public class BiologicalAssemblyTransformation
extends java.lang.Object
implements java.lang.Cloneable
Constructor and Description |
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BiologicalAssemblyTransformation()
Default Constructor
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BiologicalAssemblyTransformation(BiologicalAssemblyTransformation src)
Copy Constructor
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Modifier and Type | Method and Description |
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static BiologicalAssemblyTransformation |
combine(BiologicalAssemblyTransformation matrix1,
BiologicalAssemblyTransformation matrix2)
Returns the combination (product) of two biological assembly transformations.
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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.
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java.lang.String |
getId()
Returns the identified for this biological assembly transformation.
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Matrix |
getRotationMatrix()
Return the rotation matrix for this transformation
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Matrix |
getTransformationMatrix()
Returns the rotational and translational component of this transformation as 4x4 transformation matrix.
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double[] |
getTranslation()
Returns the translational component of this transformation
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void |
setChainId(java.lang.String chainId)
Sets the chain identified this transformation should be applied to.
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void |
setId(java.lang.String id)
Sets the identifier for this biological assembly transformation.
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void |
setRotationMatrix(Matrix rotation)
Set the rotation matrix for this transformation
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void |
setTransformationMatrix(Matrix transformation)
Sets the transformation using a 4x4 transformation matrix
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void |
setTranslation(double[] translation)
Sets the translational component of this transformation
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java.lang.String |
toXML() |
void |
toXML(PrettyXMLWriter xml) |
void |
transformPoint(double[] point)
Applies the transformation to this point.
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public BiologicalAssemblyTransformation()
public BiologicalAssemblyTransformation(BiologicalAssemblyTransformation src)
src
- public void setId(java.lang.String id)
id
- public java.lang.String getId()
public void setChainId(java.lang.String chainId)
chainId
- public java.lang.String getChainId()
public void setRotationMatrix(Matrix rotation)
rotation
- public Matrix getRotationMatrix()
public void setTranslation(double[] translation)
translation
- public double[] getTranslation()
public void setTransformationMatrix(Matrix transformation)
transformation
- public Matrix getTransformationMatrix()
public void transformPoint(double[] point)
public static BiologicalAssemblyTransformation combine(BiologicalAssemblyTransformation matrix1, BiologicalAssemblyTransformation matrix2)
matrix1
- 4x4 transformation matrixmatrix2
- 4x4 transformation matrixpublic java.lang.String toXML() throws java.io.IOException
java.io.IOException
public void toXML(PrettyXMLWriter xml) throws java.io.IOException
java.io.IOException
public static BiologicalAssemblyTransformation fromXML(java.lang.String xml) throws org.xml.sax.SAXException, java.io.IOException, javax.xml.parsers.ParserConfigurationException
org.xml.sax.SAXException
java.io.IOException
javax.xml.parsers.ParserConfigurationException
public static java.util.List<BiologicalAssemblyTransformation> fromMultiXML(java.lang.String xml) throws javax.xml.parsers.ParserConfigurationException, org.xml.sax.SAXException, java.io.IOException
javax.xml.parsers.ParserConfigurationException
org.xml.sax.SAXException
java.io.IOException