belka.geom
Class NormalModeCalculator

java.lang.Object
  extended by belka.geom.NormalModeCalculator

public class NormalModeCalculator
extends Object

The class calculates normal model for given structure from Elastic Network Model (ENM), as described in Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I, Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J. 2001 Jan;80(1):505-15.

Author:
Alexej Abyzov

Constructor Summary
NormalModeCalculator()
           
 
Method Summary
 int calculateModes(Molecule mol, double r_gamma)
          The functions generates a hessian matrix for provided molecule and calculates its eigen values and vectors.
 int calculateModes(Molecule mol, double r_gamma, boolean selected)
          The functions generates a hessian matrix for provided molecule and calculates its eigen values and vectors.
 int getNModes()
           
 void printHessian(File file)
           
 void printModes(File file)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

NormalModeCalculator

public NormalModeCalculator()
Method Detail

printHessian

public void printHessian(File file)

printModes

public void printModes(File file)

getNModes

public int getNModes()

calculateModes

public int calculateModes(Molecule mol,
                          double r_gamma)
The functions generates a hessian matrix for provided molecule and calculates its eigen values and vectors. Resides C-alpha carbons are used as a representative points.

Parameters:
mol - molecule to calculate normal modes.
r_gamma - value of gamma for rigid blocks (in unit of gamma for between blocks)

calculateModes

public int calculateModes(Molecule mol,
                          double r_gamma,
                          boolean selected)
The functions generates a hessian matrix for provided molecule and calculates its eigen values and vectors. Resides C-alpha carbons are used as a representative points.

Parameters:
mol - molecule to calculate normal modes.
r_gamma - value of gamma for rigid blocks (in unit of gamma for between blocks)
selected - flag to indicate that only selected atoms must be used.