Package ffx.potential.nonbonded.implicit

Class SurfaceAreaRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.implicit.SurfaceAreaRegion

public class SurfaceAreaRegion
extends ParallelRegion

SurfaceAreaRegion performs an analytical computation of the weighted solvent accessible surface area of each atom and the first derivatives of the area with respect to Cartesian coordinates

Literature references:

T. J. Richmond, "Solvent Accessible Surface Area and Excluded Volume in Proteins", Journal of Molecular Biology, 178, 63-89 (1984)

L. Wesson and D. Eisenberg, "Atomic Solvation Parameters Applied to Molecular Dynamics of Proteins in Solution", Protein Science, 1, 227-235 (1992)

This was ported from the TINKER "surface.f" code.

Since:

1.0

Author:

Michael J. Schnieders

Constructor Summary

Constructors

Constructor	Description
SurfaceAreaRegion(Atom[] atoms, double[] x, double[] y, double[] z, boolean[] use, int[][][] neighborLists, AtomicDoubleArray3D grad, int nt, double probe, double surfaceTension)	This class is a port of the Cavitation code in TINKER.

Method Summary

Modifier and Type	Method	Description
void	finish()	Perform finalization actions after parallel execution ends.
double[]	getArea()
double	getEnergy()
double	getResidueSurfaceArea(Residue residue)
final void	init()
void	run()	Execute parallel code.
void	setSurfaceTension(double surfaceTension)
void	start()	Perform initialization actions before parallel execution begins.

Methods inherited from class edu.rit.pj.ParallelRegion

barrier, barrier, critical, critical, criticalNonexclusive, criticalNonexclusive, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute

Methods inherited from class edu.rit.pj.ParallelConstruct

getThreadCount, getThreadIndex, isExecutingInParallel, region, team

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

SurfaceAreaRegion

public SurfaceAreaRegion(Atom[] atoms,
 double[] x,
 double[] y,
 double[] z,
 boolean[] use,
 int[][][] neighborLists,
 AtomicDoubleArray3D grad,
 int nt,
 double probe,
 double surfaceTension)

This class is a port of the Cavitation code in TINKER.

GK implicit solvents are moving to use Gaussian based definitions of surface area for efficiency.

Parameters:

atoms - Atom array.

x - X-coordinate array.

y - Y-coordinate array.

z - Z-coordinate array.

use - Specifies if the atom is used in the potential.

neighborLists - Neighbor-list array.

grad - Gradient array.

nt - Number of threads.

probe - Solvent probe radius.

surfaceTension - Surface tension.

Method Details

finish

public void finish()

Description copied from class: ParallelRegion

Perform finalization actions after parallel execution ends. Only one thread calls the finish() method.

The finish() method may be overridden in a subclass. If not overridden, the finish() method does nothing.

Overrides:

finish in class ParallelRegion

getEnergy

public double getEnergy()

getArea

public double[] getArea()

getResidueSurfaceArea

public double getResidueSurfaceArea(Residue residue)

init

public final void init()

run

public void run()

Description copied from class: ParallelRegion

Execute parallel code. All threads of the parallel team call the run() method concurrently.

The run() method must be implemented in a subclass.

Specified by:

run in class ParallelRegion

setSurfaceTension

public void setSurfaceTension(double surfaceTension)

start

public void start()

Description copied from class: ParallelRegion

Perform initialization actions before parallel execution begins. Only one thread calls the start() method.

The start() method may be overridden in a subclass. If not overridden, the start() method does nothing.

Overrides:

start in class ParallelRegion