Package jgromacs.analysis

Class GNM

java.lang.Object
jgromacs.analysis.GNM
public class GNM extends Object
Objects of this class represent a Gaussian Network Model (GNM) of a protein

  • Constructor Details

    • 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 Details

    • 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 ArrayList<Double> getMSFProfile()
      Calculates the mean square fluctuation (MSF) profile
      Returns:
      MSF profile