META-INF/
META-INF/MANIFEST.MF
org/
org/jmol/
org/jmol/symmetry/
org/jmol/symmetry/HallInfo$RotationTerm.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.HallInfo$RotationTerm extends java.lang.Object {
String inputCode
String primitiveCode
String lookupCode
String translationString
org.jmol.symmetry.Rotation rotation
org.jmol.symmetry.Translation translation
javax.vecmath.Matrix4f seitzMatrix12ths
boolean isImproper
int order
char axisType
char diagonalReferenceAxis
boolean allPositive
private final org.jmol.symmetry.HallInfo this$0
void <init> (org.jmol.symmetry.HallInfo)
void <init> (org.jmol.symmetry.HallInfo, java.lang.String, int, char)
java.lang.String dumpInfo ()
java.lang.String getXYZ (boolean)
private void getRotationInfo (java.lang.String, int, char)
}
org/jmol/symmetry/HallInfo.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.HallInfo extends java.lang.Object {
String hallSymbol
String primitiveHallSymbol
char latticeCode
String latticeExtension
boolean isCentrosymmetric
int nRotations
org.jmol.symmetry.HallInfo$RotationTerm[] rotationTerms
javax.vecmath.Point3i vector12ths
String vectorCode
void <init> (java.lang.String)
java.lang.String dumpInfo ()
private java.lang.String getLatticeDesignation ()
private java.lang.String extractLatticeInfo (java.lang.String)
private java.lang.String extractVectorInfo (java.lang.String)
private java.lang.String extractRotationInfo (java.lang.String, int, char)
}
org/jmol/symmetry/PointGroup$Operation.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.PointGroup$Operation extends java.lang.Object {
int type
int order
int index
int typeIndex
javax.vecmath.Vector3f normalOrAxis
private final org.jmol.symmetry.PointGroup this$0
void <init> (org.jmol.symmetry.PointGroup)
void <init> (org.jmol.symmetry.PointGroup, javax.vecmath.Vector3f, int)
void <init> (org.jmol.symmetry.PointGroup, javax.vecmath.Vector3f)
java.lang.String getLabel ()
}
org/jmol/symmetry/PointGroup.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.PointGroup extends java.lang.Object {
private static final int[] axesMaxN
private static final int[] nUnique
private static final int s3
private static final int s4
private static final int s5
private static final int s6
private static final int s8
private static final int s10
private static final int s12
private static final int firstProper
private static final int c2
private static final int c3
private static final int c4
private static final int c5
private static final int c6
private static final int c8
private static final int maxAxis
private int[] nAxes
private org.jmol.symmetry.PointGroup$Operation[][] axes
private int nAtoms
private float radius
private float distanceTolerance
private float linearTolerance
private float cosTolerance
private String name
private org.jmol.symmetry.PointGroup$Operation principalAxis
private org.jmol.symmetry.PointGroup$Operation principalPlane
private final javax.vecmath.Vector3f vTemp
private int centerAtomIndex
private boolean haveInversionCenter
private final javax.vecmath.Point3f center
private javax.vecmath.Point3f[] atoms
private int[] elements
private static final int ATOM_COUNT_MAX
int maxElement
int[] eCounts
static final int OPERATION_PLANE
static final int OPERATION_PROPER_AXIS
static final int OPERATION_IMPROPER_AXIS
static final int OPERATION_INVERSION_CENTER
static final String[] typeNames
int nOps
String drawInfo
String drawType
int drawIndex
java.util.Hashtable info
String textInfo
java.lang.String getName ()
static org.jmol.symmetry.PointGroup getPointGroup (org.jmol.symmetry.PointGroup, org.jmol.modelset.Atom[], java.util.BitSet, boolean, float, float)
private void <init> ()
private boolean isEqual (org.jmol.symmetry.PointGroup)
private boolean set (org.jmol.symmetry.PointGroup, org.jmol.modelset.Atom[], java.util.BitSet, boolean, float, float)
private org.jmol.symmetry.PointGroup$Operation setPrincipalAxis (int, int)
private org.jmol.symmetry.PointGroup$Operation setPrincipalPlane (int, int)
private boolean getAtomsAndElements (org.jmol.modelset.Atom[], java.util.BitSet)
private void findInversionCenter ()
private boolean checkOperation (org.jmol.util.Quaternion, javax.vecmath.Point3f, int)
private boolean isLinear (javax.vecmath.Point3f[])
private boolean isParallel (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
private boolean isPerpendicular (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
private void getElementCounts ()
private int findCAxes ()
private void getAllAxes (javax.vecmath.Vector3f)
private int getHighestOrder ()
private boolean checkAxisOrder (int, javax.vecmath.Vector3f, javax.vecmath.Point3f)
private void addAxis (int, javax.vecmath.Vector3f)
private boolean haveAxis (int, javax.vecmath.Vector3f)
private int findPlanes ()
private int getPlane (int, javax.vecmath.Vector3f, javax.vecmath.Point3f)
private void findAdditionalAxes (int)
java.lang.Object getInfo (int, boolean, boolean, java.lang.String, int, float)
boolean isDrawType (java.lang.String, int)
static void <clinit> ()
}
org/jmol/symmetry/Rotation.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.Rotation extends java.lang.Object {
String rotCode
javax.vecmath.Matrix4f seitzMatrix
javax.vecmath.Matrix4f seitzMatrixInv
static final org.jmol.symmetry.Rotation[] hallRotationTerms
void <init> ()
private void <init> (java.lang.String, java.lang.String)
static final org.jmol.symmetry.Rotation lookup (java.lang.String)
static void <clinit> ()
}
org/jmol/symmetry/SpaceGroup.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.SpaceGroup extends java.lang.Object {
int index
String hallSymbol
String hmSymbol
String hmSymbolFull
String hmSymbolExt
String hmSymbolAbbr
String hmSymbolAlternative
String hmSymbolAbbrShort
char ambiguityType
char uniqueAxis
char axisChoice
String intlTableNumber
String intlTableNumberFull
String intlTableNumberExt
org.jmol.symmetry.HallInfo hallInfo
int latticeParameter
char latticeCode
org.jmol.symmetry.SymmetryOperation[] operations
int operationCount
boolean doNormalize
org.jmol.symmetry.SymmetryOperation[] finalOperations
private static String[] canonicalSeitzList
java.util.Hashtable xyzList
String line
String term
private static int sgIndex
private static final org.jmol.symmetry.SpaceGroup[] spaceGroupDefinitions
void <init> (boolean)
private void <init> (java.lang.String)
static org.jmol.symmetry.SpaceGroup createSpaceGroup (int, java.lang.String, float[], boolean)
static int determineSpaceGroupIndex (java.lang.String)
static org.jmol.symmetry.SpaceGroup determineSpaceGroup (java.lang.String, float, float, float, float, float, float, int)
int addSymmetry (java.lang.String)
void setFinalOperations (javax.vecmath.Point3f[], int, int, boolean)
int getOperationCount ()
javax.vecmath.Matrix4f getOperation (int)
java.lang.String getXyz (int, boolean)
void newPoint (int, javax.vecmath.Point3f, javax.vecmath.Point3f, int, int, int)
java.lang.Object rotateEllipsoid (int, javax.vecmath.Point3f, javax.vecmath.Vector3f[], org.jmol.symmetry.UnitCell, javax.vecmath.Point3f, javax.vecmath.Point3f)
static java.lang.String getInfo (java.lang.String, org.jmol.api.SymmetryInterface)
java.lang.String dumpInfo (org.jmol.api.SymmetryInterface)
java.lang.String getName ()
java.lang.String getLatticeDesignation ()
void setLattice (int)
private void buildSpaceGroup (java.lang.String)
private java.lang.Object dumpCanonicalSeitzList ()
private static final java.lang.String dumpAll ()
private static final java.lang.String dumpAllSeitz ()
private void setLattice (char, boolean)
private static final org.jmol.symmetry.SpaceGroup createSpaceGroup (java.lang.String, boolean)
private static final org.jmol.symmetry.SpaceGroup determineSpaceGroup (java.lang.String)
private static final org.jmol.symmetry.SpaceGroup determineSpaceGroup (java.lang.String, org.jmol.symmetry.SpaceGroup)
private static final org.jmol.symmetry.SpaceGroup determineSpaceGroup (java.lang.String, float[])
private static final int determineSpaceGroupIndex (java.lang.String, float, float, float, float, float, float, int)
private static final char determineUniqueAxis (float, float, float, float, float, float)
private int addOperation (java.lang.String)
private void generateOperatorsFromXyzInfo (java.lang.String)
private void generateAllOperators (org.jmol.symmetry.HallInfo)
private void addSymmetry (java.lang.String, javax.vecmath.Matrix4f)
private java.lang.String extractLine ()
private java.lang.String extractTerm (char)
static void <clinit> ()
}
org/jmol/symmetry/Symmetry.class
<Unknown>
package org.jmol.symmetry
public org.jmol.symmetry.Symmetry extends java.lang.Object implements org.jmol.api.SymmetryInterface {
private org.jmol.symmetry.PointGroup pointGroup
private org.jmol.symmetry.SpaceGroup spaceGroup
private org.jmol.symmetry.SymmetryInfo symmetryInfo
private org.jmol.symmetry.UnitCell unitCell
public void <init> ()
public org.jmol.api.SymmetryInterface setPointGroup (org.jmol.api.SymmetryInterface, org.jmol.modelset.Atom[], java.util.BitSet, boolean, float, float)
public java.lang.String getPointGroupName ()
public java.lang.Object getPointGroupInfo (int, boolean, boolean, java.lang.String, int, float)
public void setSpaceGroup (boolean)
public int addSpaceGroupOperation (java.lang.String)
public void setLattice (int)
public java.lang.String getSpaceGroupName ()
public java.lang.Object getSpaceGroup ()
public void setSpaceGroup (org.jmol.api.SymmetryInterface)
public boolean createSpaceGroup (int, java.lang.String, float[], boolean)
public boolean haveSpaceGroup ()
public int determineSpaceGroupIndex (java.lang.String)
public java.lang.String getSpaceGroupInfo (java.lang.String, org.jmol.api.SymmetryInterface)
public java.lang.Object getLatticeDesignation ()
public void setFinalOperations (javax.vecmath.Point3f[], int, int, boolean)
public int getSpaceGroupOperationCount ()
public javax.vecmath.Matrix4f getSpaceGroupOperation (int)
public java.lang.String getSpaceGroupXyz (int, boolean)
public void newSpaceGroupPoint (int, javax.vecmath.Point3f, javax.vecmath.Point3f, int, int, int)
public java.lang.Object rotateEllipsoid (int, javax.vecmath.Point3f, javax.vecmath.Vector3f[], javax.vecmath.Point3f, javax.vecmath.Point3f)
public boolean haveUnitCell ()
public java.lang.String getUnitsymmetryInfo ()
public void setUnitCell (float[])
public void toCartesian (javax.vecmath.Point3f)
public java.lang.Object[] getEllipsoid (float[])
public javax.vecmath.Point3f ijkToPoint3f (int)
public void toFractional (javax.vecmath.Point3f)
public javax.vecmath.Point3f[] getUnitCellVertices ()
public javax.vecmath.Point3f getCartesianOffset ()
public float[] getNotionalUnitCell ()
public void toUnitCell (javax.vecmath.Point3f, javax.vecmath.Point3f)
public void setUnitCellOffset (javax.vecmath.Point3f)
public void setOffset (int)
public javax.vecmath.Point3f getFractionalOffset ()
public float getUnitsymmetryInfo (int)
public int getModelIndex ()
public void setModelIndex (int)
public boolean getCoordinatesAreFractional ()
public int[] getCellRange ()
public java.lang.String getSymmetryInfoString ()
public java.lang.String[] getSymmetryOperations ()
public boolean isPeriodic ()
public void setSymmetryInfo (int, java.util.Hashtable)
public float getUnitCellInfo (int)
public java.lang.String getUnitCellInfo ()
public java.lang.Object[] getSymmetryOperationDescription (int, org.jmol.api.SymmetryInterface, javax.vecmath.Point3f, java.lang.String)
}
org/jmol/symmetry/SymmetryInfo.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.SymmetryInfo extends java.lang.Object {
boolean coordinatesAreFractional
boolean isMultiCell
String spaceGroup
String[] symmetryOperations
String symmetryInfoString
int modelIndex
int[] cellRange
private javax.vecmath.Point3f periodicOriginXyz
boolean isPeriodic ()
void <init> ()
float[] setSymmetryInfo (int, java.util.Hashtable)
}
org/jmol/symmetry/SymmetryOperation.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.SymmetryOperation extends javax.vecmath.Matrix4f {
String xyzOriginal
String xyz
boolean doNormalize
boolean isFinalized
private javax.vecmath.Point4f temp
private static final String[] twelfths
javax.vecmath.Point3f atomTest
void <init> ()
void <init> (boolean)
void <init> (org.jmol.symmetry.SymmetryOperation, javax.vecmath.Point3f[], int, int, boolean)
void doFinalize ()
java.lang.String getXyz (boolean)
void newPoint (javax.vecmath.Point3f, javax.vecmath.Point3f, int, int, int)
java.lang.String dumpInfo ()
static final java.lang.String dumpSeitz (javax.vecmath.Matrix4f)
static final java.lang.String dumpCanonicalSeitz (javax.vecmath.Matrix4f)
boolean setMatrixFromXYZ (java.lang.String)
private float normalizeTwelfths (float)
static final java.lang.String getXYZFromMatrix (javax.vecmath.Matrix4f, boolean, boolean, boolean)
private static final java.lang.String twelfthsOf (float)
private static final java.lang.String xyzFraction (float, boolean, boolean)
private void setOffset (javax.vecmath.Point3f[], int, int)
private void transformCartesian (org.jmol.symmetry.UnitCell, javax.vecmath.Point3f)
javax.vecmath.Vector3f[] rotateEllipsoid (javax.vecmath.Point3f, javax.vecmath.Vector3f[], org.jmol.symmetry.UnitCell, javax.vecmath.Point3f, javax.vecmath.Point3f)
public java.lang.Object[] getProduct (org.jmol.symmetry.SymmetryOperation, org.jmol.api.SymmetryInterface, javax.vecmath.Point3f, java.lang.String)
public java.lang.Object[] getDescription (org.jmol.api.SymmetryInterface, javax.vecmath.Point3f, java.lang.String)
private static java.lang.Object[] getDescription (javax.vecmath.Matrix4f, java.lang.String, org.jmol.api.SymmetryInterface, javax.vecmath.Point3f, java.lang.String)
private static void drawLine (java.lang.StringBuffer, java.lang.String, float, javax.vecmath.Point3f, javax.vecmath.Point3f, java.lang.String)
private static java.lang.String fcoord (javax.vecmath.Tuple3f)
private static java.lang.String fc (float)
private static javax.vecmath.Tuple3f approx (javax.vecmath.Tuple3f)
private static float approx (float)
private static float approx (float, float)
public static void normalizeTranslation (javax.vecmath.Matrix4f)
static void <clinit> ()
}
org/jmol/symmetry/Translation.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.Translation extends java.lang.Object {
char translationCode
int rotationOrder
int rotationShift12ths
javax.vecmath.Point3i vectorShift12ths
static final String[] latticeTranslationData
static final int nLatticeTypes
static final org.jmol.symmetry.Translation[] hallTranslationTerms
void <init> ()
void <init> (char, int)
private void <init> (char, int, javax.vecmath.Point3i)
private void <init> (char, int, int)
static final java.lang.String getHallLatticeEquivalent (int)
static final int getLatticeIndex (char)
static final char getLatticeCode (int)
static final java.lang.String getLatticeDesignation (int)
static final java.lang.String getLatticeDesignation (char, boolean)
static final java.lang.String getLatticeExtension (char, boolean)
static void <clinit> ()
}
org/jmol/symmetry/UnitCell$Data.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.UnitCell$Data extends java.lang.Object {
double cosAlpha
double sinAlpha
double cosBeta
double sinBeta
double cosGamma
double sinGamma
double volume
double cA_
double cB_
double a_
double b_
double c_
static final double twoP2
private final org.jmol.symmetry.UnitCell this$0
void <init> (org.jmol.symmetry.UnitCell)
java.lang.Object[] getEllipsoid (float[])
}
org/jmol/symmetry/UnitCell.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.UnitCell extends java.lang.Object {
static final float toRadians
static final javax.vecmath.Point3f[] unitCubePoints
float a
float b
float c
float alpha
float beta
float gamma
boolean isPrimitive
float[] notionalUnitcell
private javax.vecmath.Matrix4f matrixCartesianToFractional
private javax.vecmath.Matrix4f matrixFractionalToCartesian
private javax.vecmath.Point3f[] vertices
private javax.vecmath.Point3f cartesianOffset
private javax.vecmath.Point3f fractionalOffset
private org.jmol.symmetry.UnitCell$Data data
void <init> (float[])
final void toCartesian (javax.vecmath.Point3f)
final void toFractional (javax.vecmath.Point3f)
private final void toFractionalUnitCell (javax.vecmath.Point3f)
private static float toFractional (float)
final void toUnitCell (javax.vecmath.Point3f, javax.vecmath.Point3f)
void setOffset (javax.vecmath.Point3f)
void setOffset (int)
static javax.vecmath.Point3f ijkToPoint3f (int)
final java.lang.String dumpInfo (boolean)
javax.vecmath.Point3f[] getVertices ()
javax.vecmath.Point3f getCartesianOffset ()
javax.vecmath.Point3f getFractionalOffset ()
float[] getNotionalUnitCell ()
float getInfo (int)
private void setUnitCell (float[])
java.lang.Object[] getEllipsoid (float[])
private void constructFractionalMatrices ()
private void calcUnitcellVertices ()
static void <clinit> ()
}