public class GNM
extends java.lang.Object
Constructor and Description |
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GNM(Structure s,
double cutoff,
int distanceBetween)
Constructs a new Gaussian Network Model
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Modifier and Type | Method and Description |
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Jama.Matrix |
getContactMatrix()
Returns the contact matrix
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Jama.Matrix |
getEigenvectorMatrix()
Returns the orthogonal matrix of eigenvectors (U)
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Jama.Matrix |
getKirchhoffMatrix()
Returns the Kirchhoff matrix
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Jama.Matrix |
getLambdaMatrix()
Returns the diagonal matrix of eigenvalues (Lambda)
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java.util.ArrayList<java.lang.Double> |
getMSFProfile()
Calculates the mean square fluctuation (MSF) profile
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public GNM(Structure s, double cutoff, int distanceBetween)
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)public Jama.Matrix getContactMatrix()
public Jama.Matrix getKirchhoffMatrix()
public Jama.Matrix getLambdaMatrix()
public Jama.Matrix getEigenvectorMatrix()
public java.util.ArrayList<java.lang.Double> getMSFProfile()