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 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.
    • 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()