scripps.mol_data
Class Molecule

java.lang.Object
  |
  +--harmonic.mz.data.ModelNode
        |
        +--harmonic.mz.data.ShapeGroup
              |
              +--scripps.mol_data.Molecule
All Implemented Interfaces:
java.awt.event.ActionListener, harmonic.mz.data.DataNode, harmonic.mz.gui.Documentable, java.util.EventListener, harmonic.mz.data.Interpolater, harmonic.meshGeom.math.MarkableObject, harmonic.mz.event.NodeListener, harmonic.mz.data.Transformable
Direct Known Subclasses:
Protein

public class Molecule
extends harmonic.mz.data.ShapeGroup


Field Summary
 java.lang.String filename
           
 
Fields inherited from class harmonic.mz.data.ShapeGroup
coordSystem, localKludge
 
Fields inherited from class harmonic.mz.data.ModelNode
_fileRoot_, _thread_, ATTRIB_CONTROL_WIDGET, ATTRIB_LISTABLE, ATTRIB_PRESENTABLE, ATTRIB_PRIVATE, ATTRIB_REMOVEABLE, ATTRIB_RENAMEABLE, ATTRIB_SHOW_CONTEXT_MENU, ATTRIB_TYPE_FILTER, ATTRIB_USERGROUP, ATTRIB_VALUE_GROUP, ATTRIB_VE_LISTENER, bCustomCS, bDebug, bValid, name
 
Constructor Summary
Molecule()
           
Molecule(java.lang.String name)
           
 
Method Summary
 void addAtomListener(AtomListener al)
           
 int expectedValidationTime()
           
 Atom findAtom(java.lang.String name)
           
 java.util.Vector getAtoms()
           
 java.util.Vector getBonds()
           
 void purgeFinal()
           
 void removeAtomListener(AtomListener al)
           
 
Methods inherited from class harmonic.mz.data.ShapeGroup
beginTransform, endTransform, getCoordSystem, getMoveableCoordSystem, getTransformable, hasFixedCS, scaleCoordSystem, translateCoordSystem
 
Methods inherited from class harmonic.mz.data.ModelNode
actionPerformed, addAll, addAlphaed, addField, addField, addField, addFields, addNetworkInput, addNetworkOutput, addNode, addNodeListener, addNodeListener, addNodes, addNodes, addToCurrent, addToGlobals, addToNetworkEditor, addToTemps, addWithUndo, allFieldsAreFinal, applyDataTransfer, areFieldsValid, assignFromMetaFields, assignFromXMLAttributes, assignFromXMLString, assignToMetaFields, assignToXMLAttributes, assignToXMLString, at, bind, canSelect, castSelection, checkFileRead, checkNetworkInput, childCount, clean, clearAttrib, clearNotified, compare, copyFrom, createControlWidget, createCopy, createXMLElement, deepCopy, defeatNodeEvents, disableEvents, enableEvents, fileRoot, finalize, findFieldElement, findNode, fromXMLNodes, getAttrib, getBound, getCatagory, getControlWidget, getCurrentNames, getDataTransfer, getDataTransferTypes, getDeleted, getDirectInputs, getDirectOutputs, getEffectors, getEntryListener, getErrorState, getFilterType, getFullName, getHandles, getInstanceURL, getInterpolater, getIsLeaf, getListable, getMark, getMetaFields, getName, getNodeChildren_V, getNodeChildren, getNodeID, getNodeParent, getObjectRep, getPresentable, getPrivate, getReferencePoolName, getRemoteOwner, getRemoveable, getRenameable, getSaveable, getSavedChildren, getSelect, getSeparateDirectInputs, getSeparateDirectOutputs, getSequenced, getSerialNo, getTags, getTentativeSelect, getTransformableParent, getTransient, getTreeName, getTypeImage, getTypeURL, getUnfoldedChildren, getUpdateTime, getUserGroup, getValidates, getValue, getXMLNodes, hasDependants, hasExternalRef, hashKey, hasValidationLock, hideControlWidget, indexOf, initControlWidget, insertNode, interpolate_Linear, interpolate_Quadratic, invalidate, isField, isFinal, isInSubtree, isInTree, isLinked, isNotified, isPurged, isSet, isTemporary, isValid, linkedTo, linksChildren, makeContextMenu, makeFixed, makePrototype, makeReferenced, makeUnreferenced, makeVisibleInGUI, markNotified, mayValidate, nodeChanged, notifyListeners, postAssignFromXMLElement, preAssignToXMLElement, printChildren, printTags, printTree, printTree, purge, pythonString, remove, removeAll, removeAll, removeHandles, removeNetworkInput, removeNetworkOutput, removeNode, removeNode, removeNode, removeNodeListener, replace, selfNodeChanged, set, setActualName, setAttrib, setBound, setCatagory, setChildrenExcept, setCoordSystem, setCurrentControlWidget, setCurrentNames, setDeleted, setEntryListener, setErrorState, setFromPrototype, setIsField, setIsLeaf, setIsSet, setListable, setMark, setMetaFields, setName, setNodeParent, setPresentable, setPrivate, setRemoteOwner, setRemoveable, setRenameable, setSaveable, setSelect, setSelect, setSequenced, setSerialNo, setTentativeSelect, setTentativeSelect, setToLink, setTransient, setTransientChildren, setUpdateTime, setUserGroup, setValidates, setValidationLock, setValue, setValueGroup, showControlWidget, showControlWidget, showControlWidget, showHandles, startRename, tag, toString, unlinkListeners, unmarkNotified, untag, updateBindable, valChanged, valChanged, validate, valueString
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

filename

public java.lang.String filename
Constructor Detail

Molecule

public Molecule()

Molecule

public Molecule(java.lang.String name)
Method Detail

purgeFinal

public void purgeFinal()
Specified by:
purgeFinal in interface harmonic.mz.data.DataNode
Overrides:
purgeFinal in class harmonic.mz.data.ShapeGroup

getAtoms

public java.util.Vector getAtoms()

getBonds

public java.util.Vector getBonds()

expectedValidationTime

public int expectedValidationTime()
Overrides:
expectedValidationTime in class harmonic.mz.data.ModelNode

addAtomListener

public void addAtomListener(AtomListener al)

removeAtomListener

public void removeAtomListener(AtomListener al)

findAtom

public Atom findAtom(java.lang.String name)