org.jmol.api
Interface SymmetryInterface
- All Known Implementing Classes:
- Symmetry
public interface SymmetryInterface
Method Summary |
void |
addSpaceGroupOperation(javax.vecmath.Matrix4f mat)
|
int |
addSpaceGroupOperation(java.lang.String xyz,
int opId)
|
boolean |
checkDistance(javax.vecmath.Point3f f1,
javax.vecmath.Point3f f2,
float distance,
float dx,
int iRange,
int jRange,
int kRange,
javax.vecmath.Point3f ptOffset)
|
boolean |
createSpaceGroup(int desiredSpaceGroupIndex,
java.lang.String name,
float[] notionalUnitCell)
|
java.lang.String |
fcoord(javax.vecmath.Tuple3f p)
|
javax.vecmath.Point3f[] |
getCanonicalCopy(float scale)
|
javax.vecmath.Point3f |
getCartesianOffset()
|
int[] |
getCellRange()
|
boolean |
getCoordinatesAreFractional()
|
java.lang.Object[] |
getEllipsoid(float[] parBorU)
|
java.lang.Object[] |
getEllipsoid(javax.vecmath.Vector3f[] vectors,
float a,
float b,
float c)
|
javax.vecmath.Point3f |
getFractionalOffset()
|
java.lang.Object |
getLatticeDesignation()
|
java.lang.String |
getMatrixFromString(java.lang.String xyz,
float[] temp,
boolean allowScaling)
|
float[] |
getNotionalUnitCell()
|
java.lang.Object |
getPointGroupInfo(int modelIndex,
boolean asDraw,
boolean asInfo,
java.lang.String type,
int index,
float scale)
|
java.lang.String |
getPointGroupName()
|
java.lang.Object |
getSpaceGroup()
|
java.lang.String |
getSpaceGroupInfo(java.lang.String name,
SymmetryInterface cellInfo)
|
java.lang.String |
getSpaceGroupName()
|
javax.vecmath.Matrix4f |
getSpaceGroupOperation(int i)
|
int |
getSpaceGroupOperationCount()
|
java.lang.String |
getSpaceGroupXyz(int i,
boolean doNormalize)
|
java.lang.String |
getSymmetryInfoString()
|
java.lang.Object[] |
getSymmetryOperationDescription(int iSym,
SymmetryInterface cellInfo,
javax.vecmath.Point3f pt1,
javax.vecmath.Point3f pt2,
java.lang.String id)
|
java.lang.String[] |
getSymmetryOperations()
|
float[] |
getUnitCellAsArray(boolean vectorsOnly)
|
java.lang.String |
getUnitCellInfo()
|
float |
getUnitCellInfo(int infoType)
|
javax.vecmath.Point3f |
getUnitCellMultiplier()
|
javax.vecmath.Point3f[] |
getUnitCellVertices()
|
boolean |
haveSpaceGroup()
|
boolean |
haveUnitCell()
|
javax.vecmath.Point3f |
ijkToPoint3f(int nnn)
|
boolean |
isPeriodic()
|
boolean |
isPolymer()
|
boolean |
isSlab()
|
void |
newSpaceGroupPoint(int i,
javax.vecmath.Point3f atom1,
javax.vecmath.Point3f atom2,
int transX,
int transY,
int transZ)
|
java.lang.Object |
rotateEllipsoid(int i,
javax.vecmath.Point3f ptTemp,
javax.vecmath.Vector3f[] axes,
javax.vecmath.Point3f ptTemp1,
javax.vecmath.Point3f ptTemp2)
|
void |
setFinalOperations(javax.vecmath.Point3f[] atoms,
int iAtomFirst,
int noSymmetryCount,
boolean doNormalize)
|
void |
setLattice(int latt)
set symmetry lattice type using Hall rotations |
void |
setMinMaxLatticeParameters(javax.vecmath.Point3i minXYZ,
javax.vecmath.Point3i maxXYZ)
|
void |
setOffset(int nnn)
|
SymmetryInterface |
setPointGroup(SymmetryInterface pointGroupPrevious,
Atom[] atomset,
java.util.BitSet bsAtoms,
boolean haveVibration,
float distanceTolerance,
float linearTolerance)
|
void |
setSpaceGroup(boolean doNormalize)
|
void |
setSpaceGroup(SymmetryInterface symmetry)
|
void |
setSymmetryInfo(int modelIndex,
java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo)
|
void |
setUnitCell(float[] notionalUnitCell)
|
void |
setUnitCellAllFractionalRelative(boolean TF)
|
void |
setUnitCellOffset(javax.vecmath.Point3f pt)
|
void |
setUnitCellOrientation(javax.vecmath.Matrix3f matUnitCellOrientation)
|
void |
toCartesian(javax.vecmath.Point3f pt,
boolean asAbsolue)
|
void |
toFractional(javax.vecmath.Point3f pt,
boolean isAbsolute)
|
void |
toUnitCell(javax.vecmath.Point3f pt,
javax.vecmath.Point3f offset)
|
setPointGroup
SymmetryInterface setPointGroup(SymmetryInterface pointGroupPrevious,
Atom[] atomset,
java.util.BitSet bsAtoms,
boolean haveVibration,
float distanceTolerance,
float linearTolerance)
getPointGroupName
java.lang.String getPointGroupName()
getPointGroupInfo
java.lang.Object getPointGroupInfo(int modelIndex,
boolean asDraw,
boolean asInfo,
java.lang.String type,
int index,
float scale)
setSpaceGroup
void setSpaceGroup(boolean doNormalize)
addSpaceGroupOperation
int addSpaceGroupOperation(java.lang.String xyz,
int opId)
setLattice
void setLattice(int latt)
- set symmetry lattice type using Hall rotations
- Parameters:
latt
- SHELX index or character lattice character P I R F A B C S T or \0
getSpaceGroupName
java.lang.String getSpaceGroupName()
getSpaceGroup
java.lang.Object getSpaceGroup()
setSpaceGroup
void setSpaceGroup(SymmetryInterface symmetry)
createSpaceGroup
boolean createSpaceGroup(int desiredSpaceGroupIndex,
java.lang.String name,
float[] notionalUnitCell)
haveSpaceGroup
boolean haveSpaceGroup()
getSpaceGroupInfo
java.lang.String getSpaceGroupInfo(java.lang.String name,
SymmetryInterface cellInfo)
getLatticeDesignation
java.lang.Object getLatticeDesignation()
setFinalOperations
void setFinalOperations(javax.vecmath.Point3f[] atoms,
int iAtomFirst,
int noSymmetryCount,
boolean doNormalize)
getSpaceGroupOperationCount
int getSpaceGroupOperationCount()
getSpaceGroupOperation
javax.vecmath.Matrix4f getSpaceGroupOperation(int i)
getSpaceGroupXyz
java.lang.String getSpaceGroupXyz(int i,
boolean doNormalize)
newSpaceGroupPoint
void newSpaceGroupPoint(int i,
javax.vecmath.Point3f atom1,
javax.vecmath.Point3f atom2,
int transX,
int transY,
int transZ)
rotateEllipsoid
java.lang.Object rotateEllipsoid(int i,
javax.vecmath.Point3f ptTemp,
javax.vecmath.Vector3f[] axes,
javax.vecmath.Point3f ptTemp1,
javax.vecmath.Point3f ptTemp2)
setUnitCellAllFractionalRelative
void setUnitCellAllFractionalRelative(boolean TF)
setUnitCell
void setUnitCell(float[] notionalUnitCell)
toCartesian
void toCartesian(javax.vecmath.Point3f pt,
boolean asAbsolue)
getEllipsoid
java.lang.Object[] getEllipsoid(float[] parBorU)
getEllipsoid
java.lang.Object[] getEllipsoid(javax.vecmath.Vector3f[] vectors,
float a,
float b,
float c)
ijkToPoint3f
javax.vecmath.Point3f ijkToPoint3f(int nnn)
toFractional
void toFractional(javax.vecmath.Point3f pt,
boolean isAbsolute)
getUnitCellVertices
javax.vecmath.Point3f[] getUnitCellVertices()
getCanonicalCopy
javax.vecmath.Point3f[] getCanonicalCopy(float scale)
getCartesianOffset
javax.vecmath.Point3f getCartesianOffset()
getNotionalUnitCell
float[] getNotionalUnitCell()
getUnitCellAsArray
float[] getUnitCellAsArray(boolean vectorsOnly)
toUnitCell
void toUnitCell(javax.vecmath.Point3f pt,
javax.vecmath.Point3f offset)
setUnitCellOffset
void setUnitCellOffset(javax.vecmath.Point3f pt)
setOffset
void setOffset(int nnn)
getUnitCellMultiplier
javax.vecmath.Point3f getUnitCellMultiplier()
getUnitCellInfo
float getUnitCellInfo(int infoType)
getCoordinatesAreFractional
boolean getCoordinatesAreFractional()
getCellRange
int[] getCellRange()
getSymmetryInfoString
java.lang.String getSymmetryInfoString()
getSymmetryOperations
java.lang.String[] getSymmetryOperations()
haveUnitCell
boolean haveUnitCell()
getUnitCellInfo
java.lang.String getUnitCellInfo()
isPeriodic
boolean isPeriodic()
setSymmetryInfo
void setSymmetryInfo(int modelIndex,
java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo)
getSymmetryOperationDescription
java.lang.Object[] getSymmetryOperationDescription(int iSym,
SymmetryInterface cellInfo,
javax.vecmath.Point3f pt1,
javax.vecmath.Point3f pt2,
java.lang.String id)
isPolymer
boolean isPolymer()
isSlab
boolean isSlab()
addSpaceGroupOperation
void addSpaceGroupOperation(javax.vecmath.Matrix4f mat)
setMinMaxLatticeParameters
void setMinMaxLatticeParameters(javax.vecmath.Point3i minXYZ,
javax.vecmath.Point3i maxXYZ)
setUnitCellOrientation
void setUnitCellOrientation(javax.vecmath.Matrix3f matUnitCellOrientation)
getMatrixFromString
java.lang.String getMatrixFromString(java.lang.String xyz,
float[] temp,
boolean allowScaling)
checkDistance
boolean checkDistance(javax.vecmath.Point3f f1,
javax.vecmath.Point3f f2,
float distance,
float dx,
int iRange,
int jRange,
int kRange,
javax.vecmath.Point3f ptOffset)
getFractionalOffset
javax.vecmath.Point3f getFractionalOffset()
fcoord
java.lang.String fcoord(javax.vecmath.Tuple3f p)