public class SymmetryOperation
extends javajs.util.M4
Modifier and Type | Field and Description |
---|---|
private static javajs.util.P3 |
atomTest |
private javajs.util.V3 |
centering |
private boolean |
doNormalize
"normalization" is the process of adjusting symmetry operator definitions
such that the center of geometry of a molecule is within the 555 unit cell
for each operation.
|
(package private) int |
index |
(package private) boolean |
isBio |
(package private) boolean |
isCenteringOp |
(package private) boolean |
isFinalized |
(package private) static String[] |
labelsXn |
(package private) static String[] |
labelsXnSub |
(package private) static String[] |
labelsXYZ |
(package private) float[] |
linearRotTrans |
private float |
magOp |
(package private) int |
modDim |
private String[] |
myLabels |
private int |
opId |
(package private) javajs.util.Matrix |
rsvs |
private javajs.util.Matrix |
sigma |
(package private) String |
subsystemCode |
(package private) int |
timeReversal |
private static String[] |
twelfths |
private boolean |
unCentered |
(package private) String |
xyz |
(package private) String |
xyzOriginal |
Constructor and Description |
---|
SymmetryOperation(SymmetryOperation op,
javajs.util.P3[] atoms,
int atomIndex,
int countOrId,
boolean doNormalize) |
Modifier and Type | Method and Description |
---|---|
(package private) static float |
approxF(float f) |
(package private) void |
doFinalize() |
(package private) String |
dumpInfo() |
(package private) static String |
dumpSeitz(javajs.util.M4 s,
boolean isCanonical) |
private static String |
fc(float x) |
(package private) static String |
fcoord(javajs.util.T3 p) |
(package private) String |
fixMagneticXYZ(javajs.util.M4 m,
String xyz,
boolean addMag) |
(package private) javajs.util.V3 |
getCentering()
assumption here is that these are in order of sets, as in ITA
|
(package private) float |
getMagneticOp()
Magnetic spin is a pseudo (or "axial") vector.
|
(package private) static String |
getMatrixFromString(SymmetryOperation op,
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
Also allows a-b,-5a-5b,-c;0,0,0 format
|
(package private) String |
getXyz(boolean normalized) |
(package private) static String |
getXYZFromMatrix(javajs.util.M4 mat,
boolean is12ths,
boolean allPositive,
boolean halfOrLess) |
(package private) static String |
getXYZFromRsVs(javajs.util.Matrix rs,
javajs.util.Matrix vs,
boolean is12ths) |
(package private) static void |
newPoint(javajs.util.M4 m,
javajs.util.P3 atom1,
javajs.util.P3 atom2,
int x,
int y,
int z) |
private static float |
normalizeTwelfths(float iValue,
boolean doNormalize) |
private static String |
plusMinus(String strT,
float x,
String sx) |
(package private) static String |
replaceXn(String xyz,
int n) |
(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(String xyz,
int modDim,
boolean allowScaling) |
private void |
setModDim(int dim) |
static void |
setOffset(javajs.util.M4 m,
javajs.util.P3[] atoms,
int atomIndex,
int count) |
(package private) void |
setSigma(String subsystemCode,
javajs.util.Matrix sigma) |
(package private) void |
setTimeReversal(int magRev)
set the time reversal, and indicate internally in xyz as appended ",m" or ",-m"
|
String |
toString()
Returns a string that contains the values of this Matrix4f.
|
(package private) static String |
twelfthsOf(float n12ths) |
private static String |
xyzFraction(float n12ths,
boolean allPositive,
boolean halfOrLess) |
determinant4, equals, getColumn, getElement, getRotationScale, getRow, getTranslation, hashCode, invert, mul, mul2, newA16, newM4, newMV, rotTrans, rotTrans2, round, scale, setA, setAsXYRotation, setAsXZRotation, setAsYZRotation, setColumn4, setColumnA, setElement, setIdentity, setM4, setMV, setRotationScale, setRowA, setToAA, setToM3, setTranslation, setZero, sub, transform, transform2, transpose
String xyzOriginal
String xyz
private boolean doNormalize
boolean isFinalized
private int opId
private javajs.util.V3 centering
private static javajs.util.P3 atomTest
private String[] myLabels
int modDim
float[] linearRotTrans
javajs.util.Matrix rsvs
boolean isBio
private javajs.util.Matrix sigma
int index
String subsystemCode
int timeReversal
private static final String[] twelfths
static final String[] labelsXYZ
static final String[] labelsXn
static final String[] labelsXnSub
private boolean unCentered
boolean isCenteringOp
private float magOp
SymmetryOperation(SymmetryOperation op, javajs.util.P3[] atoms, int atomIndex, int countOrId, boolean doNormalize)
op
- atoms
- atomIndex
- countOrId
- doNormalize
- void setSigma(String subsystemCode, javajs.util.Matrix sigma)
private void setGamma(boolean isReverse)
isReverse
- void doFinalize()
String getXyz(boolean normalized)
static void newPoint(javajs.util.M4 m, javajs.util.P3 atom1, javajs.util.P3 atom2, int x, int y, int z)
String dumpInfo()
static final String dumpSeitz(javajs.util.M4 s, boolean isCanonical)
boolean setMatrixFromXYZ(String xyz, int modDim, boolean allowScaling)
private void setModDim(int dim)
private void setMatrix(boolean isReverse)
boolean setFromMatrix(float[] offset, boolean isReverse)
static String getMatrixFromString(SymmetryOperation op, String xyz, float[] linearRotTrans, boolean allowScaling)
op
- xyz
- linearRotTrans
- allowScaling
- private static final String xyzFraction(float n12ths, boolean allPositive, boolean halfOrLess)
static final String twelfthsOf(float n12ths)
private static float normalizeTwelfths(float iValue, boolean doNormalize)
static final String getXYZFromMatrix(javajs.util.M4 mat, boolean is12ths, boolean allPositive, boolean halfOrLess)
public static void setOffset(javajs.util.M4 m, 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)
static String fcoord(javajs.util.T3 p)
private static String fc(float x)
static float approxF(float f)
static String getXYZFromRsVs(javajs.util.Matrix rs, javajs.util.Matrix vs, boolean is12ths)
public String toString()
javajs.util.M4
toString
in class javajs.util.M4
float getMagneticOp()
void setTimeReversal(int magRev)
magRev
- javajs.util.V3 getCentering()