Package org.biojava.nbio.structure.quaternary

Class BiologicalAssemblyTransformation

java.lang.Object
org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
All Implemented Interfaces:
Serializable, Cloneable
public class BiologicalAssemblyTransformation extends Object implements Cloneable, 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:

  • Constructor Details

    • BiologicalAssemblyTransformation

      public BiologicalAssemblyTransformation()
      Default Constructor

    • BiologicalAssemblyTransformation

      public BiologicalAssemblyTransformation(BiologicalAssemblyTransformation src)
      Copy Constructor
      Parameters:
      src -

  • Method Details

    • setId

      public void setId(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 String getId()
      Returns the identifier for this biological assembly transformation.
      Returns:
      biological assembly transformation identifier

    • setChainId

      public void setChainId(String chainId)
      Sets the chain identified this transformation should be applied to.
      Parameters:
      chainId -

    • getChainId

      public String getChainId()
      Returns the chain identifier 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

    • toXML

      public String toXML() throws IOException
      Throws:
      IOException

    • toXML

      public void toXML(PrettyXMLWriter xml) throws IOException
      Throws:
      IOException

    • fromXML

      public static BiologicalAssemblyTransformation fromXML(String xml) throws SAXException, IOException, ParserConfigurationException
      Throws:
      SAXException
      IOException
      ParserConfigurationException

    • fromMultiXML

      public static List<BiologicalAssemblyTransformation> fromMultiXML(String xml) throws ParserConfigurationException, SAXException, IOException
      Throws:
      ParserConfigurationException
      SAXException
      IOException

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • rotMatrixToString

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

    • translVecToString

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