scripps.vvm.graphics
Class TubeBackboneShape

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

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 TubeBackboneShape

extends VVM_RepShape

This does smooth backbone, elbowed backone, and the sharp bend backbone.

Field Summary

harmonic.mz.data.fields.IntField	elbowCircleEdges Number of circle edges per full circle of an elbow;
static int	ELBOWED
static int	LINES
harmonic.mz.data.fields.IntField	lineWidth Line width if lines are used
harmonic.mz.data.fields.IntField	pathDis Number of spline samples per residue
harmonic.mz.data.fields.ScalarField	radius Bend radius
harmonic.mz.data.TableNode	resProps Per element residue properties.
harmonic.mz.data.fields.IntField	sectionDis Number of faces around tube
static int	SHADED
static int	SHADED_AND_LINES
static int	SHARP
harmonic.mz.data.fields.BooleanField	sharpColors Whether to do a sharp color break half way between residues.
static int	SMOOTH
harmonic.mz.data.fields.IntField	smoothOrder Splining order (3 or 4)
harmonic.mz.data.fields.ExclusiveIntField	surface Shading or lines or both
static int	TRACE_C
static int	TRACE_CA
static int	TRACE_N
static int	TRACE_NCAC
static int	TRACE_P
harmonic.mz.data.fields.ExclusiveIntField	traceType Either SHARP or ELBOWED or SMOOTH

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

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

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

Method Summary

java.lang.String	areFieldsValid()
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.
boolean	isElementShowing(java.lang.Object res)
harmonic.mz.data.ModelNode	makePrototype()
Residue	residueAtPart(harmonic.viewer3D.PaintStruct p, int iPart, harmonic.meshGeom.math.Pnt3f pickedPoint) Used by the picking system.
void	setColor(TreeNodeSet set, harmonic.meshGeom.math.Clr3f clr) Set ribbon colors shown by this tube for given set
void	setColor(TreeNodeSet set, Scheme scheme) Set ribbon colors shown by this tube for given set
void	tubeTrace(harmonic.meshGeom.geom.Geom[] retgeoms, harmonic.meshGeom.geom.PolygonGeom pathGeom, float r, int dis, boolean faceColors, boolean bBigAngles)
void	validateGeometry()

Methods inherited from class scripps.vvm.graphics.VVM_RepShape

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

Methods inherited from class scripps.vvm.graphics.VVM_Shape

atomAtPart, bondAtPart

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

resProps

public harmonic.mz.data.TableNode resProps

Per element residue properties. Properties are:
ResidueColorProp

traceType

public harmonic.mz.data.fields.ExclusiveIntField traceType

Either SHARP or ELBOWED or SMOOTH

radius

public harmonic.mz.data.fields.ScalarField radius

Bend radius

smoothOrder

public harmonic.mz.data.fields.IntField smoothOrder

Splining order (3 or 4)

pathDis

public harmonic.mz.data.fields.IntField pathDis

Number of spline samples per residue

elbowCircleEdges

public harmonic.mz.data.fields.IntField elbowCircleEdges

Number of circle edges per full circle of an elbow;

sectionDis

public harmonic.mz.data.fields.IntField sectionDis

Number of faces around tube

sharpColors

public harmonic.mz.data.fields.BooleanField sharpColors

Whether to do a sharp color break half way between residues.

SHARP

public static final int SHARP

See Also:

Constant Field Values

ELBOWED

public static final int ELBOWED

See Also:

Constant Field Values

SMOOTH

public static final int SMOOTH

See Also:

Constant Field Values

TRACE_CA

public static final int TRACE_CA

See Also:

Constant Field Values

TRACE_C

public static final int TRACE_C

See Also:

Constant Field Values

TRACE_N

public static final int TRACE_N

See Also:

Constant Field Values

TRACE_P

public static final int TRACE_P

See Also:

Constant Field Values

TRACE_NCAC

public static final int TRACE_NCAC

See Also:

Constant Field Values

surface

public harmonic.mz.data.fields.ExclusiveIntField surface

Shading or lines or both

SHADED

public static final int SHADED

See Also:

Constant Field Values

LINES

public static final int LINES

See Also:

Constant Field Values

SHADED_AND_LINES

public static final int SHADED_AND_LINES

See Also:

Constant Field Values

lineWidth

public harmonic.mz.data.fields.IntField lineWidth

Line width if lines are used

Constructor Detail

TubeBackboneShape

public TubeBackboneShape(Molecule mol)

Constructs a TubeBackboneShape without adding it to database. No residues are shown be default.

TubeBackboneShape

public TubeBackboneShape()

Constructs a TubeBackboneShape without adding it to database. No residues are shown be default.

Method Detail

setColor

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

Set ribbon colors shown by this tube for given set

setColor

public void setColor(TreeNodeSet set,
                     Scheme scheme)

Set ribbon colors shown by this tube for given set

makePrototype

public harmonic.mz.data.ModelNode makePrototype()

Overrides:

makePrototype in class harmonic.mz.data.ModelNode

areFieldsValid

public java.lang.String areFieldsValid()

Overrides:

areFieldsValid in class harmonic.mz.data.ModelNode

fullInvalidate

public void fullInvalidate()

Overrides:

fullInvalidate in class VVM_RepShape

atomChanged

public void atomChanged(AtomEvent event)

Specified by:

atomChanged in interface AtomListener

Overrides:

atomChanged in class VVM_RepShape

validateGeometry

public void validateGeometry()

Overrides:

validateGeometry in class harmonic.mz.data.ShapeNode

tubeTrace

public void tubeTrace(harmonic.meshGeom.geom.Geom[] retgeoms,
                      harmonic.meshGeom.geom.PolygonGeom pathGeom,
                      float r,
                      int dis,
                      boolean faceColors,
                      boolean bBigAngles)

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

residueAtPart

public Residue residueAtPart(harmonic.viewer3D.PaintStruct p,
                             int iPart,
                             harmonic.meshGeom.math.Pnt3f pickedPoint)

Description copied from class: VVM_Shape

Used by the picking system. Return residue reference or null

Overrides:

residueAtPart in class VVM_Shape

isElementShowing

public boolean isElementShowing(java.lang.Object res)

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