ffe.lang
Class Bond

java.lang.Object
  javax.swing.tree.DefaultMutableTreeNode
      ffe.lang.FNode
          ffe.lang.Term
              ffe.lang.Bond

All Implemented Interfaces:

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

public final class Bond

extends Term

The Bond class represents a covalent bond formed between two atoms.

See Also:

Serialized Form

Nested Class Summary

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

Field Summary

static java.util.ArrayList

bondpool

Fields inherited from class ffe.lang.Term

atoms, s

Fields inherited from class ffe.lang.FNode

selected

Fields inherited from class javax.swing.tree.DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Constructor Summary

Bond(Atom a1, Atom a2, int ord)

Bond(java.lang.String n)
Simple Bond constructor that is intended to be used with the equals method

Method Summary

void	destroy()
boolean	formsAngleWith(Bond b) Check to see if this Bond and another combine to form an angle
java.util.List	getBondList() Returns an ArrayList of the Bonds that constitute this Term.
Atom	getCommonAtom(Bond b) Finds the common Atom between this Bond and Bond b
javax.media.j3d.Group	getJ3D1()
javax.media.j3d.Group	getJ3D2()
Atom	getOtherAtom(Atom a) Find the other Atom in this Bond
Atom	getOtherAtom(Bond b) Find the Atom the this Bond and Bond b don't have in common
boolean	initJ3D()
boolean	isVisible()
void	reInit(Atom a1, Atom a2, int ord)
boolean	sameGroup()
void	setAngleWith(Bond b) Specifies this Bond helps form an angle with the given Bond
void	setBondTransform3d(javax.media.j3d.Transform3D t3d, double[] pos, double[] orient, double len, boolean newRot)
void	setCylinderVisible(boolean v)
void	setWire(javax.media.j3d.LineArray l, int i)
void	setWireVisible(boolean v)
void	switchColor(Atom a)
void	switchView(int viewtype)
void	update() Update recomputes the bonds length

Methods inherited from class ffe.lang.Term

equals, getAtom, getAtomList, getBond, getID, getKey, getMM, getValue, print, setAtoms, setBonds, setID_Key, setID, setKey, setMM, setMM, setSelected, setValue, switchColor, toString

Methods inherited from class ffe.lang.FNode

drawLabel, findCenter, getFSystemNode, getList, getListIterator, getMoleculeNode, getMW, getName, getPolymerNode, getResidueNode, getTermList, isSelected, setName

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

bondpool

public static java.util.ArrayList bondpool

Constructor Detail

Bond

public Bond(Atom a1,
            Atom a2,
            int ord)

Bond

public Bond(java.lang.String n)

Simple Bond constructor that is intended to be used with the equals method

Parameters:

n - Bond id

Method Detail

destroy

public void destroy()

Overrides:

destroy in class Term

formsAngleWith

public boolean formsAngleWith(Bond b)

Check to see if this Bond and another combine to form an angle

Returns:

True if Bond b helps form an angle with this Bond

getBondList

public java.util.List getBondList()

Description copied from class: Term

Returns an ArrayList of the Bonds that constitute this Term.

Overrides:

getBondList in class Term

getCommonAtom

public Atom getCommonAtom(Bond b)

Finds the common Atom between this Bond and Bond b

Parameters:

b - Bond to compare with

Returns:

The Atom the Bonds have in common or Null if they are the same Bond or have no atom in common

getJ3D1

public javax.media.j3d.Group getJ3D1()

getJ3D2

public javax.media.j3d.Group getJ3D2()

getOtherAtom

public Atom getOtherAtom(Atom a)

Find the other Atom in this Bond

Parameters:

a - The known Atom

Returns:

The other Atom that makes up this bond, or Null if Atom a is not part of this bond

getOtherAtom

public Atom getOtherAtom(Bond b)

Find the Atom the this Bond and Bond b don't have in common

Parameters:

b - Bond to compare with

Returns:

The Atom that Bond b and this Bond do not have in common, or Null if they have no Atom in common

initJ3D

public boolean initJ3D()

reInit

public void reInit(Atom a1,
                   Atom a2,
                   int ord)

switchView

public void switchView(int viewtype)

Overrides:

switchView in class Term

switchColor

public void switchColor(Atom a)

update

public void update()

Update recomputes the bonds length

Specified by:

update in class Term

sameGroup

public boolean sameGroup()

setAngleWith

public void setAngleWith(Bond b)

Specifies this Bond helps form an angle with the given Bond

Parameters:

b - Bond that forms an angle with this Bond

setCylinderVisible

public void setCylinderVisible(boolean v)

setBondTransform3d

public void setBondTransform3d(javax.media.j3d.Transform3D t3d,
                               double[] pos,
                               double[] orient,
                               double len,
                               boolean newRot)

setWire

public void setWire(javax.media.j3d.LineArray l,
                    int i)

isVisible

public boolean isVisible()

setWireVisible

public void setWireVisible(boolean v)