public class SymmetryDesc
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private static int |
KEY_DRAW |
private static int |
KEY_POINT |
private static java.lang.String[] |
keys |
private ModelSet |
modelSet |
Constructor and Description |
---|
SymmetryDesc() |
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 java.lang.Object[] |
createInfoArray(SymmetryOperation op,
SymmetryInterface uc,
javajs.util.P3 pta00,
javajs.util.P3 ptTarget,
java.lang.String id,
float scaleFactor,
int options) |
private static void |
drawFrameLine(java.lang.String xyz,
javajs.util.P3 pt,
javajs.util.V3 v,
float width,
javajs.util.P3 ptemp,
javajs.util.SB draw1,
java.lang.String key,
java.lang.String color) |
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) |
private static void |
drawVector(javajs.util.SB draw1,
java.lang.String drawid,
java.lang.String label,
java.lang.String type,
javajs.util.T3 pt1,
javajs.util.T3 v,
java.lang.String color) |
private javajs.util.BS |
getAtom(Symmetry uc,
int iModel,
int iAtom,
javajs.util.T3 sympt) |
private static java.lang.Object |
getInfo(java.lang.Object[] info,
int type)
Return information about a symmetry operator by type:
array, angle, axis, center, draw, full, info, label, matrix4f, point, time,
plane, translation, unitcell, xyz, all,
or a negative number (-length, -1]:
{ "xyz", "xyzOriginal", "label", "draw", "fractionalTranslation",
"cartesianTranslation", "inversionCenter", "axisPoint", "axisVector",
"rotationAngle", "matrix", "unitTranslation", "centeringVector",
"timeReversal", "plane", "_type", "id" }
where "all" is the info array itself,
|
(package private) java.util.Map<java.lang.String,java.lang.Object> |
getSpaceGroupInfo(Symmetry sym,
int modelIndex,
java.lang.String sgName,
int symOp,
javajs.util.P3 pt1,
javajs.util.P3 pt2,
java.lang.String drawID,
float scaleFactor,
int nth,
boolean isFull,
boolean isForModel,
int options,
SymmetryInterface cellInfo) |
private java.lang.Object |
getSymmetryInfo(Symmetry sym,
int iModel,
int iatom,
Symmetry uc,
java.lang.String xyz,
int op,
javajs.util.P3 pt,
javajs.util.P3 pt2,
java.lang.String id,
int type,
float scaleFactor,
int nth,
int options)
multipurpose function handling a variety of tasks, including:
processing of "lattice", "list", "atom", "point", and some "draw" output
types
finding the operator in the given space group
creating a temporary space group for an xyz operator
|
(package private) java.lang.Object |
getSymopInfo(int iAtom,
java.lang.String xyz,
int op,
javajs.util.P3 pt,
javajs.util.P3 pt2,
java.lang.String id,
int type,
float scaleFactor,
int nth,
int options) |
private java.lang.Object |
getSymopInfoForPoints(Symmetry sym,
int modelIndex,
int symOp,
javajs.util.P3 pt1,
javajs.util.P3 pt2,
java.lang.String drawID,
java.lang.String stype,
float scaleFactor,
int nth,
boolean asString,
int options)
get information about a symmetry operation relating two specific points or atoms
|
private static int |
getType(java.lang.String id) |
private static java.lang.Object |
nullReturn(int type) |
private static javajs.util.P3 |
rotTransCart(SymmetryOperation op,
SymmetryInterface uc,
javajs.util.P3 pt00,
javajs.util.V3 vtrans) |
SymmetryDesc |
set(ModelSet modelSet) |
private static void |
setFractional(SymmetryInterface uc,
javajs.util.T3 pt00,
javajs.util.P3 pt01,
javajs.util.P3 offset)
Set pt01 to pt00, possibly adding offset into unit cell
|
private static java.lang.String |
strCoord(javajs.util.T3 p,
boolean isBio) |
private ModelSet modelSet
private static final java.lang.String[] keys
private static final int KEY_DRAW
private static final int KEY_POINT
public SymmetryDesc set(ModelSet modelSet)
java.lang.Object getSymopInfo(int iAtom, java.lang.String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, java.lang.String id, int type, float scaleFactor, int nth, int options)
iAtom
- xyz
- op
- pt
- pt2
- id
- type
- scaleFactor
- nth
- options
- 0 or T.offsetjava.util.Map<java.lang.String,java.lang.Object> getSpaceGroupInfo(Symmetry sym, int modelIndex, java.lang.String sgName, int symOp, javajs.util.P3 pt1, javajs.util.P3 pt2, java.lang.String drawID, float scaleFactor, int nth, boolean isFull, boolean isForModel, int options, SymmetryInterface cellInfo)
private static int getType(java.lang.String id)
private static java.lang.Object nullReturn(int type)
private static java.lang.Object getInfo(java.lang.Object[] info, int type)
info
- type
- private java.lang.Object[] createInfoArray(SymmetryOperation op, SymmetryInterface uc, javajs.util.P3 pta00, javajs.util.P3 ptTarget, java.lang.String id, float scaleFactor, int options)
op
- uc
- pta00
- optional initial atom pointptTarget
- optional target atom pointid
- scaleFactor
- scale for rotation vector onlyoptions
- 0 or T.offsetprivate 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)
private static void drawFrameLine(java.lang.String xyz, javajs.util.P3 pt, javajs.util.V3 v, float width, javajs.util.P3 ptemp, javajs.util.SB draw1, java.lang.String key, java.lang.String color)
private static void drawVector(javajs.util.SB draw1, java.lang.String drawid, java.lang.String label, java.lang.String type, javajs.util.T3 pt1, javajs.util.T3 v, java.lang.String color)
private static void setFractional(SymmetryInterface uc, javajs.util.T3 pt00, javajs.util.P3 pt01, javajs.util.P3 offset)
uc
- pt00
- pt01
- offset
- private static javajs.util.P3 rotTransCart(SymmetryOperation op, SymmetryInterface uc, javajs.util.P3 pt00, javajs.util.V3 vtrans)
private static java.lang.String strCoord(javajs.util.T3 p, boolean isBio)
private static javajs.util.T3 approx0(javajs.util.T3 pt)
private static javajs.util.T3 approx(javajs.util.T3 pt)
private java.lang.Object getSymmetryInfo(Symmetry sym, int iModel, int iatom, Symmetry uc, java.lang.String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, java.lang.String id, int type, float scaleFactor, int nth, int options)
sym
- iModel
- iatom
- uc
- xyz
- op
- pt
- pt2
- second point or offsetid
- type
- scaleFactor
- nth
- options
- 0 or T.offsetprivate javajs.util.BS getAtom(Symmetry uc, int iModel, int iAtom, javajs.util.T3 sympt)
private java.lang.Object getSymopInfoForPoints(Symmetry sym, int modelIndex, int symOp, javajs.util.P3 pt1, javajs.util.P3 pt2, java.lang.String drawID, java.lang.String stype, float scaleFactor, int nth, boolean asString, int options)
sym
- modelIndex
- symOp
- pt1
- pt2
- drawID
- stype
- scaleFactor
- nth
- asString
- options
- 0 or T.offset