org.biojava.bio.structure.quaternary

Class BiologicalAssemblyTransformation

java.lang.Object

org.biojava.bio.structure.quaternary.BiologicalAssemblyTransformation

All Implemented Interfaces:

java.lang.Cloneable

public class BiologicalAssemblyTransformation
extends java.lang.Object
implements java.lang.Cloneable

Author:

Peter Rose, Andreas Prlic, rickb

Constructor Summary

Constructors

Constructor and Description
BiologicalAssemblyTransformation() Default Constructor
BiologicalAssemblyTransformation(BiologicalAssemblyTransformation src) Copy Constructor

Method Summary

Methods

Modifier and Type	Method and Description
static BiologicalAssemblyTransformation	combine(BiologicalAssemblyTransformation matrix1, BiologicalAssemblyTransformation matrix2) Returns the combination (product) of two biological assembly transformations.
static java.util.List<BiologicalAssemblyTransformation>	fromMultiXML(java.lang.String xml)
static BiologicalAssemblyTransformation	fromXML(java.lang.String xml)
java.lang.String	getChainId() Returns the chain identifier this transformation should be applied to.
java.lang.String	getId() Returns the identified for this biological assembly transformation.
Matrix	getRotationMatrix() Return the rotation matrix for this transformation
Matrix	getTransformationMatrix() Returns the rotational and translational component of this transformation as 4x4 transformation matrix.
double[]	getTranslation() Returns the translational component of this transformation
void	setChainId(java.lang.String chainId) Sets the chain identified this transformation should be applied to.
void	setId(java.lang.String id) Sets the identifier for this biological assembly transformation.
void	setRotationMatrix(Matrix rotation) Set the rotation matrix for this transformation
void	setTransformationMatrix(Matrix transformation) Sets the transformation using a 4x4 transformation matrix
void	setTranslation(double[] translation) Sets the translational component of this transformation
java.lang.String	toXML()
void	toXML(PrettyXMLWriter xml)
void	transformPoint(double[] point) Applies the transformation to this point.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BiologicalAssemblyTransformation

public BiologicalAssemblyTransformation()

Default Constructor

BiologicalAssemblyTransformation

public BiologicalAssemblyTransformation(BiologicalAssemblyTransformation src)

Copy Constructor

Parameters:

src -

Method Detail

setId

public void setId(java.lang.String id)

Sets the identifier for this biological assembly transformation. This is usually the model number used in the biological assembly files.

Parameters:

id -

getId

public java.lang.String getId()

Returns the identified for this biological assembly transformation.

Returns:

biological assembly transformation identifier

setChainId

public void setChainId(java.lang.String chainId)

Sets the chain identified this transformation should be applied to.

Parameters:

chainId -

getChainId

public java.lang.String getChainId()

Returns the chain identifier this transformation should be applied to.

Returns:

chain identifier

setRotationMatrix

public void setRotationMatrix(Matrix rotation)

Set the rotation matrix for this transformation

Parameters:

rotation -

getRotationMatrix

public Matrix getRotationMatrix()

Return the rotation matrix for this transformation

Returns:

3x3 rotation matrix

setTranslation

public void setTranslation(double[] translation)

Sets the translational component of this transformation

Parameters:

translation -

getTranslation

public double[] getTranslation()

Returns the translational component of this transformation

Returns:

translational component

setTransformationMatrix

public void setTransformationMatrix(Matrix transformation)

Sets the transformation using a 4x4 transformation matrix

Parameters:

transformation -

getTransformationMatrix

public Matrix getTransformationMatrix()

Returns the rotational and translational component of this transformation as 4x4 transformation matrix.

Returns:

4X4 rotation matrix

transformPoint

public void transformPoint(double[] point)

Applies the transformation to this point.

combine

public static BiologicalAssemblyTransformation combine(BiologicalAssemblyTransformation matrix1,
                                       BiologicalAssemblyTransformation matrix2)

Returns the combination (product) of two biological assembly transformations.

Parameters:

matrix1 - 4x4 transformation matrix

matrix2 - 4x4 transformation matrix

Returns:

combined transformation

toXML

public java.lang.String toXML()
                       throws java.io.IOException

Throws:

java.io.IOException

toXML

public void toXML(PrettyXMLWriter xml)
           throws java.io.IOException

Throws:

java.io.IOException

fromXML

public static BiologicalAssemblyTransformation fromXML(java.lang.String xml)
                                                throws org.xml.sax.SAXException,
                                                       java.io.IOException,
                                                       javax.xml.parsers.ParserConfigurationException

Throws:

org.xml.sax.SAXException

java.io.IOException

javax.xml.parsers.ParserConfigurationException

fromMultiXML

public static java.util.List<BiologicalAssemblyTransformation> fromMultiXML(java.lang.String xml)
                                                                     throws javax.xml.parsers.ParserConfigurationException,
                                                                            org.xml.sax.SAXException,
                                                                            java.io.IOException

Throws:

javax.xml.parsers.ParserConfigurationException

org.xml.sax.SAXException

java.io.IOException