Package ffx.ui

Class FFXSystem

All Implemented Interfaces:
ROLS, Serializable, Cloneable, MutableTreeNode, TreeNode

public class FFXSystem extends MolecularAssembly
The FFXSystem class contains extensions to the generic MolecularAssembly class.
Author:
Michael J. Schnieders
See Also:
  • Field Details

    • MultiScaleLevel

      public static final int MultiScaleLevel
      Constant MultiScaleLevel=4
      See Also:
  • Constructor Details

    • FFXSystem

      public FFXSystem(File file, String description, org.apache.commons.configuration2.CompositeConfiguration properties)
      Constructor.
      Parameters:
      file - Coordinate file.
      description - Short description of the command that created this system.
      properties - Properties controlling operations on this system.
  • Method Details

    • addKeyword

      public void addKeyword(Keyword k)
      addKeyword
      Parameters:
      k - a Keyword object.
    • destroy

      public boolean destroy()
      destroy
      Overrides:
      destroy in class MolecularAssembly
      Returns:
      a boolean.
    • getKeyFile

      public File getKeyFile()
      Getter for the field keyFile.
      Returns:
      a File object.
    • setKeyFile

      public void setKeyFile(File f)
      Setter for the field keyFile.
      Parameters:
      f - a File object.
    • getKeyword

      public Keyword getKeyword(String k)
      getKeyword
      Parameters:
      k - a String object.
      Returns:
      a Keyword object.
    • getKeywords

      public Hashtable<String,Keyword> getKeywords()
      Getter for the field keywords.
      Returns:
      a Hashtable object.
    • setKeywords

      public void setKeywords(Hashtable<String,Keyword> k)
      Setter for the field keywords.
      Parameters:
      k - a Hashtable object.
    • getLogFile

      public File getLogFile()
      Getter for the field logFile.
      Returns:
      a File object.
    • setLogFile

      public void setLogFile(File f)
      Setter for the field logFile.
      Parameters:
      f - a File object.
    • getProperties

      public org.apache.commons.configuration2.CompositeConfiguration getProperties()
      Getter for the field properties.
      Overrides:
      getProperties in class MolecularAssembly
      Returns:
      a CompositeConfiguration object.
    • getTrajectory

      public Trajectory getTrajectory()
      Getter for the field trajectory.
      Returns:
      a Trajectory object.
    • setTrajectory

      public void setTrajectory(Trajectory t)
      Setter for the field trajectory.
      Parameters:
      t - a Trajectory object.
    • isClosing

      public boolean isClosing()
      isClosing
      Returns:
      a boolean.
    • setClosing

      public void setClosing(boolean b)
      Setter for the field closing.
      Parameters:
      b - a boolean.
    • isStale

      public boolean isStale()
      isStale
      Returns:
      a boolean.
    • removeKeyword

      public void removeKeyword(Keyword kd)
      removeKeyword
      Parameters:
      kd - a Keyword object.
    • setCommandDescription

      public void setCommandDescription(String command)
      Setter for the field commandDescription.
      Parameters:
      command - a String object.
    • toFFString

      public String toFFString()
      toFFString
      Returns:
      a String object.
    • toFileString

      public String toFileString()
      toFileString
      Returns:
      a String object.
    • toString

      public String toString()

      Overridden toString method returns the MSNode's name

      Returns the MSGroup's name.

      Overrides:
      toString in class MSGroup