org.jmol.adapter.smarter
Class AtomSetCollection

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

public class AtomSetCollection
extends Object


Field Summary
private  boolean allowMultiple
           
(package private)  boolean applySymmetryToBonds
           
private  int atomCount
           
private  Atom[] atoms
           
private  int[] atomSetAtomCounts
           
private  Hashtable[] atomSetAuxiliaryInfo
           
private  int[] atomSetBondCounts
           
private  Hashtable atomSetCollectionAuxiliaryInfo
           
private  int atomSetCount
           
private  int[] atomSetNumbers
           
(package private)  Hashtable atomSymbolicMap
           
private  int bondCount
           
(package private)  int bondCount0
           
(package private)  int bondIndex0
           
private  Bond[] bonds
           
(package private)  Point3f[] cartesians
           
(package private)  boolean checkSpecial
           
private  String collectionName
           
(package private)  int[] connectLast
           
(package private)  int connectNextAtomIndex
           
(package private)  int connectNextAtomSet
           
(package private)  boolean coordinatesAreFractional
           
private  int currentAtomSetIndex
           
(package private)  boolean doFixPeriodic
           
(package private)  boolean doNormalize
           
(package private)  boolean doPackUnitCell
           
 String errorMessage
           
private  String fileTypeName
           
private static int GLOBAL_CONECT
           
static int GLOBAL_FRACTCOORD
           
private static int GLOBAL_ISPDB
           
static int GLOBAL_SYMMETRY
           
static int GLOBAL_UNITCELLS
           
private static String[] globalBooleans
           
(package private)  boolean haveMappedSerials
           
(package private)  boolean haveUnitCell
           
private  boolean isTrajectory
           
private  int[] latticeCells
           
private  Point3i maxXYZ
           
private  Point3i minXYZ
           
private  boolean needEllipsoids
           
(package private)  float[] notionalUnitCell
           
static String[] notionalUnitcellTags
           
private  Point3f ptOffset
           
private  Point3f ptTemp
           
private  Point3f ptTemp1
           
private  Point3f ptTemp2
           
private  float rmaxx
           
private  float rmaxy
           
private  float rmaxz
           
private  float rminx
           
private  float rminy
           
private  float rminz
           
private  int structureCount
           
private  Structure[] structures
           
(package private)  SymmetryInterface symmetry
           
(package private)  float symmetryRange
           
private  Point3f[] trajectoryStep
           
private  int trajectoryStepCount
           
private  List trajectorySteps
           
private  Point3f unitCellOffset
           
(package private)  List vConnect
           
(package private)  VolumeDataInterface vd
           
 
Constructor Summary
AtomSetCollection(AtomSetCollection[] array)
          Creates an AtomSetCollection based on an array of AtomSetCollection
AtomSetCollection(List list)
          Creates an AtomSetCollection based on a List of AtomSetCollection or List (from zipped zip files)
AtomSetCollection(String fileTypeName, AtomSetCollectionReader atomSetCollectionReader)
           
 
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(String atomName1, String atomName2)
           
 Bond addNewBond(String atomName1, String atomName2, int order)
           
 Bond addNewBondWithMappedSerialNumbers(int atomSerial1, int atomSerial2, int order)
           
(package private)  boolean addSpaceGroupOperation(String xyz)
           
 void addStructure(Structure structure)
           
private  void addTrajectoryStep()
           
 void addVibrationVector(int iatom, float x, float y, float z)
           
 void addVibrationVector(int iatom, float vx, float vy, float vz, boolean withSymmetry)
           
private  void appendAtomProperties(int nTimes)
           
protected  void appendAtomSetCollection(int collectionIndex, AtomSetCollection collection)
          Appends an AtomSetCollection
private  void appendAtomSetCollection(List list)
           
private  void applyAllSymmetry(int maxX, int maxY, int maxZ)
           
(package private)  void applySymmetry()
           
private  void applySymmetry(int maxX, int maxY, int maxZ)
           
 void applySymmetry(List biomts, float[] notionalUnitCell, boolean applySymmetryToBonds, String filter)
           
(package private)  void applySymmetry(SymmetryInterface symmetry)
           
 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 cloneLastAtomSet(int atomCount)
           
 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(List trajectorySteps)
           
(package private)  void finish()
           
private  Point3f fixPeriodic(Point3f pt, Point3f pt0)
           
private  float fixPoint(float x, float x0)
           
(package private)  void freeze()
           
(package private)  void getAltLocLists()
           
 float[] getAnisoBorU(Atom atom)
           
 Atom getAtom(int i)
           
 int getAtomCount()
           
 int getAtomNameIndex(String atomName)
           
 Atom[] getAtoms()
           
 int getAtomSerialNumberIndex(int serialNumber)
           
(package private)  Hashtable getAtomSetAuxiliaryInfo(int atomSetIndex)
           
(package private)  Object getAtomSetAuxiliaryInfo(int index, String key)
           
 Hashtable getAtomSetCollectionAuxiliaryInfo()
           
 Object getAtomSetCollectionAuxiliaryInfo(String key)
           
 int getAtomSetCount()
           
(package private)  String getAtomSetName(int atomSetIndex)
           
(package private)  int getAtomSetNumber(int atomSetIndex)
           
 Bond getBond(int i)
           
 int getBondCount()
           
 Bond[] getBonds()
           
 String getCollectionName()
           
 int getCurrentAtomSetIndex()
           
 String getFileTypeName()
           
 int getFirstAtomSetAtomCount()
           
(package private)  void getInsertionLists()
           
 int getLastAtomSetAtomCount()
           
 int getLastAtomSetAtomIndex()
           
 int getStructureCount()
           
 Structure[] getStructures()
           
private  SymmetryInterface getSymmetry()
           
 Object getVolumeData()
           
(package private)  boolean hasAlternateLocations()
           
(package private)  boolean hasInsertions()
           
private  boolean isInSymmetryRange(Point3f c)
           
private static boolean isWithinCell(Point3f pt, int minX, int maxX, int minY, int maxY, int minZ, int maxZ)
           
(package private)  void mapAtomName(String atomName, int atomIndex)
           
(package private)  void mapMostRecentAtomName()
           
(package private)  void mapMostRecentAtomSerialNumber()
           
 void mapPartialCharge(String atomName, float charge)
           
 void newAtomSet()
           
(package private)  Atom newCloneAtom(Atom atom)
           
 void newVolumeData()
           
 void removeAtomSet()
           
 void setAnisoBorU(Atom atom, float[] data, int type)
           
 Properties setAtomNames(Properties atomIdNames)
           
 void setAtomSetAuxiliaryInfo(String key, Object value)
          Sets auxiliary information for the AtomSet
(package private)  void setAtomSetAuxiliaryInfo(String key, Object value, int atomSetIndex)
          Sets auxiliary information for an AtomSet
 void setAtomSetAuxiliaryProperty(String key, String data)
           
 void setAtomSetCollectionAuxiliaryInfo(String key, Object value)
           
 boolean setAtomSetCollectionPartialCharges(String auxKey)
          Sets the partial atomic charges based on atomSetCollection auxiliary info
 void setAtomSetEnergy(String energyString, float value)
           
 void setAtomSetFrequency(String pathKey, String label, String freq, String units)
           
 void setAtomSetName(String atomSetName)
          Sets the name for the current AtomSet
 void setAtomSetNames(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(String auxKey)
          Sets the partial atomic charges based on atomSet auxiliary info
 void setAtomSetProperties(String key, String value, int n)
          Sets the same properties for the last n atomSets.
 void setAtomSetProperty(String key, String value)
          Sets a property for the current AtomSet used specifically for creating directories and plots of frequencies and moleular energies
 void setAtomSetProperty(String key, String value, int atomSetIndex)
          Sets the a property for the an AtomSet
(package private)  void setAtomSetSpaceGroupName(String spaceGroupName)
           
 void setCheckSpecial(boolean TF)
           
 void setCollectionName(String collectionName)
           
(package private)  void setCoordinatesAreFractional(boolean coordinatesAreFractional)
           
 void setCurrentAtomSetIndex(int i)
           
 void setDoFixPeriodic()
           
(package private)  void setGlobalBoolean(int globalIndex)
           
 void setIsPDB()
           
(package private)  void setLatticeCells(int[] latticeCells, boolean applySymmetryToBonds, boolean doPackUnitCell)
           
 void setLatticeParameter(int latt)
           
(package private)  void setNoAutoBond()
           
 void setNotionalUnitCell(float[] info, Matrix3f matUnitCellOrientation, Point3f unitCellOffset)
           
private  void setSymmetryMinMax(Point3f c)
           
private  void setSymmetryOps()
           
(package private)  void setSymmetryRange(float factor)
           
 void 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)
           
(package private)  void toCartesian(SymmetryInterface symmetry)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

fileTypeName

private String fileTypeName

collectionName

private String collectionName

atomSetCollectionAuxiliaryInfo

private Hashtable atomSetCollectionAuxiliaryInfo

globalBooleans

private static final String[] globalBooleans

GLOBAL_FRACTCOORD

public static final int GLOBAL_FRACTCOORD
See Also:
Constant Field Values

GLOBAL_SYMMETRY

public static final int GLOBAL_SYMMETRY
See Also:
Constant Field Values

GLOBAL_UNITCELLS

public static final int GLOBAL_UNITCELLS
See Also:
Constant Field Values

GLOBAL_CONECT

private static final int GLOBAL_CONECT
See Also:
Constant Field Values

GLOBAL_ISPDB

private static final int GLOBAL_ISPDB
See Also:
Constant Field Values

notionalUnitcellTags

public static final String[] notionalUnitcellTags

atomCount

private int atomCount

atoms

private Atom[] atoms

bondCount

private int bondCount

bonds

private Bond[] bonds

structureCount

private int structureCount

structures

private Structure[] structures

atomSetCount

private int atomSetCount

currentAtomSetIndex

private int currentAtomSetIndex

atomSetNumbers

private int[] atomSetNumbers

atomSetAtomCounts

private int[] atomSetAtomCounts

atomSetBondCounts

private int[] atomSetBondCounts

atomSetAuxiliaryInfo

private Hashtable[] atomSetAuxiliaryInfo

latticeCells

private int[] latticeCells

errorMessage

public String errorMessage

coordinatesAreFractional

boolean coordinatesAreFractional

isTrajectory

private boolean isTrajectory

trajectoryStepCount

private int trajectoryStepCount

trajectoryStep

private Point3f[] trajectoryStep

trajectorySteps

private List trajectorySteps

doFixPeriodic

boolean doFixPeriodic

notionalUnitCell

float[] notionalUnitCell

allowMultiple

private boolean allowMultiple

vConnect

List vConnect

connectNextAtomIndex

int connectNextAtomIndex

connectNextAtomSet

int connectNextAtomSet

connectLast

int[] connectLast

symmetryRange

float symmetryRange

symmetry

SymmetryInterface symmetry

haveUnitCell

boolean haveUnitCell

doNormalize

boolean doNormalize

doPackUnitCell

boolean doPackUnitCell

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 Point3f ptOffset

unitCellOffset

private Point3f unitCellOffset

minXYZ

private Point3i minXYZ

maxXYZ

private Point3i maxXYZ

needEllipsoids

private boolean needEllipsoids

cartesians

Point3f[] cartesians

bondCount0

int bondCount0

bondIndex0

int bondIndex0

applySymmetryToBonds

boolean applySymmetryToBonds

checkSpecial

boolean checkSpecial

ptTemp

private final Point3f ptTemp

ptTemp1

private final Point3f ptTemp1

ptTemp2

private final Point3f ptTemp2

atomSymbolicMap

Hashtable atomSymbolicMap

haveMappedSerials

boolean haveMappedSerials

vd

VolumeDataInterface vd
Constructor Detail

AtomSetCollection

public AtomSetCollection(String fileTypeName,
                         AtomSetCollectionReader atomSetCollectionReader)

AtomSetCollection

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

Parameters:
array - Array of AtomSetCollection

AtomSetCollection

public AtomSetCollection(List list)
Creates an AtomSetCollection based on a List of AtomSetCollection or List (from zipped zip files)

Parameters:
list - List of AtomSetCollection
Method Detail

getFileTypeName

public String getFileTypeName()

getCollectionName

public String getCollectionName()

setCollectionName

public void setCollectionName(String collectionName)

getAtomSetCollectionAuxiliaryInfo

public Hashtable getAtomSetCollectionAuxiliaryInfo()

setIsPDB

public void setIsPDB()

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)

getStructureCount

public int getStructureCount()

getStructures

public Structure[] getStructures()

getAtomSetCount

public int getAtomSetCount()

getCurrentAtomSetIndex

public int getCurrentAtomSetIndex()

setCurrentAtomSetIndex

public void setCurrentAtomSetIndex(int i)

setDoFixPeriodic

public void setDoFixPeriodic()

appendAtomSetCollection

private void appendAtomSetCollection(List list)

setTrajectory

public void 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 Exception
Throws:
Exception

cloneFirstAtomSet

public void cloneFirstAtomSet()
                       throws Exception
Throws:
Exception

cloneFirstAtomSetWithBonds

public void cloneFirstAtomSetWithBonds(int nBonds)
                                throws Exception
Throws:
Exception

cloneLastAtomSet

public void cloneLastAtomSet()
                      throws Exception
Throws:
Exception

cloneLastAtomSet

public void cloneLastAtomSet(int atomCount)
                      throws Exception
Throws:
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(String atomName1,
                String atomName2)

addNewBond

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

addNewBond

public Bond addNewBond(String atomName1,
                       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)

addVibrationVector

public void addVibrationVector(int iatom,
                               float vx,
                               float vy,
                               float vz,
                               boolean withSymmetry)

addVibrationVector

public void addVibrationVector(int iatom,
                               float x,
                               float y,
                               float z)

setAtomSetSpaceGroupName

void setAtomSetSpaceGroupName(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

public void setNotionalUnitCell(float[] info,
                                Matrix3f matUnitCellOrientation,
                                Point3f unitCellOffset)

setGlobalBoolean

void setGlobalBoolean(int globalIndex)

addSpaceGroupOperation

boolean addSpaceGroupOperation(String xyz)

setLatticeParameter

public void setLatticeParameter(int latt)

applySymmetry

void applySymmetry()
             throws Exception
Throws:
Exception

applySymmetry

void applySymmetry(SymmetryInterface symmetry)
             throws Exception
Throws:
Exception

applySymmetry

private void applySymmetry(int maxX,
                           int maxY,
                           int maxZ)
                    throws Exception
Throws:
Exception

setSymmetryMinMax

private void setSymmetryMinMax(Point3f c)

isInSymmetryRange

private boolean isInSymmetryRange(Point3f c)

isWithinCell

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

setAnisoBorU

public void setAnisoBorU(Atom atom,
                         float[] data,
                         int type)

getAnisoBorU

public float[] getAnisoBorU(Atom atom)

applyAllSymmetry

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

setSymmetryOps

private void setSymmetryOps()

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 Exception
Throws:
Exception

applySymmetry

public void applySymmetry(List biomts,
                          float[] notionalUnitCell,
                          boolean applySymmetryToBonds,
                          String filter)

mapMostRecentAtomName

void mapMostRecentAtomName()

clearSymbolicMap

public void clearSymbolicMap()

mapMostRecentAtomSerialNumber

void mapMostRecentAtomSerialNumber()

createAtomSerialMap

public void createAtomSerialMap()

mapAtomName

void mapAtomName(String atomName,
                 int atomIndex)

getAtomNameIndex

public int getAtomNameIndex(String atomName)

getAtomSerialNumberIndex

public int getAtomSerialNumberIndex(int serialNumber)

setAtomSetCollectionAuxiliaryInfo

public void setAtomSetCollectionAuxiliaryInfo(String key,
                                              Object value)

setAtomSetCollectionPartialCharges

public boolean setAtomSetCollectionPartialCharges(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(String atomName,
                             float charge)

getAtomSetCollectionAuxiliaryInfo

public Object getAtomSetCollectionAuxiliaryInfo(String key)

addTrajectoryStep

private void addTrajectoryStep()

fixPeriodic

private Point3f fixPeriodic(Point3f pt,
                            Point3f pt0)

fixPoint

private float fixPoint(float x,
                       float x0)

finalizeTrajectory

void finalizeTrajectory(List trajectorySteps)

finalizeTrajectory

private void finalizeTrajectory(boolean addStep)

newAtomSet

public void newAtomSet()

setAtomSetName

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

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

setAtomSetNames

public void setAtomSetNames(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 needs 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(String key,
                               String value)
Sets a property for the current AtomSet used specifically for creating directories and plots of frequencies and moleular energies

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

setAtomSetProperty

public void setAtomSetProperty(String key,
                               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

setAtomSetAuxiliaryProperty

public void setAtomSetAuxiliaryProperty(String key,
                                        String data)

appendAtomProperties

private void appendAtomProperties(int nTimes)

setAtomSetAuxiliaryInfo

public void setAtomSetAuxiliaryInfo(String key,
                                    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(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

Object getAtomSetAuxiliaryInfo(int index,
                               String key)

setAtomSetAuxiliaryInfo

void setAtomSetAuxiliaryInfo(String key,
                             Object value,
                             int atomSetIndex)
Sets auxiliary information for 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(String key,
                                 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 needs 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

String getAtomSetName(int atomSetIndex)

getAtomSetAuxiliaryInfo

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 Object getVolumeData()

setAtomNames

public Properties setAtomNames(Properties atomIdNames)

setAtomSetEnergy

public void setAtomSetEnergy(String energyString,
                             float value)

setAtomSetFrequency

public void setAtomSetFrequency(String pathKey,
                                String label,
                                String freq,
                                String units)

toCartesian

void toCartesian(SymmetryInterface symmetry)