Package ffx.ui

Class UIUtils

java.lang.Object

ffx.potential.utils.PotentialsUtils

ffx.algorithms.AlgorithmUtils

ffx.ui.UIUtils

All Implemented Interfaces:

AlgorithmFunctions, PotentialsFunctions

public class UIUtils
extends AlgorithmUtils
implements AlgorithmFunctions

UIUtils implements core and extended functionality for many Force Field X algorithms and scripts, such as opening and closing structure files, basic force field evaluations, molecular dynamics, etc. This implementation performs additional tasks for the FFX graphical user interface, such as updating the GUI and tree structure. This is widely used by our scripts. The AlgorithmUtils and PotentialsUtils implementations of their respective interfaces lack the additional functionality provided here.

Author:

Jacob M. Litman, Michael J. Schnieders

Field Summary

Fields inherited from interface ffx.potential.utils.PotentialsFunctions

logger

Constructor Summary

Constructors

Constructor	Description
UIUtils(ModelingShell modelingShell, MainPanel mainPanel)

Method Summary

Modifier and Type	Method	Description
void	close(MolecularAssembly assembly)	Performs any necessary shutdown operations on a MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.
void	closeAll(MolecularAssembly[] assemblies)	Performs any necessary shutdown operations on an array of MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.
ForceFieldEnergy	energy(MolecularAssembly molecularAssembly)	Evaluates the energy of a MolecularAssembly and returns its ForceFieldEnergy object.
MolecularAssembly	getActiveAssembly()	Returns either the active assembly from the overlying UI, or the "active" molecular assembly from the last used SystemFilter.
List<String>	getArguments()	If available, returns CLI arguments; the default implementation does not have access to CLI arguments and throws UnsupportedOperationException.
AlgorithmListener	getDefaultListener()	Returns a default Listener if available (null by default).
SystemFilter	getFilter()	Returns the last SystemFilter created by this (can be null).
boolean	isLocal()	True if using a local implementation (not in a user interfaces module).
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
FFXSystem	open(String file)	open.
FFXSystem[]	open(String[] files, int nThreads)	Opens an array of files and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.
FFXSystem[]	openAll(String file)	Opens a file and returns all created MolecularAssembly objects.
FFXSystem[]	openAll(String[] files)	Opens an array of files and returns the created MolecularAssembly objects.
FFXSystem[]	openAll(String file, int nThreads)	Opens a file and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.
MolecularAssembly	openWithMutations(File file, List<PDBFilter.Mutation> mutations)	Mutates file on-the-fly as it is being opened.
double	returnEnergy(MolecularAssembly assembly)	Returns the energy of a MolecularAssembly in kcal/mol (as a double) and prints the energy evaluation
void	save(MolecularAssembly assembly, File file)	Saves the current state of a MolecularAssembly to an XYZ file.
void	saveAsPDB(MolecularAssembly[] assemblies, File file)	Saves the current state of an array of MolecularAssembly instances to a PDB file.
void	saveAsPDB(MolecularAssembly assembly, File file)	Saves the current state of a MolecularAssembly to a PDB file.
void	saveAsPDB(MolecularAssembly assembly, File file, boolean writeEnd, boolean append)
void	saveAsPDBinP1(MolecularAssembly assembly, File file)	Saves the symmetry mates of a MolecularAssembly to PDB files.
void	saveAsXYZ(MolecularAssembly assembly, File file)	Saves the current state of a MolecularAssembly to an XYZ file.
void	saveAsXYZinP1(MolecularAssembly assembly, File file)	Saves the current state of a MolecularAssembly to an XYZ file as a P1 crystal.
double	time()	Logs time elapsed since last call.

Methods inherited from class ffx.potential.utils.PotentialsUtils

energy, open, openQuietly, saveAsPDBinP1, saveAsXYZasReplicates

Methods inherited from class java.lang.Object

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

Methods inherited from interface ffx.potential.utils.PotentialsFunctions

energy, saveAsXYZasReplicates, versionFile, versionFile

Constructor Details

UIUtils

public UIUtils(ModelingShell modelingShell,
 MainPanel mainPanel)

Method Details

close

public void close(MolecularAssembly assembly)

Description copied from class: PotentialsUtils

Performs any necessary shutdown operations on a MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.

Shuts down parallel teams in the force field of the provided MolecularAssembly. Kaminsky's ParallelTeamThreads' run() methods are infinite loops, and because running threads are always GC roots, it is necessary to send them a signal to shut down to enable garbage collection.

Specified by:

close in interface PotentialsFunctions

Overrides:

close in class PotentialsUtils

Parameters:

assembly - Assembly to close.

closeAll

public void closeAll(MolecularAssembly[] assemblies)

Description copied from class: PotentialsUtils

Performs any necessary shutdown operations on an array of MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.

Shuts down parallel teams in the force fields of the provided MolecularAssemblys.

Specified by:

closeAll in interface PotentialsFunctions

Overrides:

closeAll in class PotentialsUtils

Parameters:

assemblies - Assemblies to close.

energy

public ForceFieldEnergy energy(MolecularAssembly molecularAssembly)

Description copied from class: PotentialsUtils

Evaluates the energy of a MolecularAssembly and returns its ForceFieldEnergy object.

Evaluates the energy of a MolecularAssembly and returns its ForceFieldEnergy object.

Specified by:

energy in interface PotentialsFunctions

Overrides:

energy in class PotentialsUtils

Parameters:

molecularAssembly - To evaluate

Returns:

assembly's ForceFieldEnergy.

getActiveAssembly

public MolecularAssembly getActiveAssembly()

Description copied from interface: PotentialsFunctions

Returns either the active assembly from the overlying UI, or the "active" molecular assembly from the last used SystemFilter.

Specified by:

getActiveAssembly in interface PotentialsFunctions

Returns:

A MolecularAssembly or null

getArguments

public List<String> getArguments()

Description copied from interface: PotentialsFunctions

If available, returns CLI arguments; the default implementation does not have access to CLI arguments and throws UnsupportedOperationException.

Specified by:

getArguments in interface PotentialsFunctions

Returns:

CLI arguments

getDefaultListener

public AlgorithmListener getDefaultListener()

Description copied from interface: AlgorithmFunctions

Returns a default Listener if available (null by default).

Specified by:

getDefaultListener in interface AlgorithmFunctions

Returns:

An AlgorithmListener or null.

getFilter

public SystemFilter getFilter()

Description copied from class: PotentialsUtils

Returns the last SystemFilter created by this (can be null).

Specified by:

getFilter in interface PotentialsFunctions

Overrides:

getFilter in class PotentialsUtils

Returns:

Last SystemFilter

isLocal

public boolean isLocal()

Description copied from class: PotentialsUtils

True if using a local implementation (not in a user interfaces module).

Returns true (this is the local implementation).

Specified by:

isLocal in interface PotentialsFunctions

Overrides:

isLocal in class PotentialsUtils

Returns:

If a local implementation

md

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

Description copied from class: AlgorithmUtils

Runs molecular dynamics on an assembly.

Performs molecular dynamics on a MolecularAssembly.

Specified by:

md in interface AlgorithmFunctions

Overrides:

md in class AlgorithmUtils

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)

Description copied from class: AlgorithmUtils

Relax the coordinates of a MolecularAssembly and minimize its potential energy

Minimizes a MolecularAssembly using AMOEBA potential energy.

Specified by:

minimize in interface AlgorithmFunctions

Overrides:

minimize in class AlgorithmUtils

Parameters:

assembly - a MolecularAssembly object.

eps - RMS gradient convergence criteria

Returns:

A Potential

open

public FFXSystem[] open(String[] files,
 int nThreads)

Description copied from class: PotentialsUtils

Opens an array of files and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads. Default implementation simply ignores nThreads.

Opens an array of files and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.

Specified by:

open in interface PotentialsFunctions

Overrides:

open in class PotentialsUtils

Parameters:

files - an array of String objects.

nThreads - Use non-default num threads

Returns:

Array of MolecularAssembly.

open

public FFXSystem open(String file)

Description copied from class: PotentialsUtils

open.

Specified by:

open in interface PotentialsFunctions

Overrides:

open in class PotentialsUtils

Parameters:

file - a String object.

Returns:

a MolecularAssembly object.

openAll

public FFXSystem[] openAll(String file)

Description copied from class: PotentialsUtils

Opens a file and returns all created MolecularAssembly objects.

Opens a file and returns all created MolecularAssembly objects.

Specified by:

openAll in interface PotentialsFunctions

Overrides:

openAll in class PotentialsUtils

Parameters:

file - Filename to open

Returns:

Array of MolecularAssembly.

openAll

public FFXSystem[] openAll(String[] files)

Description copied from class: PotentialsUtils

Opens an array of files and returns the created MolecularAssembly objects.

Opens an array of files and returns the created MolecularAssembly objects.

Specified by:

openAll in interface PotentialsFunctions

Overrides:

openAll in class PotentialsUtils

Parameters:

files - Filenames to open.

Returns:

Array of MolecularAssembly.

openAll

public FFXSystem[] openAll(String file,
 int nThreads)

Description copied from class: PotentialsUtils

Opens a file and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads. Default implementation simply ignores nThreads.

Opens a file and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.

Specified by:

openAll in interface PotentialsFunctions

Overrides:

openAll in class PotentialsUtils

Parameters:

file - Filename to open

nThreads - Use non-default num threads

Returns:

Array of MolecularAssembly.

openWithMutations

public MolecularAssembly openWithMutations(File file,
 List<PDBFilter.Mutation> mutations)

Mutates file on-the-fly as it is being opened. Used to open files for pHMD in fully-protonated form.

Overrides:

openWithMutations in class PotentialsUtils

Parameters:

file - a File object.

mutations - a List object.

Returns:

a MolecularAssembly object.

returnEnergy

public double returnEnergy(MolecularAssembly assembly)

Description copied from class: PotentialsUtils

Returns the energy of a MolecularAssembly in kcal/mol (as a double) and prints the energy evaluation

Returns the energy of a MolecularAssembly in kcal/mol (as a double) and prints the energy evaluation

Specified by:

returnEnergy in interface PotentialsFunctions

Overrides:

returnEnergy in class PotentialsUtils

Parameters:

assembly - To evaluate energy of

Returns:

Potential energy (kcal/mol)

save

public void save(MolecularAssembly assembly,
 File file)

Description copied from class: PotentialsUtils

Saves the current state of a MolecularAssembly to an XYZ file.

Saves the current state of a MolecularAssembly to an XYZ file.

Specified by:

save in interface PotentialsFunctions

Overrides:

save in class PotentialsUtils

Parameters:

assembly - MolecularAssembly to save

file - Destination .xyz

saveAsXYZinP1

public void saveAsXYZinP1(MolecularAssembly assembly,
 File file)

Description copied from class: PotentialsUtils

Saves the current state of a MolecularAssembly to an XYZ file as a P1 crystal.

Saves the current state of a MolecularAssembly to an XYZ file as a P1 crystal.

Specified by:

saveAsXYZinP1 in interface PotentialsFunctions

Overrides:

saveAsXYZinP1 in class PotentialsUtils

Parameters:

assembly - MolecularAssembly to save

file - Destination .xyz

saveAsPDB

public void saveAsPDB(MolecularAssembly assembly,
 File file)

Description copied from class: PotentialsUtils

Saves the current state of a MolecularAssembly to a PDB file.

Saves the current state of a MolecularAssembly to a PDB file.

Specified by:

saveAsPDB in interface PotentialsFunctions

Overrides:

saveAsPDB in class PotentialsUtils

Parameters:

assembly - MolecularAssembly to save

file - Destination .pdb

saveAsPDB

public void saveAsPDB(MolecularAssembly assembly,
 File file,
 boolean writeEnd,
 boolean append)

Description copied from class: PotentialsUtils

Saves the current state of a MolecularAssembly to a PDB file.

Specified by:

saveAsPDB in interface PotentialsFunctions

Overrides:

saveAsPDB in class PotentialsUtils

saveAsPDB

public void saveAsPDB(MolecularAssembly[] assemblies,
 File file)

Description copied from class: PotentialsUtils

Saves the current state of an array of MolecularAssembly instances to a PDB file.

Saves the current state of an array of MolecularAssemblys to a PDB file.

Specified by:

saveAsPDB in interface PotentialsFunctions

Overrides:

saveAsPDB in class PotentialsUtils

Parameters:

assemblies - MolecularAssembly array to save

file - Destination .pdb

saveAsXYZ

public void saveAsXYZ(MolecularAssembly assembly,
 File file)

Description copied from class: PotentialsUtils

Saves the current state of a MolecularAssembly to an XYZ file.

Saves the current state of a MolecularAssembly to an XYZ file.

Specified by:

saveAsXYZ in interface PotentialsFunctions

Overrides:

saveAsXYZ in class PotentialsUtils

Parameters:

assembly - MolecularAssembly to save

file - Destination .xyz

saveAsPDBinP1

public void saveAsPDBinP1(MolecularAssembly assembly,
 File file)

Description copied from class: PotentialsUtils

Saves the symmetry mates of a MolecularAssembly to PDB files.

Specified by:

saveAsPDBinP1 in interface PotentialsFunctions

Overrides:

saveAsPDBinP1 in class PotentialsUtils

Parameters:

assembly - To save

file - Destination file

time

public double time()

Description copied from class: AlgorithmUtils

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 AlgorithmUtils

Returns:

Time.