CrystalTransform (biojava 5.3.0 API)

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

All Implemented Interfaces:

Serializable
```
public class CrystalTransform
extends Object
implements Serializable
```
Representation of a transformation in a crystal: - a transformation id (each of the transformations in a space group, 0 to m) - a crystal translation The transformation matrix in crystal basis is stored, representing the basic transformation together with the crystal translation. Contains methods to check for equivalent transformations.

Author:

duarte_j

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type Field and Description

static javax.vecmath.Matrix4d IDENTITY

Fields
Modifier and Type	Field and Description
`static javax.vecmath.Matrix4d`	`IDENTITY`

Constructor Summary

Constructors
Constructor and Description
`CrystalTransform(CrystalTransform transform)` Copy constructor
`CrystalTransform(SpaceGroup sg)` Creates a new CrystalTransform representing the identity transform in cell (0,0,0)
`CrystalTransform(SpaceGroup sg, int transformId)` Represents the n-th transform

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`javax.vecmath.Point3i`	`getCrystalTranslation()`
`javax.vecmath.Matrix4d`	`getMatTransform()`
`int`	`getTransformId()`
`TransformType`	`getTransformType()` Returns the TransformType of this transformation: AU, crystal translation, fractional translation , 2 3 4 6-fold rotations, 2 3 4 6-fold screw rotations, -1 -3 -2 -4 -6 inversions/rotoinversions.
`javax.vecmath.Vector3d`	`getTranslScrewComponent()`
`static javax.vecmath.Vector3d`	`getTranslScrewComponent(javax.vecmath.Matrix4d m)` Given a transformation matrix containing a rotation and translation returns the screw component of the rotation.
`boolean`	`isEquivalent(CrystalTransform other)` Returns true if the given CrystalTransform is equivalent to this one.
`boolean`	`isFractionalTranslation()` Tells whether this transformation contains a fractional translational component (whatever its rotational component).
`boolean`	`isIdentity()` Tells whether this transformation is the identity: no rotation and no translation
`boolean`	`isPureCrystalTranslation()` Tells whether this transformation is a pure crystal lattice translation, i.e. no rotational component and an integer translation vector.
`boolean`	`isPureTranslation()` Tells whether this transformation is a pure translation: either a pure crystal (lattice) translation or a fractional (within unit cell) translation: space groups Ixxx, Cxxx, Fxxx have operators with fractional translations within the unit cell.
`boolean`	`isRotation()` Tells whether this transformation is a rotation disregarding the translational component, i.e. either pure rotation or screw rotation, but not improper rotation.
`void`	`setMatTransform(javax.vecmath.Matrix4d matTransform)`
`void`	`setTransformId(int transformId)`
`String`	`toString()`
`String`	`toXYZString()` Expresses this transformation in terms of x,y,z fractional coordinates.
`void`	`translate(javax.vecmath.Point3i translation)`

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

- Field Detail
  - IDENTITY
```
public static final javax.vecmath.Matrix4d IDENTITY
```
- Constructor Detail
  - CrystalTransform
```
public CrystalTransform(SpaceGroup sg)
```
    Creates a new CrystalTransform representing the identity transform in cell (0,0,0)
  - CrystalTransform
```
public CrystalTransform(SpaceGroup sg,
                        int transformId)
```
    Represents the n-th transform
    
    Parameters:
    
    sg -
    
    transformId -
  - CrystalTransform
```
public CrystalTransform(CrystalTransform transform)
```
    Copy constructor
    
    Parameters:
    
    transform -
- Method Detail
  - getMatTransform
```
public javax.vecmath.Matrix4d getMatTransform()
```
  - setMatTransform
```
public void setMatTransform(javax.vecmath.Matrix4d matTransform)
```
  - getCrystalTranslation
```
public javax.vecmath.Point3i getCrystalTranslation()
```
  - translate
```
public void translate(javax.vecmath.Point3i translation)
```
  - isEquivalent
```
public boolean isEquivalent(CrystalTransform other)
```
    Returns true if the given CrystalTransform is equivalent to this one. Two crystal transforms are equivalent if one is the inverse of the other, i.e. their transformation matrices multiplication is equal to the identity.
    
    Parameters:
    
    other -
    
    Returns:
  - isPureCrystalTranslation
```
public boolean isPureCrystalTranslation()
```
    Tells whether this transformation is a pure crystal lattice translation, i.e. no rotational component and an integer translation vector.
    
    Returns:
  - isIdentity
```
public boolean isIdentity()
```
    Tells whether this transformation is the identity: no rotation and no translation
    
    Returns:
  - isPureTranslation
```
public boolean isPureTranslation()
```
    Tells whether this transformation is a pure translation: either a pure crystal (lattice) translation or a fractional (within unit cell) translation: space groups Ixxx, Cxxx, Fxxx have operators with fractional translations within the unit cell.
    
    Returns:
  - isFractionalTranslation
```
public boolean isFractionalTranslation()
```
    Tells whether this transformation contains a fractional translational component (whatever its rotational component). A fractional translation together with a rotation means a screw axis.
    
    Returns:
  - isRotation
```
public boolean isRotation()
```
    Tells whether this transformation is a rotation disregarding the translational component, i.e. either pure rotation or screw rotation, but not improper rotation.
    
    Returns:
  - getTransformType
```
public TransformType getTransformType()
```
    Returns the TransformType of this transformation: AU, crystal translation, fractional translation , 2 3 4 6-fold rotations, 2 3 4 6-fold screw rotations, -1 -3 -2 -4 -6 inversions/rotoinversions.
    
    Returns:
  - getTranslScrewComponent
```
public javax.vecmath.Vector3d getTranslScrewComponent()
```
  - getTransformId
```
public int getTransformId()
```
  - setTransformId
```
public void setTransformId(int transformId)
```
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - toXYZString
```
public String toXYZString()
```
    Expresses this transformation in terms of x,y,z fractional coordinates. Examples:
    
    Returns:
  - getTranslScrewComponent
```
public static javax.vecmath.Vector3d getTranslScrewComponent(javax.vecmath.Matrix4d m)
```
    Given a transformation matrix containing a rotation and translation returns the screw component of the rotation. See http://www.crystallography.fr/mathcryst/pdf/Gargnano/Aroyo_Gargnano_1.pdf
    
    Parameters:
    
    m -
    
    Returns:

Class CrystalTransform

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

IDENTITY

Constructor Detail

CrystalTransform

CrystalTransform

CrystalTransform

Method Detail

getMatTransform

setMatTransform

getCrystalTranslation

translate

isEquivalent

isPureCrystalTranslation

isIdentity

isPureTranslation

isFractionalTranslation

isRotation

getTransformType

getTranslScrewComponent

getTransformId

setTransformId

toString

toXYZString

getTranslScrewComponent