Class GNM


  • public class GNM
    extends java.lang.Object
    Objects of this class represent a Gaussian Network Model (GNM) of a protein
    • Constructor Summary

      Constructors 
      Constructor Description
      GNM​(Structure s, double cutoff, int distanceBetween)
      Constructs a new Gaussian Network Model
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Jama.Matrix getContactMatrix()
      Returns the contact matrix
      Jama.Matrix getEigenvectorMatrix()
      Returns the orthogonal matrix of eigenvectors (U)
      Jama.Matrix getKirchhoffMatrix()
      Returns the Kirchhoff matrix
      Jama.Matrix getLambdaMatrix()
      Returns the diagonal matrix of eigenvalues (Lambda)
      java.util.ArrayList<java.lang.Double> getMSFProfile()
      Calculates the mean square fluctuation (MSF) profile
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • GNM

        public GNM​(Structure s,
                   double cutoff,
                   int distanceBetween)
        Constructs a new Gaussian Network Model
        Parameters:
        s - structure to be modelled
        cutoff - distance cutoff
        distanceBetween - which atoms are used for calculating the distances (ALPHACARBON: alpha carbon atoms, CLOSEST: closest atoms of two residues, CLOSESTHEAVY: closest heavy atoms of two residues)
    • Method Detail

      • getContactMatrix

        public Jama.Matrix getContactMatrix()
        Returns the contact matrix
        Returns:
        contact matrix
      • getKirchhoffMatrix

        public Jama.Matrix getKirchhoffMatrix()
        Returns the Kirchhoff matrix
        Returns:
        Kirchhoff matrix
      • getLambdaMatrix

        public Jama.Matrix getLambdaMatrix()
        Returns the diagonal matrix of eigenvalues (Lambda)
        Returns:
        Lambda matrix
      • getEigenvectorMatrix

        public Jama.Matrix getEigenvectorMatrix()
        Returns the orthogonal matrix of eigenvectors (U)
        Returns:
        U matrix
      • getMSFProfile

        public java.util.ArrayList<java.lang.Double> getMSFProfile()
        Calculates the mean square fluctuation (MSF) profile
        Returns:
        MSF profile