org.jmol.adapter.smarter

Class AtomSetCollection

public class AtomSetCollection extends Object

Field Summary
booleanapplySymmetryToBonds
intatomCount
Atom[]atoms
int[]atomSetAtomCounts
Hashtable[]atomSetAuxiliaryInfo
HashtableatomSetCollectionAuxiliaryInfo
PropertiesatomSetCollectionProperties
intatomSetCount
String[]atomSetNames
int[]atomSetNumbers
Properties[]atomSetProperties
HashtableatomSymbolicMap
intbondCount
intbondCount0
intbondIndex0
Bond[]bonds
Point3f[]cartesians
booleancheckSpecial
StringcollectionName
int[]connectLast
intconnectNextAtomIndex
intconnectNextAtomSet
booleancoordinatesAreFractional
intcurrentAtomSetIndex
booleandoNormalize
StringerrorMessage
StringfileTypeName
static String[]globalBooleans
static intGLOBAL_FRACTCOORD
static intGLOBAL_latticeCells
static intGLOBAL_SYMMETRY
booleanhaveMappedSerials
booleanisLatticeRange
booleanisTrajectory
int[]latticeCells
static String[]notionalUnitcellTags
float[]notionalUnitCell
intnTrajectories
Point3fptTemp
Point3fptTemp1
Point3fptTemp2
floatrmaxx
floatrmaxy
floatrmaxz
floatrminx
floatrminy
floatrminz
intstructureCount
Structure[]structures
SymmetryInterfacesymmetry
floatsymmetryRange
Vectortrajectories
Point3f[]trajectory
VectorvConnect
VolumeDataInterfacevd
Constructor Summary
AtomSetCollection(String fileTypeName)
AtomSetCollection(AtomSetCollection[] array)
Creates an AtomSetCollection based on an array of AtomSetCollection
AtomSetCollection(Vector list)
Creates an AtomSetCollection based on a Vector of AtomSetCollection or Vector (from zipped zip files)
Method Summary
voidaddAtom(Atom atom)
voidaddAtomWithMappedName(Atom atom)
voidaddAtomWithMappedSerialNumber(Atom atom)
voidaddBond(Bond bond)
voidaddConnection(int[] is)
AtomaddNewAtom()
BondaddNewBond(int atomIndex1, int atomIndex2)
BondaddNewBond(String atomName1, String atomName2)
BondaddNewBond(int atomIndex1, int atomIndex2, int order)
BondaddNewBond(String atomName1, String atomName2, int order)
BondaddNewBondWithMappedSerialNumbers(int atomSerial1, int atomSerial2, int order)
booleanaddSpaceGroupOperation(String xyz)
voidaddStructure(Structure structure)
voidaddTrajectory()
voidappendAtomSetCollection(Vector list)
protected voidappendAtomSetCollection(int collectionIndex, AtomSetCollection collection)
Appends an AtomSetCollection
voidapplyAllSymmetry(int maxX, int maxY, int maxZ)
voidapplySymmetry()
voidapplySymmetry(SymmetryInterface symmetry)
voidapplySymmetry(int maxX, int maxY, int maxZ)
voidapplySymmetry(Vector biomts, boolean applySymmetryToBonds, String filter)
voidclearSymbolicMap()
voidcloneAtomSetProperties(int index)
Clones the properties of an atom set and associated it with the current atom set.
voidcloneFirstAtomSet()
voidcloneFirstAtomSetWithBonds(int nBonds)
voidcloneLastAtomSet()
voidcloneLastAtomSetProperties()
Clones the properties of the last atom set and associates it with the current atom set.
voidconnectAll(int maxSerial)
voidcreateAtomSerialMap()
voiddiscardPreviousAtoms()
voidfinalizeTrajectories()
voidfinish()
voidfreeze()
voidgetAltLocLists()
AtomgetAtom(int i)
intgetAtomCount()
intgetAtomNameIndex(String atomName)
Atom[]getAtoms()
intgetAtomSerialNumberIndex(int serialNumber)
ObjectgetAtomSetAuxiliaryInfo(int index, String key)
HashtablegetAtomSetAuxiliaryInfo(int atomSetIndex)
ObjectgetAtomSetCollectionAuxiliaryInfo(String key)
StringgetAtomSetCollectionProperty(String key)
intgetAtomSetCount()
StringgetAtomSetName(int atomSetIndex)
intgetAtomSetNumber(int atomSetIndex)
PropertiesgetAtomSetProperties(int atomSetIndex)
BondgetBond(int i)
intgetBondCount()
Bond[]getBonds()
intgetCurrentAtomSetIndex()
intgetFirstAtomSetAtomCount()
voidgetInsertionLists()
intgetLastAtomSetAtomCount()
intgetLastAtomSetAtomIndex()
SymmetryInterfacegetSymmetry()
ObjectgetVolumeData()
booleanhasAlternateLocations()
booleanhasInsertions()
booleanisInSymmetryRange(Point3f c)
voidmapAtomName(String atomName, int atomIndex)
voidmapMostRecentAtomName()
voidmapMostRecentAtomSerialNumber()
voidmapPartialCharge(String atomName, float charge)
voidnewAtomSet()
AtomnewCloneAtom(Atom atom)
voidnewVolumeData()
voidremoveAtomSet()
voidsetApplySymmetryToBonds(boolean TF)
PropertiessetAtomNames(Properties atomIdNames)
voidsetAtomSetAuxiliaryInfo(String key, Object value)
Sets auxiliary information for the AtomSet
voidsetAtomSetAuxiliaryInfo(String key, Object value, int atomSetIndex)
Sets auxiliary information for the an AtomSet
voidsetAtomSetCollectionAuxiliaryInfo(String key, Object value)
booleansetAtomSetCollectionPartialCharges(String auxKey)
Sets the partial atomic charges based on atomSetCollection auxiliary info
voidsetAtomSetCollectionProperty(String key, String value)
Sets a property for the AtomSetCollection
voidsetAtomSetName(String atomSetName)
Sets the name for the current AtomSet
voidsetAtomSetName(String atomSetName, int atomSetIndex)
Sets the name for an AtomSet
voidsetAtomSetNames(String atomSetName, int n)
Sets the atom set names of the last n atomSets
voidsetAtomSetNumber(int atomSetNumber)
Sets the number for the current AtomSet
booleansetAtomSetPartialCharges(String auxKey)
Sets the partial atomic charges based on atomSet auxiliary info
voidsetAtomSetProperties(String key, String value, int n)
Sets the same properties for the last n atomSets.
voidsetAtomSetProperty(String key, String value)
Sets a property for the AtomSet
voidsetAtomSetProperty(String key, String value, int atomSetIndex)
Sets the a property for the an AtomSet
voidsetAtomSetSpaceGroupName(String spaceGroupName)
voidsetCheckSpecial(boolean TF)
voidsetCollectionName(String collectionName)
voidsetCoordinatesAreFractional(boolean coordinatesAreFractional)
voidsetFileTypeName(String type)
Just sets the overall file type after the fact.
voidsetGlobalBoolean(int globalIndex)
voidsetLatticeCells(int[] latticeCells, boolean applySymmetryToBonds)
voidsetLatticeParameter(int latt)
booleansetNotionalUnitCell(float[] info)
voidsetSymmetryMinMax(Point3f c)
voidsetSymmetryRange(float factor)
booleansetTrajectory()
voidsetVolumetricOrigin(float x, float y, float z)
voidsetVolumetricVector(int i, float x, float y, float z)
voidsetVoxelCounts(int nPointsX, int nPointsY, int nPointsZ)
voidsetVoxelData(float[][][] voxelData)
intsymmetryAddAtoms(int iAtomFirst, int noSymmetryCount, int transX, int transY, int transZ, int baseCount, int pt, int iCellOpPt)

Field Detail

applySymmetryToBonds

boolean applySymmetryToBonds

atomCount

int atomCount

atoms

Atom[] atoms

atomSetAtomCounts

int[] atomSetAtomCounts

atomSetAuxiliaryInfo

Hashtable[] atomSetAuxiliaryInfo

atomSetCollectionAuxiliaryInfo

Hashtable atomSetCollectionAuxiliaryInfo

atomSetCollectionProperties

Properties atomSetCollectionProperties

atomSetCount

int atomSetCount

atomSetNames

String[] atomSetNames

atomSetNumbers

int[] atomSetNumbers

atomSetProperties

Properties[] atomSetProperties

atomSymbolicMap

Hashtable atomSymbolicMap

bondCount

int bondCount

bondCount0

int bondCount0

bondIndex0

int bondIndex0

bonds

Bond[] bonds

cartesians

Point3f[] cartesians

checkSpecial

boolean checkSpecial

collectionName

String collectionName

connectLast

int[] connectLast

connectNextAtomIndex

int connectNextAtomIndex

connectNextAtomSet

int connectNextAtomSet

coordinatesAreFractional

boolean coordinatesAreFractional

currentAtomSetIndex

int currentAtomSetIndex

doNormalize

boolean doNormalize

errorMessage

public String errorMessage

fileTypeName

String fileTypeName

globalBooleans

static final String[] globalBooleans

GLOBAL_FRACTCOORD

static final int GLOBAL_FRACTCOORD

GLOBAL_latticeCells

static final int GLOBAL_latticeCells

GLOBAL_SYMMETRY

static final int GLOBAL_SYMMETRY

haveMappedSerials

boolean haveMappedSerials

isLatticeRange

boolean isLatticeRange

isTrajectory

boolean isTrajectory

latticeCells

int[] latticeCells

notionalUnitcellTags

public static final String[] notionalUnitcellTags

notionalUnitCell

float[] notionalUnitCell

nTrajectories

int nTrajectories

ptTemp

private final Point3f ptTemp

ptTemp1

private final Point3f ptTemp1

ptTemp2

private final Point3f ptTemp2

rmaxx

private float rmaxx

rmaxy

private float rmaxy

rmaxz

private float rmaxz

rminx

private float rminx

rminy

private float rminy

rminz

private float rminz

structureCount

int structureCount

structures

Structure[] structures

symmetry

SymmetryInterface symmetry

symmetryRange

float symmetryRange

trajectories

Vector trajectories

trajectory

Point3f[] trajectory

vConnect

Vector vConnect

vd

VolumeDataInterface vd

Constructor Detail

AtomSetCollection

public AtomSetCollection(String fileTypeName)

AtomSetCollection

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

Parameters: array Array of AtomSetCollection

AtomSetCollection

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

Parameters: list Vector of AtomSetCollection

Method Detail

addAtom

public void addAtom(Atom atom)

addAtomWithMappedName

public void addAtomWithMappedName(Atom atom)

addAtomWithMappedSerialNumber

public void addAtomWithMappedSerialNumber(Atom atom)

addBond

public void addBond(Bond bond)

addConnection

public void addConnection(int[] is)

addNewAtom

public Atom addNewAtom()

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)

addSpaceGroupOperation

boolean addSpaceGroupOperation(String xyz)

addStructure

public void addStructure(Structure structure)

addTrajectory

void addTrajectory()

appendAtomSetCollection

private void appendAtomSetCollection(Vector list)

appendAtomSetCollection

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

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

applyAllSymmetry

private void applyAllSymmetry(int maxX, int maxY, int maxZ)

applySymmetry

void applySymmetry()

applySymmetry

void applySymmetry(SymmetryInterface symmetry)

applySymmetry

void applySymmetry(int maxX, int maxY, int maxZ)

applySymmetry

public void applySymmetry(Vector biomts, boolean applySymmetryToBonds, String filter)

clearSymbolicMap

private void clearSymbolicMap()

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.

cloneFirstAtomSet

public void cloneFirstAtomSet()

cloneFirstAtomSetWithBonds

public void cloneFirstAtomSetWithBonds(int nBonds)

cloneLastAtomSet

public void cloneLastAtomSet()

cloneLastAtomSetProperties

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

connectAll

public void connectAll(int maxSerial)

createAtomSerialMap

public void createAtomSerialMap()

discardPreviousAtoms

public void discardPreviousAtoms()

finalizeTrajectories

void finalizeTrajectories()

finish

void finish()

freeze

void freeze()

getAltLocLists

void getAltLocLists()

getAtom

public Atom getAtom(int i)

getAtomCount

public int getAtomCount()

getAtomNameIndex

public int getAtomNameIndex(String atomName)

getAtoms

public Atom[] getAtoms()

getAtomSerialNumberIndex

public int getAtomSerialNumberIndex(int serialNumber)

getAtomSetAuxiliaryInfo

Object getAtomSetAuxiliaryInfo(int index, String key)

getAtomSetAuxiliaryInfo

Hashtable getAtomSetAuxiliaryInfo(int atomSetIndex)

getAtomSetCollectionAuxiliaryInfo

public Object getAtomSetCollectionAuxiliaryInfo(String key)

getAtomSetCollectionProperty

String getAtomSetCollectionProperty(String key)

getAtomSetCount

public int getAtomSetCount()

getAtomSetName

String getAtomSetName(int atomSetIndex)

getAtomSetNumber

int getAtomSetNumber(int atomSetIndex)

getAtomSetProperties

Properties getAtomSetProperties(int atomSetIndex)

getBond

public Bond getBond(int i)

getBondCount

public int getBondCount()

getBonds

public Bond[] getBonds()

getCurrentAtomSetIndex

public int getCurrentAtomSetIndex()

getFirstAtomSetAtomCount

public int getFirstAtomSetAtomCount()

getInsertionLists

void getInsertionLists()

getLastAtomSetAtomCount

public int getLastAtomSetAtomCount()

getLastAtomSetAtomIndex

public int getLastAtomSetAtomIndex()

getSymmetry

private SymmetryInterface getSymmetry()

getVolumeData

public Object getVolumeData()

hasAlternateLocations

boolean hasAlternateLocations()

hasInsertions

boolean hasInsertions()

isInSymmetryRange

private boolean isInSymmetryRange(Point3f c)

mapAtomName

void mapAtomName(String atomName, int atomIndex)

mapMostRecentAtomName

void mapMostRecentAtomName()

mapMostRecentAtomSerialNumber

void mapMostRecentAtomSerialNumber()

mapPartialCharge

public void mapPartialCharge(String atomName, float charge)

newAtomSet

public void newAtomSet()

newCloneAtom

Atom newCloneAtom(Atom atom)

newVolumeData

public void newVolumeData()

removeAtomSet

public void removeAtomSet()

setApplySymmetryToBonds

void setApplySymmetryToBonds(boolean TF)

setAtomNames

public Properties setAtomNames(Properties atomIdNames)

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

setAtomSetAuxiliaryInfo

void setAtomSetAuxiliaryInfo(String key, 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

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

setAtomSetCollectionProperty

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

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

setAtomSetName

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

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

setAtomSetName

public void setAtomSetName(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(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.

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

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 need these set

setAtomSetProperty

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

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

setAtomSetSpaceGroupName

void setAtomSetSpaceGroupName(String spaceGroupName)

setCheckSpecial

public void setCheckSpecial(boolean TF)

setCollectionName

public void setCollectionName(String collectionName)

setCoordinatesAreFractional

void setCoordinatesAreFractional(boolean coordinatesAreFractional)

setFileTypeName

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

Parameters: type

setGlobalBoolean

void setGlobalBoolean(int globalIndex)

setLatticeCells

void setLatticeCells(int[] latticeCells, boolean applySymmetryToBonds)

setLatticeParameter

public void setLatticeParameter(int latt)

setNotionalUnitCell

boolean setNotionalUnitCell(float[] info)

setSymmetryMinMax

private void setSymmetryMinMax(Point3f c)

setSymmetryRange

void setSymmetryRange(float factor)

setTrajectory

boolean setTrajectory()

setVolumetricOrigin

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

setVolumetricVector

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

setVoxelCounts

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

setVoxelData

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

symmetryAddAtoms

private int symmetryAddAtoms(int iAtomFirst, int noSymmetryCount, int transX, int transY, int transZ, int baseCount, int pt, int iCellOpPt)