Class FFXSystem

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.MSGroup

ffx.potential.MolecularAssembly

ffx.ui.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:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class MolecularAssembly

MolecularAssembly.FractionalMode

Field Summary

Fields

Modifier and Type	Field	Description
static final int	MultiScaleLevel	Constant MultiScaleLevel=4

Fields inherited from class MolecularAssembly

forceField

Fields inherited from class MSGroup

angleTime, angleTorsionTime, bondTime, improperTorsionTime, outOfPlaneBendTime, piOrbitalTorsionTime, stretchBendTime, stretchTorsionTime, torsionTime, torsionTorsionTime, ureyBradleyTime

Fields inherited from class MSNode

selected

Fields inherited from class DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Fields inherited from interface ROLS

MaxLengthScale

Constructor Summary

Constructors

Constructor	Description
FFXSystem(File file, String description, org.apache.commons.configuration2.CompositeConfiguration properties)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	addKeyword(Keyword k)	addKeyword
boolean	destroy()	destroy
File	getKeyFile()	Getter for the field keyFile.
Keyword	getKeyword(String k)	getKeyword
Hashtable<String,Keyword>	getKeywords()	Getter for the field keywords.
File	getLogFile()	Getter for the field logFile.
org.apache.commons.configuration2.CompositeConfiguration	getProperties()	Getter for the field properties.
Trajectory	getTrajectory()	Getter for the field trajectory.
boolean	isClosing()	isClosing
boolean	isStale()	isStale
void	removeKeyword(Keyword kd)	removeKeyword
void	setClosing(boolean b)	Setter for the field closing.
void	setCommandDescription(String command)	Setter for the field commandDescription.
void	setKeyFile(File f)	Setter for the field keyFile.
void	setKeywords(Hashtable<String,Keyword> k)	Setter for the field keywords.
void	setLogFile(File f)	Setter for the field logFile.
void	setTrajectory(Trajectory t)	Setter for the field trajectory.
String	toFFString()	toFFString
String	toFileString()	toFileString
String	toString()

Methods inherited from class MolecularAssembly

addHeaderLine, addMSNode, applyRandomDensity, applyRandomSymOp, center, centerAt, centerView, computeFractionalCoordinates, createBox, deleteMolecule, detach, finalize, findAtom, findAtom, fractionalCount, getActiveAtomArray, getAllBondedEntities, getAlternateLocation, getArchiveFile, getAtomArray, getAtomFromWireVertex, getBackBoneAtoms, getBranchGroup, getChain, getChainNames, getChains, getCharge, getCrystal, getCurrentCycle, getCycles, getExtent, getFile, getForceField, getFractionalMode, getHeaderLines, getIons, getMass, getMoleculeArray, getMoleculeNumbers, getMolecules, getNeuralNetworkIdentity, getNodeList, getNodeList, getOffset, getOriginToRot, getParallelTeam, getPolymer, getPotentialEnergy, getResidue, getResidueList, getTransformGroup, getWater, getWireFrame, hasDeuterium, isVisible, loadVRML, moveAllIntoUnitCell, moveCenter, moveToFractionalCoordinates, removeLeaves, rotateAbout, sceneGraphChange, setAlternateLocation, setArchiveFile, setChainIDAndRenumberMolecules, setColor, setCrystal, setCurrentCycle, setCycles, setFile, setForceField, setFractionalMode, setOccupancy, setOccupancy, setOffset, setPotential, setView, setWireWidth

Methods inherited from class MSGroup

assignBondedTerms, conatainsAltLoc, conformationEquals, createJoint, createJoint, findDangelingAtoms, getAngles, getAtomByName, getAtomNode, getAtomNode, getAtomNode, getAtomNodeList, getBond, getBond, getBonds, getCenter, getDanglingAtoms, getMatchDeuterium, getMultiScaleCenter, getTermNode, getTorsions, isFinalized, print, reOrderAtoms, setAngles, setAngleTorsions, setAtomicAltLoc, setAtomNode, setBonds, setCenter, setDanglingAtoms, setFinalized, setImproperTorsions, setMatchDeuterium, setOutOfPlaneBends, setPiOrbitalTorsions, setStretchBends, setStretchTorsions, setTerms, setTorsions, setTorsionTorsions, setUreyBradleys, update, updateAtoms, updateBonds

Methods inherited from class MSNode

contains, drawLabel, equals, getAngleList, getAngleTorsionList, getAtomList, getAtomList, getBondList, getCenter, getChildList, getFirstActiveHeavyAtom, getImproperTorsionList, getList, getList, getMSCount, getMSNode, getMW, getName, getOutOfPlaneBendList, getPiOrbitalTorsionList, getStretchBendList, getStretchTorsionList, getTorsionList, getTorsionTorsionList, getTotalMass, getUreyBradleyList, hashCode, isSelected, removeChild, setName, setSelected

Methods inherited from class DefaultMutableTreeNode

add, breadthFirstEnumeration, children, clone, depthFirstEnumeration, getAllowsChildren, getChildAfter, getChildAt, getChildBefore, getChildCount, getDepth, getFirstChild, getFirstLeaf, getIndex, getLastChild, getLastLeaf, getLeafCount, getLevel, getNextLeaf, getNextNode, getNextSibling, getParent, getPath, getPathToRoot, getPreviousLeaf, getPreviousNode, getPreviousSibling, getRoot, getSharedAncestor, getSiblingCount, getUserObject, getUserObjectPath, insert, isLeaf, isNodeAncestor, isNodeChild, isNodeDescendant, isNodeRelated, isNodeSibling, isRoot, pathFromAncestorEnumeration, postorderEnumeration, preorderEnumeration, remove, remove, removeAllChildren, removeFromParent, setAllowsChildren, setParent, setUserObject

Methods inherited from class Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Details

MultiScaleLevel

public static final int MultiScaleLevel

Constant MultiScaleLevel=4

See Also:

• Constant Field Values

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