ffe.lang
Class FSystem

java.lang.Object
  javax.swing.tree.DefaultMutableTreeNode
      ffe.lang.FNode
          ffe.lang.FGroup
              ffe.lang.FSystem

All Implemented Interfaces:

java.lang.Cloneable, javax.swing.tree.MutableTreeNode, java.io.Serializable, javax.swing.tree.TreeNode

public final class FSystem

extends FGroup

The FSystem class contains the information needed to represent one system in Force Field Explorer.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class javax.swing.tree.DefaultMutableTreeNode

Field Summary

static double

KCAL_TO_KJ

Fields inherited from class ffe.lang.FNode

selected

Fields inherited from class javax.swing.tree.DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Constructor Summary

FSystem(java.lang.String name, boolean bk)

FSystem(java.lang.String name, FNode Polymers, boolean bk)

Method Summary

void	addAltLocation(java.lang.String s)
void	addFNode(FNode o) Abstract method that should specify how to add various FNode subclasses (such as Atoms, Residues and Polymers) to the FGroup
void	addKeyword(Keyword k)
void	CenterAt(double[] d)
void	centerFSystem()
void	centerView(boolean rot, boolean trans)
void	createBox()
void	createLists()
javax.media.j3d.BranchGroup	createScene(boolean zero) The FSystem Branchgroup has two TransformGroups between it and the "base" node where gemoetry is attached.
void	destroy()
void	detach()
void	finalize(boolean finalizeGroups) Abstact method that should specify how to finalize a FGroup
java.lang.String[]	getAltLocations()
Atom	getAtomFromWireVertex(int i)
java.util.List	getAtomList() Returns an ArrayList of all Atoms below the present FNode.
java.util.ArrayList	getBackBoneAtoms()
java.util.List	getBondList() Returns an ArrayList of all Bonds below the present FNode.
javax.media.j3d.BranchGroup	getBranchGroup()
java.lang.String[]	getChainNames()
int	getCurrentCycle()
int	getCycles()
double	getEnergy()
java.lang.String	getEnergyString()
double	getExtent()
java.io.File	getFile()
byte	getFileType()
java.io.File	getKeyFile()
Keyword	getKeyword(java.lang.String k)
java.util.Hashtable	getKeywords()
java.io.File	getLogFile()
MMFilter	getMMFilter()
java.util.List	getMoleculeList()
javax.vecmath.Vector3d	getOffset()
java.lang.String	getParameterFile()
Polymer	getPolymer(java.lang.String chainName, boolean create)
Residue	getResidue(java.lang.String chainName, int resNum, java.lang.String resName, boolean create)
java.util.ArrayList	getResidueList()
java.lang.String	getStepString()
double	getTemperature()
java.util.ArrayList	getTermList() Returns an ArrayList of all Terms below the present FNode.
double	getTime()
java.lang.String	getTimeString()
Trajectory	getTrajectory()
javax.media.j3d.TransformGroup	getTransformGroup()
javax.media.j3d.Node	getWireFrame()
void	initAtoms(FNode f)
void	initAtoms(java.util.List f)
void	initBonds(FNode f)
void	initBonds(java.util.List f)
boolean	isClosing()
boolean	isOptimization()
boolean	isSimulation()
boolean	isVisible()
void	MoveCenter(double[] d)
void	removeJ3D()
void	removeKeyword(Keyword kd)
protected void	removeLeaves()
void	rotateAbout(javax.vecmath.Vector3d v) Rotate about a point in given in the System's Local Coordinates
void	setAngle(double[] a)
void	setBox(double[] b)
void	setClosing(boolean b)
void	setCurrentCycle(int c)
void	setCycles(int c)
void	setEnergy(double e)
void	setFile(java.io.File f)
void	setFileType(byte ftype)
void	setForceField(java.lang.String f)
void	setKeyFile(java.io.File f)
void	setKeywords(java.util.Hashtable k)
void	setLogFile(java.io.File f)
void	setMMFilter(MMFilter m)
void	setOffset(javax.vecmath.Vector3d o)
void	setSimulation(int type)
void	setStep(int s)
void	setTemperature(double t)
void	setTime(double t)
void	setTrajectory(Trajectory t)
void	setVRML(javax.media.j3d.BranchGroup v)
void	setWireWidth(float f)
void	sidePolymerCOM()
void	switchColor(int colortype, javax.vecmath.Color3f color, javax.media.j3d.Material mat)
void	switchView(int viewtype)
java.lang.String	toFFString()
java.lang.String	toFileString()
java.lang.String	toString() Returns the Moieties name.

Methods inherited from class ffe.lang.FGroup

collectBonds, ConstructGeometry, findCenter, findDangelingAtoms, getAngles, getBond, getBond, getBonds, getBondsKnown, getCenter, getDangelingAtoms, getDihedrals, getFGroupList, getFGroups, getFNode, getFNode, getTerms, isFinalized, joiner, joiner, print, reInit, setAngles, setBonds, setBondsKnown, setCenter, setDangelingAtoms, setDihedrals, setFGroups, setFinalized, setTerms, updateAtoms, updateBonds

Methods inherited from class ffe.lang.FNode

drawLabel, equals, getFSystemNode, getList, getListIterator, getMoleculeNode, getMW, getName, getPolymerNode, getResidueNode, isSelected, setName, setSelected

Methods inherited from class javax.swing.tree.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 java.lang.Object

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

Field Detail

KCAL_TO_KJ

public static final double KCAL_TO_KJ

See Also:

Constant Field Values

Constructor Detail

FSystem

public FSystem(java.lang.String name,
               boolean bk)

FSystem

public FSystem(java.lang.String name,
               FNode Polymers,
               boolean bk)

Method Detail

addKeyword

public void addKeyword(Keyword k)

getKeyword

public Keyword getKeyword(java.lang.String k)

getKeywords

public java.util.Hashtable getKeywords()

setKeywords

public void setKeywords(java.util.Hashtable k)

removeLeaves

protected void removeLeaves()

Overrides:

removeLeaves in class FGroup

removeKeyword

public void removeKeyword(Keyword kd)

addFNode

public void addFNode(FNode o)

Description copied from class: FGroup

Abstract method that should specify how to add various FNode subclasses (such as Atoms, Residues and Polymers) to the FGroup

Specified by:

addFNode in class FGroup

destroy

public void destroy()

Overrides:

destroy in class FGroup

getBranchGroup

public javax.media.j3d.BranchGroup getBranchGroup()

getTransformGroup

public javax.media.j3d.TransformGroup getTransformGroup()

finalize

public void finalize(boolean finalizeGroups)

Description copied from class: FGroup

Abstact method that should specify how to finalize a FGroup

Specified by:

finalize in class FGroup

createLists

public void createLists()

switchView

public void switchView(int viewtype)

Overrides:

switchView in class FNode

setWireWidth

public void setWireWidth(float f)

isVisible

public boolean isVisible()

setEnergy

public void setEnergy(double e)

setTime

public void setTime(double t)

setTemperature

public void setTemperature(double t)

switchColor

public void switchColor(int colortype,
                        javax.vecmath.Color3f color,
                        javax.media.j3d.Material mat)

Overrides:

switchColor in class FGroup

toFFString

public java.lang.String toFFString()

toString

public java.lang.String toString()

Description copied from class: FGroup

Returns the Moieties name.

Overrides:

toString in class FGroup

toFileString

public java.lang.String toFileString()

createScene

public javax.media.j3d.BranchGroup createScene(boolean zero)

The FSystem Branchgroup has two TransformGroups between it and the "base" node where gemoetry is attached. If the point between the two transformations is where user rotation occurs. For example, if rotating about the center of mass of the system, the RotToCOM transformation will be an identity transformation (ie. none). If rotation is about some atom or group of atoms within the system, then the RotToCOM transformation will be a translation from that point to the COM.

Parameters:

zero - boolean

Returns:

BranchGroup

getWireFrame

public javax.media.j3d.Node getWireFrame()

createBox

public void createBox()

removeJ3D

public void removeJ3D()

rotateAbout

public void rotateAbout(javax.vecmath.Vector3d v)

Rotate about a point in given in the System's Local Coordinates

Parameters:

v - Vector3d

centerView

public void centerView(boolean rot,
                       boolean trans)

initAtoms

public void initAtoms(FNode f)

initAtoms

public void initAtoms(java.util.List f)

initBonds

public void initBonds(FNode f)

initBonds

public void initBonds(java.util.List f)

detach

public void detach()

getEnergy

public double getEnergy()

getExtent

public double getExtent()

centerFSystem

public void centerFSystem()

CenterAt

public void CenterAt(double[] d)

MoveCenter

public void MoveCenter(double[] d)

getBackBoneAtoms

public java.util.ArrayList getBackBoneAtoms()

getResidueList

public java.util.ArrayList getResidueList()

sidePolymerCOM

public void sidePolymerCOM()

getPolymer

public Polymer getPolymer(java.lang.String chainName,
                          boolean create)

getResidue

public Residue getResidue(java.lang.String chainName,
                          int resNum,
                          java.lang.String resName,
                          boolean create)

setLogFile

public void setLogFile(java.io.File f)

getLogFile

public java.io.File getLogFile()

setFile

public void setFile(java.io.File f)

getFile

public java.io.File getFile()

setKeyFile

public void setKeyFile(java.io.File f)

getKeyFile

public java.io.File getKeyFile()

setMMFilter

public void setMMFilter(MMFilter m)

setOffset

public void setOffset(javax.vecmath.Vector3d o)

getOffset

public javax.vecmath.Vector3d getOffset()

getMMFilter

public MMFilter getMMFilter()

getAtomList

public java.util.List getAtomList()

Description copied from class: FNode

Returns an ArrayList of all Atoms below the present FNode.

Overrides:

getAtomList in class FNode

getBondList

public java.util.List getBondList()

Description copied from class: FNode

Returns an ArrayList of all Bonds below the present FNode.

Overrides:

getBondList in class FNode

getMoleculeList

public java.util.List getMoleculeList()

getTemperature

public double getTemperature()

getTermList

public java.util.ArrayList getTermList()

Description copied from class: FNode

Returns an ArrayList of all Terms below the present FNode.

Overrides:

getTermList in class FNode

getTime

public double getTime()

getTrajectory

public Trajectory getTrajectory()

setTrajectory

public void setTrajectory(Trajectory t)

setStep

public void setStep(int s)

setAngle

public void setAngle(double[] a)

setBox

public void setBox(double[] b)

setClosing

public void setClosing(boolean b)

isSimulation

public boolean isSimulation()

isOptimization

public boolean isOptimization()

setSimulation

public void setSimulation(int type)

getTimeString

public java.lang.String getTimeString()

getStepString

public java.lang.String getStepString()

getEnergyString

public java.lang.String getEnergyString()

isClosing

public boolean isClosing()

setFileType

public void setFileType(byte ftype)

setForceField

public void setForceField(java.lang.String f)

getFileType

public byte getFileType()

addAltLocation

public void addAltLocation(java.lang.String s)

getAltLocations

public java.lang.String[] getAltLocations()

getChainNames

public java.lang.String[] getChainNames()

getParameterFile

public java.lang.String getParameterFile()

getAtomFromWireVertex

public Atom getAtomFromWireVertex(int i)

setCurrentCycle

public void setCurrentCycle(int c)

setVRML

public void setVRML(javax.media.j3d.BranchGroup v)

getCurrentCycle

public int getCurrentCycle()

setCycles

public void setCycles(int c)

getCycles

public int getCycles()