Package org.jmol.symmetry

Class SpaceGroup

java.lang.Object

org.jmol.symmetry.SpaceGroup

class SpaceGroup
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
(package private) char	ambiguityType
private static String	ambiguousNames
(package private) char	axisChoice
private static String[]	canonicalSeitzList
(package private) String	crystalClass
(package private) boolean	doNormalize
(package private) SymmetryOperation[]	finalOperations
(package private) HallInfo	hallInfo
(package private) String	hallSymbol
(package private) String	hmSymbol
(package private) String	hmSymbolAbbr
(package private) String	hmSymbolAbbrShort
(package private) String	hmSymbolAlternative
(package private) String	hmSymbolExt
(package private) String	hmSymbolFull
private static Map<Integer,javajs.util.Lst<SpaceGroup>>	htByOpCount
(package private) int	index
private Map<String,Object>	info
(package private) String	intlTableNumber
(package private) String	intlTableNumberExt
(package private) String	intlTableNumberFull
(package private) boolean	isBilbao
(package private) boolean	isBio
(package private) boolean	isSSG
private static String	lastInfo
(package private) int	latticeOp
(package private) int	latticeParameter
(package private) String	latticeType
private int	modDim
(package private) String	name
private static int	NAME_HALL
private static int	NAME_HM
private static int	NAME_UNK
private Integer	nHallOperators
(package private) int	operationCount
(package private) SymmetryOperation[]	operations
private static SpaceGroup[]	SG
private static int	sgIndex
private static String[]	STR_SG	intlNo:options;nOps;schoenflies;hermannMauguin;Hall;BilbaoFlag
(package private) char	uniqueAxis
(package private) Map<String,Integer>	xyzList

Constructor Summary

Constructors

Modifier	Constructor	Description
private	SpaceGroup(int index, String cifLine, boolean doInit)

Method Summary

Modifier and Type	Method	Description
(package private) boolean	addLatticeVectors(javajs.util.Lst<float[]> lattvecs)
private int	addOp(SymmetryOperation op, String xyz0, boolean isSpecial)
private int	addOperation(String xyz0, int opId, boolean allowScaling)
(package private) int	addSymmetry(String xyz, int opId, boolean allowScaling)
(package private) int	addSymmetrySM(String xyz, javajs.util.M4 operation)
private void	buildSpaceGroup(String cifLine)
private int	checkXYZlist(String xyz)
private static SpaceGroup	createSGFromList(String name, javajs.util.Lst<?> data)
(package private) static SpaceGroup	createSpaceGroup(int desiredSpaceGroupIndex, String name, Object data, int modDim)
private static SpaceGroup	createSpaceGroupN(String name)
private static SpaceGroup[]	createSpaceGroups()
private static SpaceGroup	determineSpaceGroup(String name, float a, float b, float c, float alpha, float beta, float gamma, int lastIndex)
private static int	determineSpaceGroupIndex(String name, float a, float b, float c, float alpha, float beta, float gamma, int lastIndex)
private static SpaceGroup	determineSpaceGroupN(String name)
(package private) static SpaceGroup	determineSpaceGroupNA(String name, float[] unitCellParams)
private static SpaceGroup	determineSpaceGroupNS(String name, SpaceGroup sg)
private static char	determineUniqueAxis(float a, float b, float c, float alpha, float beta, float gamma)
private static String	dumpAll()
private static String	dumpAllSeitz()
private Object	dumpCanonicalSeitzList()
(package private) String	dumpInfo()
(package private) Object	dumpInfoObj()
private static SpaceGroup	findSpaceGroup(int opCount, String s)
private void	generateAllOperators(HallInfo h)
private void	generateOperatorsFromXyzInfo(String xyzInfo)
private static String	getCanonicalSeitz(int i)
private String	getCanonicalSeitzList()
(package private) SpaceGroup	getDerivedSpaceGroup()
private Map<String,Object>	getInfo(SymmetryInterface cellInfo)
(package private) static Object	getInfo(SpaceGroup sg, String spaceGroup, SymmetryInterface cellInfo, boolean asMap)
(package private) String	getLatticeDesignation()
(package private) String	getName()
(package private) static SpaceGroup	getNull(boolean doInit, boolean doNormalize, boolean doFinalize)
(package private) javajs.util.M4	getOperation(int i)
(package private) int	getOperationCount()
javajs.util.M4	getRawOperation(int i)
(package private) int	getSiteMultiplicity(javajs.util.P3 pt, UnitCell unitCell)
private static SpaceGroup[]	getSpaceGroups()
(package private) String	getXyz(int i, boolean doNormalize)
private void	init(boolean addXYZ)
(package private) void	newPoint(int i, javajs.util.P3 atom1, javajs.util.P3 atom2, int transX, int transY, int transZ)
(package private) void	setFinalOperations(javajs.util.P3[] atoms, int atomIndex, int count, boolean doNormalize)
private void	setHMSymbol(String name)
private void	setLattice(char latticeCode, boolean isCentrosymmetric)
(package private) void	setLatticeParam(int latticeParameter)
void	setName(String name)
private static String	toCap(String s, int n)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

index

int index

isSSG

boolean isSSG

name

String name

hallSymbol

String hallSymbol

crystalClass

String crystalClass

hmSymbol

String hmSymbol

hmSymbolFull

String hmSymbolFull

hmSymbolExt

String hmSymbolExt

hmSymbolAbbr

String hmSymbolAbbr

hmSymbolAlternative

String hmSymbolAlternative

hmSymbolAbbrShort

String hmSymbolAbbrShort

ambiguityType

char ambiguityType

uniqueAxis

char uniqueAxis

axisChoice

char axisChoice

intlTableNumber

String intlTableNumber

intlTableNumberFull

String intlTableNumberFull

intlTableNumberExt

String intlTableNumberExt

hallInfo

HallInfo hallInfo

latticeParameter

int latticeParameter

operations

SymmetryOperation[] operations

finalOperations

SymmetryOperation[] finalOperations

operationCount

int operationCount

latticeOp

int latticeOp

xyzList

Map<String,Integer> xyzList

modDim

private int modDim

doNormalize

boolean doNormalize

isBio

boolean isBio

isBilbao

boolean isBilbao

latticeType

String latticeType

nHallOperators

private Integer nHallOperators

info

private Map<String,Object> info

canonicalSeitzList

private static String[] canonicalSeitzList

NAME_UNK

private static final int NAME_UNK

See Also:

Constant Field Values

NAME_HM

private static final int NAME_HM

See Also:

Constant Field Values

NAME_HALL

private static final int NAME_HALL

See Also:

Constant Field Values

sgIndex

private static int sgIndex

ambiguousNames

private static String ambiguousNames

lastInfo

private static String lastInfo

SG

private static SpaceGroup[] SG

htByOpCount

private static Map<Integer,javajs.util.Lst<SpaceGroup>> htByOpCount

STR_SG

private static String[] STR_SG

intlNo:options;nOps;schoenflies;hermannMauguin;Hall;BilbaoFlag

Constructor Detail

SpaceGroup

private SpaceGroup(int index,
                   String cifLine,
                   boolean doInit)

Method Detail

getNull

static SpaceGroup getNull(boolean doInit,
                          boolean doNormalize,
                          boolean doFinalize)

init

private void init(boolean addXYZ)

createSpaceGroup

static SpaceGroup createSpaceGroup(int desiredSpaceGroupIndex,
                                   String name,
                                   Object data,
                                   int modDim)

createSGFromList

private static SpaceGroup createSGFromList(String name,
                                           javajs.util.Lst<?> data)

Parameters:

name -

data - Lst<SymmetryOperation> or Lst<M4>

Returns:

a new SpaceGroup if successful or null

addSymmetry

int addSymmetry(String xyz,
                int opId,
                boolean allowScaling)

setFinalOperations

void setFinalOperations(javajs.util.P3[] atoms,
                        int atomIndex,
                        int count,
                        boolean doNormalize)

getOperationCount

int getOperationCount()

getOperation

javajs.util.M4 getOperation(int i)

getXyz

String getXyz(int i,
              boolean doNormalize)

newPoint

void newPoint(int i,
              javajs.util.P3 atom1,
              javajs.util.P3 atom2,
              int transX,
              int transY,
              int transZ)

getInfo

static Object getInfo(SpaceGroup sg,
                      String spaceGroup,
                      SymmetryInterface cellInfo,
                      boolean asMap)

getInfo

private Map<String,Object> getInfo(SymmetryInterface cellInfo)

dumpInfo

String dumpInfo()

Returns:

detailed information

dumpInfoObj

Object dumpInfoObj()

Returns:

detailed information

getName

String getName()

getLatticeDesignation

String getLatticeDesignation()

setLatticeParam

void setLatticeParam(int latticeParameter)

dumpCanonicalSeitzList

private Object dumpCanonicalSeitzList()

Returns:

either a String or a SpaceGroup, depending on index.

getDerivedSpaceGroup

SpaceGroup getDerivedSpaceGroup()

Returns:

a known space group or null

getCanonicalSeitzList

private String getCanonicalSeitzList()

findSpaceGroup

private static SpaceGroup findSpaceGroup(int opCount,
                                         String s)

dumpAll

private static final String dumpAll()

dumpAllSeitz

private static final String dumpAllSeitz()

getCanonicalSeitz

private static String getCanonicalSeitz(int i)

setLattice

private void setLattice(char latticeCode,
                        boolean isCentrosymmetric)

createSpaceGroupN

private static final SpaceGroup createSpaceGroupN(String name)

addOperation

private int addOperation(String xyz0,
                         int opId,
                         boolean allowScaling)

checkXYZlist

private int checkXYZlist(String xyz)

addOp

private int addOp(SymmetryOperation op,
                  String xyz0,
                  boolean isSpecial)

generateOperatorsFromXyzInfo

private void generateOperatorsFromXyzInfo(String xyzInfo)

generateAllOperators

private void generateAllOperators(HallInfo h)

addSymmetrySM

int addSymmetrySM(String xyz,
                  javajs.util.M4 operation)

determineSpaceGroupN

private static final SpaceGroup determineSpaceGroupN(String name)

determineSpaceGroupNS

private static final SpaceGroup determineSpaceGroupNS(String name,
                                                      SpaceGroup sg)

determineSpaceGroupNA

static final SpaceGroup determineSpaceGroupNA(String name,
                                              float[] unitCellParams)

determineSpaceGroup

private static final SpaceGroup determineSpaceGroup(String name,
                                                    float a,
                                                    float b,
                                                    float c,
                                                    float alpha,
                                                    float beta,
                                                    float gamma,
                                                    int lastIndex)

determineSpaceGroupIndex

private static final int determineSpaceGroupIndex(String name,
                                                  float a,
                                                  float b,
                                                  float c,
                                                  float alpha,
                                                  float beta,
                                                  float gamma,
                                                  int lastIndex)

determineUniqueAxis

private static final char determineUniqueAxis(float a,
                                              float b,
                                              float c,
                                              float alpha,
                                              float beta,
                                              float gamma)

buildSpaceGroup

private void buildSpaceGroup(String cifLine)

setHMSymbol

private void setHMSymbol(String name)

toCap

private static String toCap(String s,
                            int n)

toString

public String toString()

Overrides:

toString in class Object

getSpaceGroups

private static SpaceGroup[] getSpaceGroups()

createSpaceGroups

private static SpaceGroup[] createSpaceGroups()

addLatticeVectors

boolean addLatticeVectors(javajs.util.Lst<float[]> lattvecs)

Parameters:

lattvecs - could be magnetic centering, in which case there is an additional lattice parameter that is time reversal

Returns:

true if successful

getSiteMultiplicity

int getSiteMultiplicity(javajs.util.P3 pt,
                        UnitCell unitCell)

setName

public void setName(String name)

getRawOperation

public javajs.util.M4 getRawOperation(int i)