Package org.biojava.nbio.structure.quaternary

Class BiologicalAssemblyTransformation

java.lang.Object

org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<BiologicalAssemblyTransformation>

public class BiologicalAssemblyTransformation
extends java.lang.Object
implements java.lang.Cloneable, java.lang.Comparable<BiologicalAssemblyTransformation>, java.io.Serializable

The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file. It contains both the actual transformation (rotation+translation) and the chain identifier to which it should be applied.

Author:

Peter Rose, Andreas Prlic, rickb, Jose Duarte

See Also:

CrystalTransform, Serialized Form

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
static BiologicalAssemblyTransformation	combine(BiologicalAssemblyTransformation matrix1, BiologicalAssemblyTransformation matrix2)	Returns the combination (product) of two biological assembly transformations.
int	compareTo(BiologicalAssemblyTransformation other)
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 (asym id) that this transformation should be applied to.
java.lang.String	getId()	Returns the identifier for this biological assembly transformation.
javax.vecmath.Matrix4d	getTransformationMatrix()	Return the transformation (both rotational and translational component) as a 4x4 transformation matrix.
boolean	isIdentity()	Tells whether this transformation is in identity.
static java.lang.String	rotMatrixToString(javax.vecmath.Matrix4d m)
void	setChainId(java.lang.String chainId)	Sets the chain identifier (asym id) that this transformation should be applied to.
void	setId(java.lang.String id)	Sets the identifier for this biological assembly transformation.
void	setRotationMatrix(double[][] m)
void	setTransformationMatrix(javax.vecmath.Matrix4d transformation)	Sets the transformation using a 4x4 transformation matrix
void	setTranslation(double[] t)
java.lang.String	toString()
java.lang.String	toXML()
void	toXML(PrettyXMLWriter xml)
void	transformPoint(double[] point)	Applies the transformation to given point.
static java.lang.String	translVecToString(javax.vecmath.Matrix4d m)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, 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 identifier for this biological assembly transformation.

Returns:

biological assembly transformation identifier

setChainId

public void setChainId(java.lang.String chainId)

Sets the chain identifier (asym id) that this transformation should be applied to.

Parameters:

chainId -

getChainId

public java.lang.String getChainId()

Returns the chain identifier (asym id) that this transformation should be applied to.

Returns:

chain identifier

setTransformationMatrix

public void setTransformationMatrix(javax.vecmath.Matrix4d transformation)

Sets the transformation using a 4x4 transformation matrix

Parameters:

transformation -

getTransformationMatrix

public javax.vecmath.Matrix4d getTransformationMatrix()

Return the transformation (both rotational and translational component) as a 4x4 transformation matrix. The transformation is in orthonormal (cartesian coordinates). If required to be converted to crystal coordinates then use CrystalCell.transfToCrystal(Matrix4d) Note that this is a reference to the variable, thus it remains linked to this object's transformation field. The user must deep copy it if need changing it.

Returns:

4x4 transformation matrix

setRotationMatrix

public void setRotationMatrix(double[][] m)

setTranslation

public void setTranslation(double[] t)

transformPoint

public void transformPoint(double[] point)

Applies the transformation to given point.

combine

public static BiologicalAssemblyTransformation combine(BiologicalAssemblyTransformation matrix1,
                                                       BiologicalAssemblyTransformation matrix2)

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

Parameters:

matrix1 -

matrix2 -

Returns:

combined transformation

isIdentity

public boolean isIdentity()

Tells whether this transformation is in identity.

Returns:

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

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

rotMatrixToString

public static java.lang.String rotMatrixToString(javax.vecmath.Matrix4d m)

translVecToString

public static java.lang.String translVecToString(javax.vecmath.Matrix4d m)

compareTo

public int compareTo(BiologicalAssemblyTransformation other)

Specified by:

compareTo in interface java.lang.Comparable<BiologicalAssemblyTransformation>