Package ffx.algorithms

Class AlgorithmUtils

java.lang.Object

ffx.potential.utils.PotentialsUtils

ffx.algorithms.AlgorithmUtils

All Implemented Interfaces:

AlgorithmFunctions, PotentialsFunctions

Direct Known Subclasses:

UIUtils

public class AlgorithmUtils
extends PotentialsUtils
implements AlgorithmFunctions

AlgorithmUtils, on top of the core functionality of PotentialsUtils, implements additional functionality such as molecular dynamics and L-BFGS local optimization. This implementation does not do anything on top of what is specified by the interface, and is used primarily by tests. It is also potentially useful for third parties who would like to use FFX without its graphical user interface.

Author:

Jacob M. Litman, Michael J. Schnieders

Constructor Summary

Constructors

Constructor	Description
AlgorithmUtils()	Constructor for AlgorithmUtils.

Method Summary

Modifier and Type	Method	Description
void	md(MolecularAssembly assembly, int nStep, double timeStep, double printInterval, double saveInterval, double temperature, boolean initVelocities, File dyn)	Runs molecular dynamics on an assembly.
Potential	minimize(MolecularAssembly assembly, double eps)	Relax the coordinates of a MolecularAssembly and minimize its potential energy
double	time()	Logs time elapsed since last call.

Methods inherited from class ffx.potential.utils.PotentialsUtils

close, closeAll, energy, energy, getFilter, isLocal, open, open, open, openAll, openAll, openAll, openQuietly, openWithMutations, returnEnergy, save, saveAsPDB, saveAsPDB, saveAsPDB, saveAsPDBinP1, saveAsPDBinP1, saveAsXYZ, saveAsXYZasReplicates, saveAsXYZinP1

Methods inherited from class java.lang.Object

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

Methods inherited from interface ffx.algorithms.AlgorithmFunctions

getDefaultListener

Methods inherited from interface ffx.potential.utils.PotentialsFunctions

close, closeAll, energy, energy, getActiveAssembly, getArguments, getFilter, isLocal, open, open, openAll, openAll, openAll, returnEnergy, save, saveAsPDB, saveAsPDB, saveAsPDB, saveAsPDBinP1, saveAsXYZ, saveAsXYZasReplicates, saveAsXYZinP1, versionFile, versionFile

Constructor Details

AlgorithmUtils

public AlgorithmUtils()

Constructor for AlgorithmUtils.

Method Details

md

public void md(MolecularAssembly assembly,
 int nStep,
 double timeStep,
 double printInterval,
 double saveInterval,
 double temperature,
 boolean initVelocities,
 File dyn)

Runs molecular dynamics on an assembly.

Performs molecular dynamics on a MolecularAssembly.

Specified by:

md in interface AlgorithmFunctions

Parameters:

assembly - a MolecularAssembly object.

nStep - Timesteps

timeStep - Time per step

printInterval - a double.

saveInterval - a double.

temperature - a double.

initVelocities - Initialize velocities from Maxwell-Boltzmann distribution

dyn - Dynamics file

minimize

public Potential minimize(MolecularAssembly assembly,
 double eps)

Relax the coordinates of a MolecularAssembly and minimize its potential energy

Minimizes a MolecularAssembly using AMOEBA potential energy.

Specified by:

minimize in interface AlgorithmFunctions

Parameters:

assembly - a MolecularAssembly object.

eps - RMS gradient convergence criteria

Returns:

A Potential

time

public double time()

Logs time elapsed since last call.

Logs time since this interface was created and the last time this method was called.

Logs time since this interface was created and the last time this method was called. May be more elegant to replace this by using protected variables and simply inheriting the time() function.

Specified by:

time in interface PotentialsFunctions

Overrides:

time in class PotentialsUtils

Returns:

Time.