Package ffx.potential.parsers

Class BARFilter

java.lang.Object

ffx.potential.parsers.BARFilter

public class BARFilter
extends Object

The BARFilter class parses TINKER bar(*.BAR) files.

Since:

1.0

Author:

Rose A. Gogal

Constructor Summary

Constructors

Constructor	Description
BARFilter(File barFile)	BARFilter constructor
BARFilter(File xyzFile, double[] e1l1, double[] e1l2, double[] e2l1, double[] e2l2, double[] volume1, double[] volume2, double temp)	BARFilter constructor
BARFilter(File barFile, int startingSnap, int endingSnap)	BARFilter constructor

Method Summary

Modifier and Type	Method	Description
double[]	getE1l1()
double[]	getE1l2()
double[]	getE2l1()
double[]	getE2l2()
File	getFile()
int	getSnaps()
double[]	getVolume1()
double[]	getVolume2()
boolean	readFile()	Read TINKER bar files and parse the snapshots into energy arrays
boolean	writeFile(String saveFile, boolean isPBC)	Write TINKER bar files
boolean	writeFile(String saveFile, boolean isPBC, boolean append)	Write TINKER bar files

Methods inherited from class java.lang.Object

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

Constructor Details

BARFilter

public BARFilter(File barFile)

BARFilter constructor

Parameters:

barFile - a List object.

BARFilter

public BARFilter(File barFile,
 int startingSnap,
 int endingSnap)

BARFilter constructor

Parameters:

barFile - a List object.

startingSnap - a List object.

endingSnap - a List object.

BARFilter

public BARFilter(File xyzFile,
 double[] e1l1,
 double[] e1l2,
 double[] e2l1,
 double[] e2l2,
 double[] volume1,
 double[] volume2,
 double temp)

BARFilter constructor

Parameters:

xyzFile - a List object.

e1l1 - energy in ensemble 1 at lambda 1

e1l2 - energy in ensemble 1 at lambda 2

e2l1 - energy in ensemble 2 at lambda 1

e2l2 - energy in ensemble 2 at lambda 2

volume1 - volume in ensemble 1

volume2 - volume in ensemble 2

temp - temperature

Method Details

readFile

public boolean readFile()

Read TINKER bar files and parse the snapshots into energy arrays

Returns:

True if the file was read successfully.

writeFile

public boolean writeFile(String saveFile,
 boolean isPBC)

Write TINKER bar files

Parameters:

saveFile - The file to write to.

isPBC - include volume in the output file.

Returns:

True if successful.

writeFile

public boolean writeFile(String saveFile,
 boolean isPBC,
 boolean append)

Write TINKER bar files

Parameters:

saveFile - The file to write to.

isPBC - include volume in the output file.

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

Returns:

True if successful.

getE1l1

public double[] getE1l1()

getE2l1

public double[] getE2l1()

getE2l2

public double[] getE2l2()

getE1l2

public double[] getE1l2()

getVolume1

public double[] getVolume1()

getVolume2

public double[] getVolume2()

getSnaps

public int getSnaps()

getFile

public File getFile()