org.biojava.nbio.structure.xtal

Class CrystalTransform

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

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

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.
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.
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: