Package ffx.potential.nonbonded.implicit

Class ConnollyRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.implicit.ConnollyRegion

public class ConnollyRegion
extends ParallelRegion

ConnollyRegion uses the algorithms from the AMS/VAM programs of Michael Connolly to compute the analytical molecular surface area and volume of a collection of spherical atoms; thus it implements Fred Richards' molecular surface definition as a set of analytically defined spherical and toroidal polygons.

Numerical derivatives of the volume are available.

Literature references: M. L. Connolly, "Analytical Molecular Surface Calculation", Journal of Applied Crystallography, 16, 548-558 (1983)

M. L. Connolly, "Computation of Molecular Volume", Journal of the American Chemical Society, 107, 1118-1124 (1985)

C. E. Kundrot, J. W. Ponder and F. M. Richards, "Algorithms for Calculating Excluded Volume and Its Derivatives as a Function of Molecular Conformation and Their Use in Energy Minimization", Journal of Computational Chemistry, 12, 402-409 (1991)

Since:

1.0

Author:

Guowei Qi, Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
static final double	DEFAULT_WIGGLE	Default size of a vector to randomly perturb coordinates.

Constructor Summary

Constructors

Constructor	Description
ConnollyRegion(Atom[] atoms, double[] baseRadius, int nThreads)	ConnollyRegion constructor.

Method Summary

Modifier and Type	Method	Description
double	getExclude()
double	getProbe()
double	getSurfaceArea()
double	getVolume()
double[][]	getVolumeGradient()
void	init(Atom[] atoms, boolean gradient)	Initialize this VolumeRegion instance for an energy evaluation.
void	run()	Execute parallel code.
void	runVolume()	Execute the VolumeRegion with a private, single threaded ParallelTeam.
void	setExclude(double exclude)
void	setProbe(double probe)
void	setWiggle(double wiggle)	Apply a random perturbation to the atomic coordinates to avoid numerical instabilities for various linear, planar and symmetric structures.
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, finish

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

Field Details

DEFAULT_WIGGLE

public static final double DEFAULT_WIGGLE

Default size of a vector to randomly perturb coordinates.

See Also:

• Constant Field Values

Constructor Details

ConnollyRegion

public ConnollyRegion(Atom[] atoms,
 double[] baseRadius,
 int nThreads)

ConnollyRegion constructor.

Parameters:

atoms - Array of atom instances.

baseRadius - Base radius for each atom (no added probe).

nThreads - Number of threads.

Method Details

getExclude

public double getExclude()

setExclude

public void setExclude(double exclude)

getProbe

public double getProbe()

setProbe

public void setProbe(double probe)

getSurfaceArea

public double getSurfaceArea()

getVolume

public double getVolume()

getVolumeGradient

public double[][] getVolumeGradient()

init

public void init(Atom[] atoms,
 boolean gradient)

Initialize this VolumeRegion instance for an energy evaluation.

Currently the number of atoms cannot change.

Parameters:

atoms - Array of atoms.

gradient - Compute the atomic coordinate gradient.

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

runVolume

public void runVolume()

Execute the VolumeRegion with a private, single threaded ParallelTeam.

setWiggle

public void setWiggle(double wiggle)

Apply a random perturbation to the atomic coordinates to avoid numerical instabilities for various linear, planar and symmetric structures.

Parameters:

wiggle - Size of the random vector move in Angstroms.

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