jgromacs.analysis
Class GNM

java.lang.Object
  jgromacs.analysis.GNM

public class GNM
extends java.lang.Object

Objects of this class represent a Gaussian Network Model (GNM) of a protein

Constructor Summary

GNM(Structure s, double cutoff, int distanceBetween)
Constructs a new Gaussian Network Model

Method Summary

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

equals, 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