Package ffx.potential.parsers

Class MergeFilter

java.lang.Object

ffx.potential.parsers.SystemFilter

ffx.potential.parsers.MergeFilter

public class MergeFilter
extends SystemFilter

The MergeFilter class allows Force Field X to treat merging of Systems just like opening a file from a hard disk or socket.

Since:

1.0

Author:

Michael J. Schnieders

Nested Class Summary

Nested classes/interfaces inherited from class ffx.potential.parsers.SystemFilter

SystemFilter.Versioning

Field Summary

Fields inherited from class ffx.potential.parsers.SystemFilter

atomList, bondList, dieOnMissingAtom, fileRead, files, fileType, forceField, lambdaPattern, properties, standardizeAtomNames, systems, vdwH

Constructor Summary

Constructors

Constructor	Description
MergeFilter(MolecularAssembly f, ArrayList<Atom> a, ArrayList<Bond> b)	Constructor for MergeFilter.

Method Summary

Modifier and Type	Method	Description
void	closeReader()	Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
boolean	readFile()	This method is different for each subclass and must be overridden.
boolean	readNext()	Reads the next model if applicable (currently, ARC and PDB files only).
boolean	readNext(boolean resetPosition)	Reads the next model if applicable (currently, ARC files only).
boolean	readNext(boolean resetPosition, boolean print)	Reads the next model if applicable (currently, ARC files only).
boolean	readNext(boolean resetPosition, boolean print, boolean parse)	Reads the next model if applicable (currently, ARC files only).
boolean	writeFile(File saveFile, boolean append, String[] extraLines)	This method is different for each subclass and must be overridden.

Methods inherited from class ffx.potential.parsers.SystemFilter

applyAtomProperties, atomListToSet, countNumModels, fileRead, getActiveMolecularSystem, getAtomList, getFile, getFiles, getLastReadLambda, getMolecularAssemblyArray, getRemarkLines, getSnapshot, getType, previousVersion, setFile, setFileRead, setFiles, setForceField, setProperties, setType, setVersioning, version, writeFile

Methods inherited from class java.lang.Object

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

Constructor Details

MergeFilter

public MergeFilter(MolecularAssembly f,
 ArrayList<Atom> a,
 ArrayList<Bond> b)

Constructor for MergeFilter.

Parameters:

f - a MolecularAssembly object.

a - a ArrayList object.

b - a ArrayList object.

Method Details

closeReader

public void closeReader()

Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.

Specified by:

closeReader in class SystemFilter

readFile

public boolean readFile()

This method is different for each subclass and must be overridden.

Specified by:

readFile in class SystemFilter

Returns:

a boolean.

readNext

public boolean readNext(boolean resetPosition)

Reads the next model if applicable (currently, ARC files only).

Specified by:

readNext in class SystemFilter

Parameters:

resetPosition - Resets to first frame.

Returns:

If next model read.

readNext

public boolean readNext(boolean resetPosition,
 boolean print)

Reads the next model if applicable (currently, ARC files only).

Specified by:

readNext in class SystemFilter

Parameters:

resetPosition - Resets to first frame.

print - Flag to print.

Returns:

If next model read.

readNext

public boolean readNext(boolean resetPosition,
 boolean print,
 boolean parse)

Reads the next model if applicable (currently, ARC files only).

Specified by:

readNext in class SystemFilter

Parameters:

resetPosition - Resets to first frame.

print - Flag to print.

parse - Parse data in file. May want to skip structures for parallel jobs.

Returns:

If next model read.

readNext

public boolean readNext()

Reads the next model if applicable (currently, ARC and PDB files only).

Specified by:

readNext in class SystemFilter

Returns:

If next model read.

writeFile

public boolean writeFile(File saveFile,
 boolean append,
 String[] extraLines)

This method is different for each subclass and must be overridden.

If the append flag is true, "saveFile" will be appended to. Otherwise, the default versioning scheme will be applied.

Specified by:

writeFile in class SystemFilter

Parameters:

saveFile - a File object.

append - a boolean.

extraLines - Additional lines to append to a comments section, or null.

Returns:

a boolean.