Class Joint

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.Joint

All Implemented Interfaces:

ROLS, Serializable, Cloneable, MutableTreeNode, TreeNode

public class Joint
extends MSNode

The Joint class contains the geometry produced by the FGroup Joiner method.

Since:

1.0

Author:

Michael J. Schnieders

See Also:

• Serialized Form

Field Summary

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
Joint()	Default Constructor
Joint(MSGroup group1, MSGroup group2, MSNode bondNode, MSNode angleNode, MSNode stretchBendNode, MSNode ureyBradleyNode, MSNode outOfPlaneNode, MSNode torsionNode, MSNode improperTorsionNode, MSNode stretchTorsionNode, MSNode angleTorsionNode, MSNode piOrbitalTorsionNode, MSNode torsionTorsionNode)	Constructs a Joint between Group 1 and Group 2.
Joint(String name)	Constructor for Joint.

Method Summary

Modifier and Type	Method	Description
void	merge(Joint j)	merge
void	setColor(RendererCache.ColorModel newColorModel)	setColor
void	setView(RendererCache.ViewModel newViewModel, List<org.jogamp.java3d.BranchGroup> newShapes)	setView
String	toString()

Methods inherited from class MSNode

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

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

Constructor Details

Joint

public Joint()

Default Constructor

Joint

public Joint(String name)

Constructor for Joint.

Parameters:

name - a String object.

Joint

public Joint(MSGroup group1,
 MSGroup group2,
 MSNode bondNode,
 MSNode angleNode,
 MSNode stretchBendNode,
 MSNode ureyBradleyNode,
 MSNode outOfPlaneNode,
 MSNode torsionNode,
 MSNode improperTorsionNode,
 MSNode stretchTorsionNode,
 MSNode angleTorsionNode,
 MSNode piOrbitalTorsionNode,
 MSNode torsionTorsionNode)

Constructs a Joint between Group 1 and Group 2.

Parameters:

group1 - a MSGroup object.

group2 - a MSGroup object.

bondNode - a MSNode object.

angleNode - a MSNode object.

stretchBendNode - a MSNode object.

ureyBradleyNode - a MSNode object.

outOfPlaneNode - a MSNode object.

torsionNode - a MSNode object.

improperTorsionNode - a MSNode object.

stretchTorsionNode - a MSNode object.

angleTorsionNode - a MSNode object.

piOrbitalTorsionNode - a MSNode object.

torsionTorsionNode - a MSNode object.

Method Details

merge

public void merge(Joint j)

merge

Parameters:

j - a Joint object.

setColor

public void setColor(RendererCache.ColorModel newColorModel)

setColor

Parameters:

newColorModel - a RendererCache.ColorModel object.

setView

public void setView(RendererCache.ViewModel newViewModel,
 List<org.jogamp.java3d.BranchGroup> newShapes)

setView

Specified by:

setView in interface ROLS

Overrides:

setView in class MSNode

Parameters:

newViewModel - a RendererCache.ViewModel object.

newShapes - a List object.

toString

public String toString()

Overridden toString method returns the MSNode's name

Overridden toString method returns: "Joint: m1 Name - m2 Name"

Overrides:

toString in class MSNode