class SymmetryOperation
extends javajs.util.M4
Modifier and Type | Field and Description |
---|---|
private javajs.util.P3 |
atomTest |
private boolean |
doNormalize |
(package private) int |
index |
private boolean |
isBio |
(package private) boolean |
isFinalized |
(package private) static java.lang.String[] |
labelsXn |
(package private) static java.lang.String[] |
labelsXnSub |
(package private) static java.lang.String[] |
labelsXYZ |
(package private) float[] |
linearRotTrans |
(package private) int |
modDim |
private java.lang.String[] |
myLabels |
private int |
opId |
(package private) javajs.util.Matrix |
rsvs |
private javajs.util.Matrix |
sigma |
(package private) java.lang.String |
subsystemCode |
private static java.lang.String[] |
twelfths |
(package private) java.lang.String |
xyz |
(package private) java.lang.String |
xyzOriginal |
Constructor and Description |
---|
SymmetryOperation(SymmetryOperation op,
javajs.util.P3[] atoms,
int atomIndex,
int countOrId,
boolean doNormalize) |
Modifier and Type | Method and Description |
---|---|
private static javajs.util.T3 |
approx(javajs.util.T3 pt) |
private static javajs.util.T3 |
approx0(javajs.util.T3 pt) |
private static float |
approxF(float f) |
private java.lang.String |
coord(javajs.util.T3 p) |
(package private) void |
doFinalize() |
private static void |
drawLine(javajs.util.SB s,
java.lang.String id,
float diameter,
javajs.util.P3 pt0,
javajs.util.P3 pt1,
java.lang.String color) |
(package private) static java.lang.String |
dumpCanonicalSeitz(javajs.util.M4 s) |
(package private) java.lang.String |
dumpInfo() |
(package private) static java.lang.String |
dumpSeitz(javajs.util.M4 s) |
private static java.lang.String |
fc(float x) |
(package private) static java.lang.String |
fcoord(javajs.util.T3 p) |
(package private) java.lang.Object[] |
getDescription(ModelSet modelSet,
SymmetryInterface uc,
javajs.util.P3 pt00,
javajs.util.P3 ptTarget,
java.lang.String id) |
(package private) static java.lang.String |
getMatrixFromString(SymmetryOperation op,
java.lang.String xyz,
float[] linearRotTrans,
boolean allowScaling)
Convert the Jones-Faithful notation
"x, -z+1/2, y" or "x1, x3-1/2, x2, x5+1/2, -x6+1/2, x7..."
to a linear array
|
(package private) java.lang.String |
getXyz(boolean normalized) |
(package private) static java.lang.String |
getXYZFromMatrix(javajs.util.M4 mat,
boolean is12ths,
boolean allPositive,
boolean halfOrLess) |
static java.lang.String |
getXYZFromRsVs(javajs.util.Matrix rs,
javajs.util.Matrix vs,
boolean is12ths) |
(package private) void |
newPoint(javajs.util.P3 atom1,
javajs.util.P3 atom2,
int x,
int y,
int z) |
static void |
normalizeTranslation(javajs.util.M4 operation) |
private static float |
normalizeTwelfths(float iValue,
boolean doNormalize) |
private static java.lang.String |
plusMinus(java.lang.String strT,
float x,
java.lang.String sx) |
(package private) javajs.util.V3[] |
rotateAxes(javajs.util.V3[] vectors,
UnitCell unitcell,
javajs.util.P3 ptTemp,
javajs.util.M3 mTemp) |
(package private) boolean |
setFromMatrix(float[] offset,
boolean isReverse) |
private void |
setGamma(boolean isReverse)
rsvs is the superspace group rotation-translation matrix.
|
private void |
setMatrix(boolean isReverse) |
(package private) boolean |
setMatrixFromXYZ(java.lang.String xyz,
int modDim,
boolean allowScaling) |
private void |
setOffset(javajs.util.P3[] atoms,
int atomIndex,
int count) |
(package private) void |
setSigma(java.lang.String subsystemCode,
javajs.util.Matrix sigma) |
java.lang.String |
toString()
Returns a string that contains the values of this Matrix4f.
|
private static java.lang.String |
twelfthsOf(float n12ths) |
private static java.lang.String |
xyzFraction(float n12ths,
boolean allPositive,
boolean halfOrLess) |
determinant, equals, getColumn, getElement, getRotationScale, getRow, getTranslation, hashCode, invert, invertM, mul, mul2, newA16, newM4, newMV, rotTrans, rotTrans2, setA, setColumn4, setColumnA, setElement, setIdentity, setM4, setMV, setRotationScale, setRowA, setToAA, setToM3, setTranslation, setZero, sub, transform, transform2, transpose
java.lang.String xyzOriginal
java.lang.String xyz
private boolean doNormalize
boolean isFinalized
private int opId
private javajs.util.P3 atomTest
private java.lang.String[] myLabels
int modDim
float[] linearRotTrans
javajs.util.Matrix rsvs
private boolean isBio
private javajs.util.Matrix sigma
int index
java.lang.String subsystemCode
private static final java.lang.String[] twelfths
static final java.lang.String[] labelsXYZ
static final java.lang.String[] labelsXn
static final java.lang.String[] labelsXnSub
SymmetryOperation(SymmetryOperation op, javajs.util.P3[] atoms, int atomIndex, int countOrId, boolean doNormalize)
op
- atoms
- atomIndex
- countOrId
- doNormalize
- void setSigma(java.lang.String subsystemCode, javajs.util.Matrix sigma)
private void setGamma(boolean isReverse)
isReverse
- void doFinalize()
java.lang.String getXyz(boolean normalized)
void newPoint(javajs.util.P3 atom1, javajs.util.P3 atom2, int x, int y, int z)
java.lang.String dumpInfo()
static final java.lang.String dumpSeitz(javajs.util.M4 s)
static final java.lang.String dumpCanonicalSeitz(javajs.util.M4 s)
boolean setMatrixFromXYZ(java.lang.String xyz, int modDim, boolean allowScaling)
private void setMatrix(boolean isReverse)
boolean setFromMatrix(float[] offset, boolean isReverse)
static java.lang.String getMatrixFromString(SymmetryOperation op, java.lang.String xyz, float[] linearRotTrans, boolean allowScaling)
op
- xyz
- linearRotTrans
- allowScaling
- private static final java.lang.String xyzFraction(float n12ths, boolean allPositive, boolean halfOrLess)
private static final java.lang.String twelfthsOf(float n12ths)
private static java.lang.String plusMinus(java.lang.String strT, float x, java.lang.String sx)
private static float normalizeTwelfths(float iValue, boolean doNormalize)
static final java.lang.String getXYZFromMatrix(javajs.util.M4 mat, boolean is12ths, boolean allPositive, boolean halfOrLess)
private void setOffset(javajs.util.P3[] atoms, int atomIndex, int count)
javajs.util.V3[] rotateAxes(javajs.util.V3[] vectors, UnitCell unitcell, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)
java.lang.Object[] getDescription(ModelSet modelSet, SymmetryInterface uc, javajs.util.P3 pt00, javajs.util.P3 ptTarget, java.lang.String id)
modelSet
- TODOuc
- pt00
- ptTarget
- id
- private java.lang.String coord(javajs.util.T3 p)
private static void drawLine(javajs.util.SB s, java.lang.String id, float diameter, javajs.util.P3 pt0, javajs.util.P3 pt1, java.lang.String color)
static java.lang.String fcoord(javajs.util.T3 p)
private static java.lang.String fc(float x)
private static javajs.util.T3 approx0(javajs.util.T3 pt)
private static javajs.util.T3 approx(javajs.util.T3 pt)
private static float approxF(float f)
public static void normalizeTranslation(javajs.util.M4 operation)
public static java.lang.String getXYZFromRsVs(javajs.util.Matrix rs, javajs.util.Matrix vs, boolean is12ths)
public java.lang.String toString()
javajs.util.M4
toString
in class javajs.util.M4