scripps.vvm.graphics
Class MolSurfaceShape

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

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 MolSurfaceShape

extends VVM_RepShape

This is the solvent accessable surface representation of a molecule. This uses the famous MSMS program to calculate

Field Summary

harmonic.mz.data.fields.ScalarField	atomOffset Offset factor for atom size
harmonic.mz.data.TableNode	atomProps Holdes the per-element atom properties.
harmonic.mz.data.fields.ScalarField	atomScale Scale factor for atom size
boolean	bSurfaceValid
harmonic.mz.data.fields.ScalarField	probeRadius Size of imaginary solvent molecule used in generating surface
harmonic.mz.data.fields.BooleanField	vertexColors This can be used to defeat vertex coloring if needed
harmonic.mz.data.fields.ScalarField	vertexDensity Density of verticies on generated surface

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

MolSurfaceShape()
Constructs a MolSurfaceShape

MolSurfaceShape(Molecule mol)
Constructs a MolSurfaceShape

Method Summary

java.lang.String	areFieldsValid()
Atom	atomAtPart(harmonic.viewer3D.PaintStruct p, int itri, harmonic.meshGeom.math.Pnt3f pickedPoint) Used by the picking system.
void	atomChanged(AtomEvent event)
harmonic.meshGeom.geom.IndexedTriangleArrayGeom	createSurface()
harmonic.meshGeom.geom.Geom	fastGeometry(harmonic.meshGeom.geom.ArrayGeom geom)
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 surface for the given set
void	setAtomColor(TreeNodeSet set, Scheme scheme) Set atom color shown by this surface for the given set
void	setAtomInclusion(TreeNodeSet set, boolean bShow) Set atom inclusion shown by this surface for the given set
void	setAtomInclusion(TreeNodeSet set, Scheme scheme) Set atom inclusion shown by this surface for the given set
void	setAtomRadius(TreeNodeSet set, float radius) Set atom radius shown by this surface for the given set
void	setAtomRadius(TreeNodeSet set, Scheme scheme) Set atom radius shown by this surface for the given set
boolean	shouldSpawnThread()
void	validateAttribs()
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, show, show, transferAttributes, transferAttributes, transform, transformFields, translateCoordSystem, validate, 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

Holdes the per-element atom properties. Properties include:
IncludeAtomProp AtomColorProp AtomRadiusProp

vertexColors

public harmonic.mz.data.fields.BooleanField vertexColors

This can be used to defeat vertex coloring if needed

vertexDensity

public harmonic.mz.data.fields.ScalarField vertexDensity

Density of verticies on generated surface

probeRadius

public harmonic.mz.data.fields.ScalarField probeRadius

Size of imaginary solvent molecule used in generating surface

atomScale

public harmonic.mz.data.fields.ScalarField atomScale

Scale factor for atom size

atomOffset

public harmonic.mz.data.fields.ScalarField atomOffset

Offset factor for atom size

bSurfaceValid

public boolean bSurfaceValid

Constructor Detail

MolSurfaceShape

public MolSurfaceShape(Molecule mol)

Constructs a MolSurfaceShape

MolSurfaceShape

public MolSurfaceShape()

Constructs a MolSurfaceShape

Method Detail

setAtomInclusion

public void setAtomInclusion(TreeNodeSet set,
                             boolean bShow)

Set atom inclusion shown by this surface for the given set

setAtomInclusion

public void setAtomInclusion(TreeNodeSet set,
                             Scheme scheme)

Set atom inclusion shown by this surface for the given set

setAtomColor

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

Set atom color shown by this surface for the given set

setAtomColor

public void setAtomColor(TreeNodeSet set,
                         Scheme scheme)

Set atom color shown by this surface for the given set

setAtomRadius

public void setAtomRadius(TreeNodeSet set,
                          float radius)

Set atom radius shown by this surface for the given set

setAtomRadius

public void setAtomRadius(TreeNodeSet set,
                          Scheme scheme)

Set atom radius shown by this surface for the given set

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

areFieldsValid

public java.lang.String areFieldsValid()

Overrides:

areFieldsValid in class harmonic.mz.data.ModelNode

shouldSpawnThread

public boolean shouldSpawnThread()

Overrides:

shouldSpawnThread in class harmonic.mz.data.ShapeNode

validateAttribs

public void validateAttribs()

Overrides:

validateAttribs in class harmonic.mz.data.ShapeNode

validateGeometry

public void validateGeometry()

Overrides:

validateGeometry in class harmonic.mz.data.ShapeNode

fastGeometry

public harmonic.meshGeom.geom.Geom fastGeometry(harmonic.meshGeom.geom.ArrayGeom geom)

createSurface

public harmonic.meshGeom.geom.IndexedTriangleArrayGeom createSurface()

atomAtPart

public Atom atomAtPart(harmonic.viewer3D.PaintStruct p,
                       int itri,
                       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