belka.geom
Class NormalModeCalculator
java.lang.Object
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
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 |
NormalModeCalculator
public NormalModeCalculator()
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.