scripps.vvm.graphics
Class CPKShape

java.lang.Object
  |
  +--harmonic.mz.data.ModelNode
        |
        +--harmonic.mz.data.ShapeNode
              |
              +--scripps.vvm.graphics.VVM_Shape
                    |
                    +--scripps.vvm.graphics.VVM_RepShape
                          |
                          +--scripps.vvm.graphics.CPKShape

All Implemented Interfaces:

java.awt.event.ActionListener, AtomListener, harmonic.mz.data.DataNode, harmonic.mz.gui.Documentable, java.util.EventListener, harmonic.mz.data.Interpolater, harmonic.meshGeom.math.MarkableObject, harmonic.mz.event.NodeListener, harmonic.viewer3D.ShapeOwner, harmonic.mz.data.Transformable

public class CPKShape

extends VVM_RepShape

This represends a set of atoms with spheres.

Field Summary

harmonic.mz.data.TableNode	atomProps Per element atom properties.
harmonic.mz.data.fields.IntField	maxBalls Maximum balls to alow
harmonic.mz.data.fields.IntField	sphereDis Fineness of sphere shapes

Fields inherited from class scripps.vvm.graphics.VVM_RepShape

molField, type

Fields inherited from class harmonic.mz.data.ShapeNode

ANY_GEOM, ARRAY_GEOM, ATTRIBUTE_FIELD_TYPE, bAssignMaterialColors, bAttribsValid, bBaseGeometryValid, bSelectionValid, bTSelectionValid, bVisibilityValid, coordSystem, COORDSYSTEM_FIELD_TYPE, existingPainters, fastPainters, GEOMETRY_FIELD_TYPE, LINES_GEOM, localKludge, material, painters, POINT_GEOM, POLYGON_GEOM, REGION_GEOM, SOLID_GEOM, SURFACE_GEOM, transparency, visibility

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

CPKShape()
Constructs a CPKShape without adding it to database.

CPKShape(Molecule mol)
Constructs a CPKShape without adding it to database.

Method Summary

java.lang.String	areFieldsValid()
Atom	atomAtPart(harmonic.viewer3D.PaintStruct p, int iPart, harmonic.meshGeom.math.Pnt3f pickedPoint) Used by the picking system.
void	atomChanged(AtomEvent event)
void	fullInvalidate()
java.lang.String[]	getDomains() Return a list of domains used by this class
harmonic.mz.data.TableNode	getElementDataTable(java.lang.String domainType) Like getElementProps() except return the ElementListNode object at the domain
java.util.Vector	getElementProps(java.lang.String domainType) Return vector of meta data objects for the domain.
harmonic.mz.data.ModelNode	makePrototype()
void	nodeChanged(harmonic.mz.event.NodeEvent event)
void	setAtomColor(TreeNodeSet set, harmonic.meshGeom.math.Clr3f clr) Set atom color shown by this CPK for the given set
void	setAtomColor(TreeNodeSet set, Scheme scheme) Set atom color shown by this CPK for the given set
void	setAtomRadius(TreeNodeSet set, float radius) Set atom radius shown by this CPK for the given set
void	setAtomRadius(TreeNodeSet set, Scheme scheme) Set atom radius shown by this CPK for the given set
void	setAtomShape(TreeNodeSet set, int shape) Set atom shape shown by this CPK for the given set
void	setAtomShape(TreeNodeSet set, Scheme scheme) Set atom shape shown by this CPK for the given set
void	validateGeometry()

Methods inherited from class scripps.vvm.graphics.VVM_RepShape

defineTable, expectedValidationTime, getMol, prop, purge, selfNodeChanged, setDefaultProps, setMol, validateMol

Methods inherited from class scripps.vvm.graphics.VVM_Shape

bondAtPart, residueAtPart

Methods inherited from class harmonic.mz.data.ShapeNode

addFastGeometry, addFastGeometry, addFastGeometry, addFastGeometry, addFastPainter, addGeometry, addGeometry, addGeometry, addGeometry, addNetworkOutput, addPainter, addWithUndo, beginTransform, bigValidation, calcGeometricProps, calcSurfaceArea, calcVolume, checkRequirements, clearFastGeometries, clearFastPainters, clearGeometries, clearGeometryCache, clearPainters, defaultPickPriority, endTransform, fastPainterCount, findPointSnaps, getCachedGeometries, getCachedGeometry, getChildRequirements, getCoordSystem, getDataTransfer, getDataTransferTypes, getDragable, getEdges, getFastPainter, getFastPainters, getFitable, getGDIEdges, getGeom, getGeom, getGeomAt, getGeoms, getGeoms, getGeoms, getGlobalPerLocal, getILAEdges, getMoveableCoordSystem, getObjectChildren, getPainter, getPainter, getPainters, getPainters, getPainters, getPaintOnTransient, getPickable, getPointSnaps, getRequirements, getSerializeGeometry, getShapeDefOwner, getTransformable, getTypeImage, getViewpointDependantGeometry, getVisibility, hasFixedCS, hasGeometryLock, hide, hide, invalidate, invalidateAttribs, invalidateCoordSystem, invalidateGeometry, invalidateGeometryDependants, isAttribsValid, isGeomComposite, isGeometryValid, isSelectionValid, isTentativeSelectionValid, isVisibilityValid, makeContextMenu_ShapeFns, makeContextMenu, painterCount, processMouseDragged, processMouseEntered, processMouseExited, processMouseMoved, processMousePressed, processMouseReleased, purgeFinal, removeFastPainter, removePainter, scaleCoordSystem, setDragable, setExclusiveVisibility, setFieldCoordSystems, setFitable, setMoveableCoordSystem, setPaintOnTransient, setPickable, setPickPriority, setSelect, setSerializeGeometry, setTempVisibility, setTentativeSelect, setTransform, setTransient, setViewpointDependantGeometry, setVisibility, shouldSpawnThread, show, show, transferAttributes, transferAttributes, transform, transformFields, translateCoordSystem, validate, validateAttribs, validateSelection, validateTransform

Methods inherited from class harmonic.mz.data.ModelNode

actionPerformed, addAll, addAlphaed, addField, addField, addField, addFields, addNetworkInput, addNode, addNodeListener, addNodeListener, addNodes, addNodes, addToCurrent, addToGlobals, addToNetworkEditor, addToTemps, allFieldsAreFinal, applyDataTransfer, 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, 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, getTypeURL, getUnfoldedChildren, getUpdateTime, getUserGroup, getValidates, getValue, getXMLNodes, hasDependants, hasExternalRef, hashKey, hasValidationLock, hideControlWidget, indexOf, initControlWidget, insertNode, interpolate_Linear, interpolate_Quadratic, isField, isFinal, isInSubtree, isInTree, isLinked, isNotified, isPurged, isSet, isTemporary, isValid, linkedTo, linksChildren, makeFixed, makeReferenced, makeUnreferenced, makeVisibleInGUI, markNotified, mayValidate, notifyListeners, postAssignFromXMLElement, preAssignToXMLElement, printChildren, printTags, printTree, printTree, pythonString, remove, removeAll, removeAll, removeHandles, removeNetworkInput, removeNetworkOutput, removeNode, removeNode, removeNode, removeNodeListener, replace, 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, setSequenced, setSerialNo, setTentativeSelect, setToLink, setTransientChildren, setUpdateTime, setUserGroup, setValidates, setValidationLock, setValue, setValueGroup, showControlWidget, showControlWidget, showControlWidget, showHandles, startRename, tag, toString, unlinkListeners, unmarkNotified, untag, updateBindable, valChanged, valChanged, valueString

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

atomProps

public harmonic.mz.data.TableNode atomProps

Per element atom properties. These properties include: AtomColorProp AtomRadiusProp AtomShapeProp

maxBalls

public harmonic.mz.data.fields.IntField maxBalls

Maximum balls to alow

sphereDis

public harmonic.mz.data.fields.IntField sphereDis

Fineness of sphere shapes

Constructor Detail

CPKShape

public CPKShape(Molecule mol)

Constructs a CPKShape without adding it to database.

CPKShape

public CPKShape()

Constructs a CPKShape without adding it to database. The super classes 'mol' field needs to be set to a loaded Molecule. No atoms are shown by default.

Method Detail

setAtomColor

public void setAtomColor(TreeNodeSet set,
                         harmonic.meshGeom.math.Clr3f clr)

Set atom color shown by this CPK for the given set

setAtomColor

public void setAtomColor(TreeNodeSet set,
                         Scheme scheme)

Set atom color shown by this CPK for the given set

setAtomRadius

public void setAtomRadius(TreeNodeSet set,
                          float radius)

Set atom radius shown by this CPK for the given set

setAtomRadius

public void setAtomRadius(TreeNodeSet set,
                          Scheme scheme)

Set atom radius shown by this CPK for the given set

setAtomShape

public void setAtomShape(TreeNodeSet set,
                         int shape)

Set atom shape shown by this CPK for the given set

setAtomShape

public void setAtomShape(TreeNodeSet set,
                         Scheme scheme)

Set atom shape shown by this CPK for the given set

areFieldsValid

public java.lang.String areFieldsValid()

Overrides:

areFieldsValid in class harmonic.mz.data.ModelNode

makePrototype

public harmonic.mz.data.ModelNode makePrototype()

Overrides:

makePrototype in class harmonic.mz.data.ModelNode

nodeChanged

public void nodeChanged(harmonic.mz.event.NodeEvent event)

Specified by:

nodeChanged in interface harmonic.mz.event.NodeListener

Overrides:

nodeChanged in class VVM_RepShape

atomChanged

public void atomChanged(AtomEvent event)

Specified by:

atomChanged in interface AtomListener

Overrides:

atomChanged in class VVM_RepShape

fullInvalidate

public void fullInvalidate()

Overrides:

fullInvalidate in class VVM_RepShape

validateGeometry

public void validateGeometry()

Overrides:

validateGeometry in class harmonic.mz.data.ShapeNode

atomAtPart

public Atom atomAtPart(harmonic.viewer3D.PaintStruct p,
                       int iPart,
                       harmonic.meshGeom.math.Pnt3f pickedPoint)

Description copied from class: VVM_Shape

Used by the picking system. Return atom reference or null

Overrides:

atomAtPart in class VVM_Shape

getDomains

public java.lang.String[] getDomains()

Description copied from class: VVM_RepShape

Return a list of domains used by this class

Overrides:

getDomains in class VVM_RepShape

getElementProps

public java.util.Vector getElementProps(java.lang.String domainType)

Description copied from class: VVM_RepShape

Return vector of meta data objects for the domain. The meta data objects are sub classes of the ElementProperty class

Overrides:

getElementProps in class VVM_RepShape

getElementDataTable

public harmonic.mz.data.TableNode getElementDataTable(java.lang.String domainType)

Description copied from class: VVM_RepShape

Like getElementProps() except return the ElementListNode object at the domain

Overrides:

getElementDataTable in class VVM_RepShape