SpaceGroup (biojava 4.2.1 API)

java.lang.Object
- org.biojava.nbio.structure.xtal.SpaceGroup

All Implemented Interfaces:

Serializable
```
public class SpaceGroup
extends Object
implements Serializable
```
A crystallographic space group. We store the standard numeric identifier, the international short symbol and the transformations corresponding to each space group (as Matrix4ds and in algebraic notation). The information for all (protein crystallography) space groups can be parsed from the XML file in the resource directory. See: http://en.wikipedia.org/wiki/Space_group

Author:

duarte_j

See Also:

SymoplibParser, Serialized Form

Field Summary

Fields
Modifier and Type Field and Description

protected static double DELTA

Fields
Modifier and Type	Field and Description
`protected static double`	`DELTA`

Constructor Summary

Constructors
Constructor and Description
`SpaceGroup(int id, int multiplicity, int primitiveMultiplicity, String shortSymbol, String altShortSymbol, BravaisLattice bravLattice)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addTransformation(String transfAlgebraic)`
`boolean`	`areInSameAxis(int tId1, int tId2)` Returns true if both given transform ids belong to the same crystallographic axis (a, b or c) For two non-rotation transformations (i.e.
`protected static boolean`	`deltaComp(double d1, double d2, double delta)`
`boolean`	`equals(Object o)`
`static String`	`getAlgebraicFromMatrix(javax.vecmath.Matrix4d m)`
`String`	`getAltShortSymbol()` Gets the alternative international short name (as sometimes used in PDB), e.g.
`int`	`getAxisFoldType(int transformId)` Given a transformId returns the type of axis of rotation: 1 (no rotation), 2, 3, 4 or 6 -fold and for improper rotations: -1, -2, -3, -4 and -6
`int[]`	`getAxisTypes()`
`BravaisLattice`	`getBravLattice()`
`javax.vecmath.Vector3d`	`getCellTranslation(int i)`
`javax.vecmath.Vector3d[]`	`getCellTranslations()`
`static Pattern`	`getCoordpat()`
`static double`	`getDelta()`
`int`	`getId()` Gets the standard numeric identifier for the space group.
`static javax.vecmath.Matrix4d`	`getMatrixFromAlgebraic(String transfAlgebraic)`
`int`	`getMultiplicity()`
`static Pattern`	`getNonenantpat()`
`int`	`getNumOperators()` Gets the number of symmetry operators corresponding to this SpaceGroup (counting the identity operator)
`int`	`getPrimitiveMultiplicity()`
`static javax.vecmath.AxisAngle4d`	`getRotAxisAndAngle(javax.vecmath.Matrix3d m)` Given a rotation matrix calculates the rotation axis and angle for it.
`javax.vecmath.AxisAngle4d`	`getRotAxisAngle(int transformId)`
`static int`	`getRotAxisType(javax.vecmath.Matrix4d m)` Given a transformation matrix containing a rotation returns the type of rotation: 1 for identity, 2 for 2-fold rotation, 3 for 3-fold rotation, 4 for 4-fold rotation, 6 for 6-fold rotation, -1 for inversions, -2 for mirror planes, -3 for 3-fold improper rotation, -4 for 4-fold improper rotation and -6 for 6-fold improper rotation
`static long`	`getSerialversionuid()`
`String`	`getShortSymbol()` Gets the international short name (as used in PDB), e.g.
`static Pattern`	`getSplitpat1()`
`static Pattern`	`getSplitpat2()`
`static Pattern`	`getTranscoefpat()`
`List<String>`	`getTransfAlgebraic()`
`String`	`getTransfAlgebraic(int i)` Gets a transformation algebraic string given its index.
`javax.vecmath.Matrix4d`	`getTransformation(int i)` Gets a transformation by index expressed in crystal axes basis.
`List<javax.vecmath.Matrix4d>`	`getTransformations()` Gets all transformations except for the identity in crystal axes basis.
`protected void`	`initializeCellTranslations()`
`boolean`	`isEnantiomorphic()`
`static SpaceGroup`	`parseSpaceGroup(String shortName)` Get the space group for the given international short name, using the PDB format, e.g.
`void`	`setAltShortSymbol(String altShortSymbol)`
`void`	`setAxisTypes(int[] axisTypes)`
`void`	`setBravLattice(BravaisLattice bravLattice)`
`void`	`setId(int id)`
`void`	`setMultiplicity(int multiplicity)`
`void`	`setPrimitiveMultiplicity(int primitiveMultiplicity)`
`void`	`setShortSymbol(String shortSymbol)`
`void`	`setTransfAlgebraic(List<String> transfAlgebraic)`
`String`	`toString()`
`String`	`toXML()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - DELTA
```
protected static final double DELTA
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - SpaceGroup
```
public SpaceGroup(int id,
                  int multiplicity,
                  int primitiveMultiplicity,
                  String shortSymbol,
                  String altShortSymbol,
                  BravaisLattice bravLattice)
```
- Method Detail
  - parseSpaceGroup
```
public static SpaceGroup parseSpaceGroup(String shortName)
```
    Get the space group for the given international short name, using the PDB format, e.g. 'P 21 21 21' or 'C 1 c 1'
    
    Parameters:
    
    shortName -
    
    Returns:
    
    the SpaceGroup or null if the shortName is not valid
    
    See Also:
    
    SymoplibParser.getSpaceGroup(String)
  - addTransformation
```
public void addTransformation(String transfAlgebraic)
```
  - initializeCellTranslations
```
protected void initializeCellTranslations()
```
  - getMultiplicity
```
public int getMultiplicity()
```
  - getPrimitiveMultiplicity
```
public int getPrimitiveMultiplicity()
```
  - getCellTranslations
```
public javax.vecmath.Vector3d[] getCellTranslations()
```
  - getCellTranslation
```
public javax.vecmath.Vector3d getCellTranslation(int i)
```
  - getMatrixFromAlgebraic
```
public static javax.vecmath.Matrix4d getMatrixFromAlgebraic(String transfAlgebraic)
```
  - getId
```
public int getId()
```
    Gets the standard numeric identifier for the space group. See for example http://en.wikipedia.org/wiki/Space_group or the IUCr crystallographic tables
    
    Returns:
  - getShortSymbol
```
public String getShortSymbol()
```
    Gets the international short name (as used in PDB), e.g. "P 21 21 21" or "C 1 c 1"
    
    Returns:
  - getAltShortSymbol
```
public String getAltShortSymbol()
```
    Gets the alternative international short name (as sometimes used in PDB), e.g. "I 1 2 1" instead of "I 2"
    
    Returns:
  - getTransformations
```
public List<javax.vecmath.Matrix4d> getTransformations()
```
    Gets all transformations except for the identity in crystal axes basis.
    
    Returns:
  - getRotAxisAngle
```
public javax.vecmath.AxisAngle4d getRotAxisAngle(int transformId)
```
  - areInSameAxis
```
public boolean areInSameAxis(int tId1,
                             int tId2)
```
    Returns true if both given transform ids belong to the same crystallographic axis (a, b or c) For two non-rotation transformations (i.e. identity operators) it returns true
    
    Parameters:
    
    tId1 -
    
    tId2 -
    
    Returns:
  - getAxisFoldType
```
public int getAxisFoldType(int transformId)
```
    Given a transformId returns the type of axis of rotation: 1 (no rotation), 2, 3, 4 or 6 -fold and for improper rotations: -1, -2, -3, -4 and -6
    
    Parameters:
    
    transformId -
    
    Returns:
  - getTransformation
```
public javax.vecmath.Matrix4d getTransformation(int i)
```
    Gets a transformation by index expressed in crystal axes basis. Index 0 corresponds always to the identity transformation. Beware the returned Matrix4d is not a copy but it stays linked to the one stored in this SpaceGroup object
    
    Parameters:
    
    i -
    
    Returns:
  - getTransfAlgebraic
```
public String getTransfAlgebraic(int i)
```
    Gets a transformation algebraic string given its index. Index 0 corresponds always to the identity transformation.
    
    Parameters:
    
    i -
    
    Returns:
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class Object
  - getNumOperators
```
public int getNumOperators()
```
    Gets the number of symmetry operators corresponding to this SpaceGroup (counting the identity operator)
    
    Returns:
  - getAlgebraicFromMatrix
```
public static String getAlgebraicFromMatrix(javax.vecmath.Matrix4d m)
```
  - deltaComp
```
protected static boolean deltaComp(double d1,
                                   double d2,
                                   double delta)
```
  - getBravLattice
```
public BravaisLattice getBravLattice()
```
  - isEnantiomorphic
```
public boolean isEnantiomorphic()
```
  - getRotAxisAndAngle
```
public static javax.vecmath.AxisAngle4d getRotAxisAndAngle(javax.vecmath.Matrix3d m)
```
    Given a rotation matrix calculates the rotation axis and angle for it. The angle is calculated from the trace, the axis from the eigenvalue decomposition. If given matrix is improper rotation or identity matrix then axis (0,0,0) and angle 0 are returned.
    
    Parameters:
    
    m -
    
    Returns:
    
    Throws:
    
    IllegalArgumentException - if given matrix is not a rotation matrix (determinant not 1 or -1)
  - getRotAxisType
```
public static int getRotAxisType(javax.vecmath.Matrix4d m)
```
    Given a transformation matrix containing a rotation returns the type of rotation: 1 for identity, 2 for 2-fold rotation, 3 for 3-fold rotation, 4 for 4-fold rotation, 6 for 6-fold rotation, -1 for inversions, -2 for mirror planes, -3 for 3-fold improper rotation, -4 for 4-fold improper rotation and -6 for 6-fold improper rotation
    
    Parameters:
    
    m -
    
    Returns:
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - toXML
```
public String toXML()
```
  - getTransfAlgebraic
```
public List<String> getTransfAlgebraic()
```
  - setTransfAlgebraic
```
public void setTransfAlgebraic(List<String> transfAlgebraic)
```
  - getAxisTypes
```
public int[] getAxisTypes()
```
  - setAxisTypes
```
public void setAxisTypes(int[] axisTypes)
```
  - getSerialversionuid
```
public static long getSerialversionuid()
```
  - getSplitpat1
```
public static Pattern getSplitpat1()
```
  - getSplitpat2
```
public static Pattern getSplitpat2()
```
  - getCoordpat
```
public static Pattern getCoordpat()
```
  - getTranscoefpat
```
public static Pattern getTranscoefpat()
```
  - getNonenantpat
```
public static Pattern getNonenantpat()
```
  - getDelta
```
public static double getDelta()
```
  - setId
```
public void setId(int id)
```
  - setMultiplicity
```
public void setMultiplicity(int multiplicity)
```
  - setPrimitiveMultiplicity
```
public void setPrimitiveMultiplicity(int primitiveMultiplicity)
```
  - setShortSymbol
```
public void setShortSymbol(String shortSymbol)
```
  - setAltShortSymbol
```
public void setAltShortSymbol(String altShortSymbol)
```
  - setBravLattice
```
public void setBravLattice(BravaisLattice bravLattice)
```

Class SpaceGroup

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DELTA

Constructor Detail

SpaceGroup

Method Detail

parseSpaceGroup

addTransformation

initializeCellTranslations

getMultiplicity

getPrimitiveMultiplicity

getCellTranslations

getCellTranslation

getMatrixFromAlgebraic

getId

getShortSymbol

getAltShortSymbol

getTransformations

getRotAxisAngle

areInSameAxis

getAxisFoldType

getTransformation

getTransfAlgebraic

equals

getNumOperators

getAlgebraicFromMatrix

deltaComp

getBravLattice

isEnantiomorphic

getRotAxisAndAngle

getRotAxisType

toString

toXML

getTransfAlgebraic

setTransfAlgebraic

getAxisTypes

setAxisTypes

getSerialversionuid

getSplitpat1

getSplitpat2

getCoordpat

getTranscoefpat

getNonenantpat

getDelta

setId

setMultiplicity

setPrimitiveMultiplicity

setShortSymbol

setAltShortSymbol

setBravLattice