class SymmetryOperation
extends javajs.util.M4
Modifier and Type | Field and Description |
---|---|
private javajs.util.P3 |
atomTest |
private boolean |
doNormalize |
private boolean |
isBio |
(package private) boolean |
isFinalized |
(package private) static String[] |
labelsXn |
(package private) static String[] |
labelsXnSub |
(package private) static String[] |
labelsXYZ |
(package private) float[] |
linearRotTrans |
(package private) int |
modDim |
private String[] |
myLabels |
private int |
opId |
(package private) javajs.util.Matrix |
rsvs |
private javajs.util.P3 |
temp3 |
private static String[] |
twelfths |
(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 |
---|---|
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 String |
coord(javajs.util.T3 p) |
(package private) void |
doFinalize() |
private static void |
drawLine(javajs.util.SB s,
String id,
float diameter,
javajs.util.P3 pt0,
javajs.util.P3 pt1,
String color) |
(package private) static String |
dumpCanonicalSeitz(javajs.util.M4 s) |
(package private) String |
dumpInfo() |
(package private) static String |
dumpSeitz(javajs.util.M4 s) |
private static String |
fc(float x) |
(package private) static String |
fcoord(javajs.util.T3 p) |
(package private) Object[] |
getDescription(ModelSet modelSet,
SymmetryInterface uc,
javajs.util.P3 pt00,
javajs.util.P3 ptTarget,
String id) |
(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 that consists of
[3*x + 1][3*x + 1][3*x + 1][4*0][modDim*x+1] [modDim*x+1] [modDim*x+1]...
|
(package private) String |
getXyz(boolean normalized) |
(package private) static String |
getXYZFromMatrix(javajs.util.M4 mat,
boolean is12ths,
boolean allPositive,
boolean halfOrLess) |
static 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 transX,
int transY,
int transZ) |
static void |
normalizeTranslation(javajs.util.M4 operation) |
private static float |
normalizeTwelfths(float iValue,
boolean doNormalize) |
private static String |
plusMinus(String strT,
float x,
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()
rsvs is the superspace group rotation-translation matrix.
|
(package private) boolean |
setMatrixFromXYZ(String xyz,
int modDim) |
private void |
setOffset(javajs.util.P3[] atoms,
int atomIndex,
int count) |
String |
toString()
Returns a string that contains the values of this Matrix4f.
|
private static String |
twelfthsOf(float n12ths) |
private static String |
xyzFraction(float n12ths,
boolean allPositive,
boolean halfOrLess) |
determinant, equals, get, getColumn, getElement, getRotationScale, getRow, hashCode, invert, invertM, mul2, mulM4, newA, newM, newMV, rotate, rotX, rotY, rotZ, setA, setAA, setColumn, setColumn4, setElement, setIdentity, setM, setM3, setMV, setRotationScale, setRow, setTranslation, setZero, sub, toA, transform, transform2, transform4, transformT2, transpose
String xyzOriginal
String xyz
private boolean doNormalize
boolean isFinalized
private int opId
private javajs.util.P3 atomTest
private javajs.util.P3 temp3
private String[] myLabels
int modDim
float[] linearRotTrans
javajs.util.Matrix rsvs
private boolean isBio
private static final String[] twelfths
static final String[] labelsXYZ
static final String[] labelsXn
static final String[] labelsXnSub
SymmetryOperation(SymmetryOperation op, javajs.util.P3[] atoms, int atomIndex, int countOrId, boolean doNormalize)
op
- atoms
- atomIndex
- countOrId
- doNormalize
- private void setGamma()
void doFinalize()
String getXyz(boolean normalized)
void newPoint(javajs.util.P3 atom1, javajs.util.P3 atom2, int transX, int transY, int transZ)
String dumpInfo()
static final String dumpSeitz(javajs.util.M4 s)
static final String dumpCanonicalSeitz(javajs.util.M4 s)
boolean setMatrixFromXYZ(String xyz, int modDim)
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)
private 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)
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)
Object[] getDescription(ModelSet modelSet, SymmetryInterface uc, javajs.util.P3 pt00, javajs.util.P3 ptTarget, String id)
modelSet
- TODOuc
- pt00
- ptTarget
- id
- private String coord(javajs.util.T3 p)
private static void drawLine(javajs.util.SB s, String id, float diameter, javajs.util.P3 pt0, javajs.util.P3 pt1, String color)
static String fcoord(javajs.util.T3 p)
private static 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 String getXYZFromRsVs(javajs.util.Matrix rs, javajs.util.Matrix vs, boolean is12ths)
public String toString()
javajs.util.M4
toString
in class javajs.util.M4