Package jgromacs.analysis
Class GNM
- java.lang.Object
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- jgromacs.analysis.GNM
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public class GNM extends java.lang.Object
Objects of this class represent a Gaussian Network Model (GNM) of a protein
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Jama.Matrix
getContactMatrix()
Returns the contact matrixJama.Matrix
getEigenvectorMatrix()
Returns the orthogonal matrix of eigenvectors (U)Jama.Matrix
getKirchhoffMatrix()
Returns the Kirchhoff matrixJama.Matrix
getLambdaMatrix()
Returns the diagonal matrix of eigenvalues (Lambda)java.util.ArrayList<java.lang.Double>
getMSFProfile()
Calculates the mean square fluctuation (MSF) profile
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Constructor Detail
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GNM
public GNM(Structure s, double cutoff, int distanceBetween)
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)
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Method Detail
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getContactMatrix
public Jama.Matrix getContactMatrix()
Returns the contact matrix- Returns:
- contact matrix
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getKirchhoffMatrix
public Jama.Matrix getKirchhoffMatrix()
Returns the Kirchhoff matrix- Returns:
- Kirchhoff matrix
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getLambdaMatrix
public Jama.Matrix getLambdaMatrix()
Returns the diagonal matrix of eigenvalues (Lambda)- Returns:
- Lambda matrix
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getEigenvectorMatrix
public Jama.Matrix getEigenvectorMatrix()
Returns the orthogonal matrix of eigenvectors (U)- Returns:
- U matrix
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getMSFProfile
public java.util.ArrayList<java.lang.Double> getMSFProfile()
Calculates the mean square fluctuation (MSF) profile- Returns:
- MSF profile
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