org.jmol.symmetry
Class SymmetryOperation
java.lang.Object
javax.vecmath.Matrix4f
org.jmol.symmetry.SymmetryOperation
- All Implemented Interfaces:
- Serializable, Cloneable
class SymmetryOperation
- extends Matrix4f
Fields inherited from class javax.vecmath.Matrix4f |
m00, m01, m02, m03, m10, m11, m12, m13, m20, m21, m22, m23, m30, m31, m32, m33 |
Method Summary |
private static float |
approx(float f)
|
private static float |
approx(float f,
float n)
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private static Tuple3f |
approx(Tuple3f pt)
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private static Tuple3f |
approx0(Tuple3f pt)
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(package private) void |
doFinalize()
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private static void |
drawLine(StringBuffer s,
String id,
float diameter,
Point3f pt0,
Point3f pt1,
String color)
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(package private) static String |
dumpCanonicalSeitz(Matrix4f s)
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(package private) String |
dumpInfo()
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(package private) static String |
dumpSeitz(Matrix4f s)
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private static String |
fc(float x)
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private static String |
fcoord(Tuple3f p)
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Object[] |
getDescription(int isym,
SymmetryInterface uc,
Point3f pt00,
Point3f ptTarget,
String id)
|
private static Object[] |
getDescription(int isym,
SymmetryOperation m,
String xyzOriginal,
SymmetryInterface uc,
Point3f pt00,
Point3f ptTarget,
String id)
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(package private) String |
getXyz(boolean normalized)
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(package private) static String |
getXYZFromMatrix(Matrix4f mat,
boolean is12ths,
boolean allPositive,
boolean halfOrLess)
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(package private) void |
newPoint(Point3f atom1,
Point3f atom2,
int transX,
int transY,
int transZ)
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static void |
normalizeTranslation(Matrix4f operation)
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private float |
normalizeTwelfths(float iValue)
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(package private) Vector3f[] |
rotateEllipsoid(Point3f cartCenter,
Vector3f[] vectors,
UnitCell unitcell,
Point3f ptTemp1,
Point3f ptTemp2)
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(package private) boolean |
setMatrixFromXYZ(String xyz)
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private void |
setOffset(Point3f[] atoms,
int atomIndex,
int count)
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private void |
transformCartesian(UnitCell unitcell,
Point3f pt)
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private static String |
twelfthsOf(float n12ths)
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private static String |
xyzFraction(float n12ths,
boolean allPositive,
boolean halfOrLess)
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Methods inherited from class javax.vecmath.Matrix4f |
add, add, add, add, clone, determinant, epsilonEquals, equals, equals, get, get, get, get, get, getColumn, getColumn, getElement, getM00, getM01, getM02, getM03, getM10, getM11, getM12, getM13, getM20, getM21, getM22, getM23, getM30, getM31, getM32, getM33, getRotationScale, getRow, getRow, getScale, hashCode, invert, invert, mul, mul, mul, mul, mulTransposeBoth, mulTransposeLeft, mulTransposeRight, negate, negate, rotX, rotY, rotZ, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, setColumn, setColumn, setColumn, setElement, setIdentity, setM00, setM01, setM02, setM03, setM10, setM11, setM12, setM13, setM20, setM21, setM22, setM23, setM30, setM31, setM32, setM33, setRotation, setRotation, setRotation, setRotation, setRotation, setRotationScale, setRow, setRow, setRow, setScale, setTranslation, setZero, sub, sub, toString, transform, transform, transform, transform, transform, transform, transpose, transpose |
xyzOriginal
String xyzOriginal
xyz
String xyz
doNormalize
boolean doNormalize
isFinalized
boolean isFinalized
opId
int opId
temp3
private Point3f temp3
twelfths
private static final String[] twelfths
atomTest
Point3f atomTest
SymmetryOperation
SymmetryOperation()
SymmetryOperation
SymmetryOperation(boolean doNormalize,
int opId)
SymmetryOperation
SymmetryOperation(SymmetryOperation op,
Point3f[] atoms,
int atomIndex,
int count,
boolean doNormalize)
doFinalize
void doFinalize()
getXyz
String getXyz(boolean normalized)
newPoint
void newPoint(Point3f atom1,
Point3f atom2,
int transX,
int transY,
int transZ)
dumpInfo
String dumpInfo()
dumpSeitz
static final String dumpSeitz(Matrix4f s)
dumpCanonicalSeitz
static final String dumpCanonicalSeitz(Matrix4f s)
setMatrixFromXYZ
boolean setMatrixFromXYZ(String xyz)
normalizeTwelfths
private float normalizeTwelfths(float iValue)
getXYZFromMatrix
static final String getXYZFromMatrix(Matrix4f mat,
boolean is12ths,
boolean allPositive,
boolean halfOrLess)
twelfthsOf
private static final String twelfthsOf(float n12ths)
xyzFraction
private static final String xyzFraction(float n12ths,
boolean allPositive,
boolean halfOrLess)
setOffset
private void setOffset(Point3f[] atoms,
int atomIndex,
int count)
transformCartesian
private void transformCartesian(UnitCell unitcell,
Point3f pt)
rotateEllipsoid
Vector3f[] rotateEllipsoid(Point3f cartCenter,
Vector3f[] vectors,
UnitCell unitcell,
Point3f ptTemp1,
Point3f ptTemp2)
getDescription
public Object[] getDescription(int isym,
SymmetryInterface uc,
Point3f pt00,
Point3f ptTarget,
String id)
- Parameters:
isym
- uc
- pt00
- ptTarget
- id
-
- Returns:
- Object[] containing:
[0] xyz (Jones-Faithful calculated from matrix)
[1] xyzOriginal (Provided by calling method)
[2] info ("C2 axis", for example)
[3] draw commands
[4] translation vector (fractional)
[5] translation vector (Cartesian)
[6] inversion point
[7] axis point
[8] axis vector (defines plane if angle = 0
[9] angle of rotation
[10] matrix representation
getDescription
private static Object[] getDescription(int isym,
SymmetryOperation m,
String xyzOriginal,
SymmetryInterface uc,
Point3f pt00,
Point3f ptTarget,
String id)
drawLine
private static void drawLine(StringBuffer s,
String id,
float diameter,
Point3f pt0,
Point3f pt1,
String color)
fcoord
private static String fcoord(Tuple3f p)
fc
private static String fc(float x)
approx0
private static Tuple3f approx0(Tuple3f pt)
approx
private static Tuple3f approx(Tuple3f pt)
approx
private static float approx(float f)
approx
private static float approx(float f,
float n)
normalizeTranslation
public static void normalizeTranslation(Matrix4f operation)