Package jgromacs.analysis
Class GNM
java.lang.Object
jgromacs.analysis.GNM
Objects of this class represent a Gaussian Network Model (GNM) of a protein
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionJama.Matrix
Returns the contact matrixJama.Matrix
Returns the orthogonal matrix of eigenvectors (U)Jama.Matrix
Returns the Kirchhoff matrixJama.Matrix
Returns the diagonal matrix of eigenvalues (Lambda)Calculates the mean square fluctuation (MSF) profile
-
Constructor Details
-
GNM
Constructs a new Gaussian Network Model- Parameters:
s
- structure to be modelledcutoff
- distance cutoffdistanceBetween
- 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
Calculates the mean square fluctuation (MSF) profile- Returns:
- MSF profile
-