Class BiologicalAssemblyTransformation

  • 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
    • Constructor Detail

      • BiologicalAssemblyTransformation

        public BiologicalAssemblyTransformation()
        Default Constructor
    • 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 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
      • 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.
      • 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)