Class BiologicalAssemblyTransformation
- java.lang.Object
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- org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
public class BiologicalAssemblyTransformation extends java.lang.Object implements java.lang.Cloneable, 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, duarte_j
- See Also:
CrystalTransform
, Serialized Form
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Constructor Summary
Constructors Constructor Description BiologicalAssemblyTransformation()
Default ConstructorBiologicalAssemblyTransformation(BiologicalAssemblyTransformation src)
Copy Constructor
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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 identifier for this biological assembly transformation.javax.vecmath.Matrix4d
getTransformationMatrix()
Return the transformation (both rotational and translational component) as a 4x4 transformation matrix.static java.lang.String
rotMatrixToString(javax.vecmath.Matrix4d m)
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(double[][] m)
void
setTransformationMatrix(javax.vecmath.Matrix4d transformation)
Sets the transformation using a 4x4 transformation matrixvoid
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)
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Constructor Detail
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BiologicalAssemblyTransformation
public BiologicalAssemblyTransformation()
Default Constructor
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BiologicalAssemblyTransformation
public BiologicalAssemblyTransformation(BiologicalAssemblyTransformation src)
Copy Constructor- Parameters:
src
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Method Detail
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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
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getId
public java.lang.String getId()
Returns the identifier for this biological assembly transformation.- Returns:
- biological assembly transformation identifier
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setChainId
public void setChainId(java.lang.String chainId)
Sets the chain identified this transformation should be applied to.- Parameters:
chainId
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getChainId
public java.lang.String getChainId()
Returns the chain identifier this transformation should be applied to.- Returns:
- chain identifier
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setTransformationMatrix
public void setTransformationMatrix(javax.vecmath.Matrix4d transformation)
Sets the transformation using a 4x4 transformation matrix- Parameters:
transformation
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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 useCrystalCell.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
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setRotationMatrix
public void setRotationMatrix(double[][] m)
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setTranslation
public void setTranslation(double[] t)
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transformPoint
public void transformPoint(double[] point)
Applies the transformation to given point.
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combine
public static BiologicalAssemblyTransformation combine(BiologicalAssemblyTransformation matrix1, BiologicalAssemblyTransformation matrix2)
Returns the combination (product) of two biological assembly transformations.- Parameters:
matrix1
-matrix2
-- Returns:
- combined transformation
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toXML
public java.lang.String toXML() throws java.io.IOException
- Throws:
java.io.IOException
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toXML
public void toXML(PrettyXMLWriter xml) throws java.io.IOException
- Throws:
java.io.IOException
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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
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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
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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rotMatrixToString
public static java.lang.String rotMatrixToString(javax.vecmath.Matrix4d m)
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translVecToString
public static java.lang.String translVecToString(javax.vecmath.Matrix4d m)
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