Package org.biojava.spark.function

Class AlignmentTools

  • All Implemented Interfaces:
    java.io.Serializable
    public class AlignmentTools
extends java.lang.Object
implements java.io.Serializable
    Class to calculate the TM Score between two Atom arrays.
    Author:
    Anthony Bradley
    See Also:
    Serialized Form

    • Constructor Summary

      Constructors 
      Constructor Description
      AlignmentTools()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static org.biojava.nbio.structure.align.model.AFPChain getBiojavaAlignment​(org.biojava.nbio.structure.Atom[] ca1, org.biojava.nbio.structure.Atom[] ca2, java.lang.String alignmentMethod)
      Performs an alignment and returns the AFPChain scores between two C-alpha Atom arrays.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • AlignmentTools

        public AlignmentTools()

    • Method Detail

      • getBiojavaAlignment

        public static org.biojava.nbio.structure.align.model.AFPChain getBiojavaAlignment​(org.biojava.nbio.structure.Atom[] ca1,
                                                                                  org.biojava.nbio.structure.Atom[] ca2,
                                                                                  java.lang.String alignmentMethod)
        Performs an alignment and returns the AFPChain scores between two C-alpha Atom arrays.
        Parameters:
        ca1 - the first C-alpha array
        ca2 - the second C-alpha array
        alignmentMethod - the string specifying the alignment method
        Returns:
        the AFPChain pf the scores between the two input Atom array