ffe.lang
Class Molecule

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

All Implemented Interfaces:

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

public class Molecule

extends FGroup

The Molecule class is a general container used for simple compounds or in cases where more specialized classes have not been implemented.

See Also:

Serialized Form

Nested Class Summary

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

Field Summary

Fields inherited from class ffe.lang.FNode

selected

Fields inherited from class javax.swing.tree.DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Constructor Summary

Molecule()

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

Method Summary

void	addFNode(FNode o) Allows adding Atom FNodes to the Molecule.
void	finalize(boolean finalizeGeometry) Abstact method that should specify how to finalize a FGroup

Methods inherited from class ffe.lang.FGroup

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

Methods inherited from class ffe.lang.FNode

drawLabel, equals, getAtomList, getBondList, getFSystemNode, getList, getListIterator, getMoleculeNode, getMW, getName, getPolymerNode, getResidueNode, getTermList, isSelected, setName, setSelected, switchView

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

Constructor Detail

Molecule

public Molecule()

Molecule

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

Method Detail

addFNode

public void addFNode(FNode o)

Allows adding Atom FNodes to the Molecule.

Specified by:

addFNode in class FGroup

finalize

public void finalize(boolean finalizeGeometry)

Description copied from class: FGroup

Abstact method that should specify how to finalize a FGroup

Specified by:

finalize in class FGroup