.lang.String key,
                                    java.lang.Object value)
Sets auxiliary information for the AtomSet

Parameters:
key - The key for the property
value - The value to be associated with the key

setAtomSetPartialCharges

boolean setAtomSetPartialCharges(java.lang.String auxKey)
Sets the partial atomic charges based on atomSet auxiliary info

Parameters:
auxKey - The auxiliary key name that contains the charges
Returns:
true if the data exist; false if not

getAtomSetAuxiliaryInfo

java.lang.Object getAtomSetAuxiliaryInfo(int index,
                                         java.lang.String key)

setAtomSetProperty

public void setAtomSetProperty(java.lang.String key,
                               java.lang.String value,
                               int atomSetIndex)
Sets the a property for the an AtomSet

Parameters:
key - The key for the property
value - The value for the property
atomSetIndex - The index of the AtomSet to get the property

setAtomSetAuxiliaryInfo

void setAtomSetAuxiliaryInfo(java.lang.String key,
                             java.lang.Object value,
                             int atomSetIndex)
Sets auxiliary information for the an AtomSet

Parameters:
key - The key for the property
value - The value for the property
atomSetIndex - The index of the AtomSet to get the property

setAtomSetProperties

public void setAtomSetProperties(java.lang.String key,
                                 java.lang.String value,
                                 int n)
Sets the same properties for the last n atomSets.

Parameters:
key - The key for the property
value - The value of the property
n - The number of last AtomSets that need these set

cloneLastAtomSetProperties

public void cloneLastAtomSetProperties()
Clones the properties of the last atom set and associates it with the current atom set.


cloneAtomSetProperties

void cloneAtomSetProperties(int index)
Clones the properties of an atom set and associated it with the current atom set.

Parameters:
index - The index of the atom set whose properties are to be cloned.

getAtomSetNumber

int getAtomSetNumber(int atomSetIndex)

getAtomSetName

java.lang.String getAtomSetName(int atomSetIndex)

getAtomSetProperties

java.util.Properties getAtomSetProperties(int atomSetIndex)

getAtomSetAuxiliaryInfo

java.util.Hashtable getAtomSetAuxiliaryInfo(int atomSetIndex)

hasAlternateLocations

boolean hasAlternateLocations()

getAltLocLists

void getAltLocLists()

hasInsertions

boolean hasInsertions()

getInsertionLists

void getInsertionLists()

newVolumeData

public void newVolumeData()

setVoxelCounts

public void setVoxelCounts(int nPointsX,
                           int nPointsY,
                           int nPointsZ)

setVolumetricVector

public void setVolumetricVector(int i,
                                float x,
                                float y,
                                float z)

setVolumetricOrigin

public void setVolumetricOrigin(float x,
                                float y,
                                float z)

setVoxelData

public void setVoxelData(float[][][] voxelData)

getVolumeData

public java.lang.Object getVolumeData()

setAtomNames

public java.util.Properties setAtomNames(java.util.Properties atomIdNames)