scripps.vvm.graphics
Class RibbonBackboneShape

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

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 RibbonBackboneShape

extends VVM_RepShape

Field Summary

harmonic.mz.data.fields.ScalarField	arrowMajorSize Thickest arrow width
harmonic.mz.data.fields.BooleanField	arrows Whether to add arrows to strands or not
harmonic.mz.data.fields.BooleanField	circularTurns Whether turns and loops are square
harmonic.mz.data.fields.BooleanField	fancyHelix If true helix is colored differently on its sides and inner and outer flat
harmonic.mz.data.fields.BooleanField	fancyStrand If true strand is colored differently on its sides and inner and outer flat
harmonic.mz.data.fields.ColorField	helixInsideColor Color for helix inside flat, blended with residue color, if fanceHelix is true
harmonic.mz.data.fields.ColorField	helixOutsideColor Color for helix outside flat, blended with residue color, if fanceHelix is true
harmonic.mz.data.fields.ColorField	helixSideColor Color for helix side, blended with residue color, if fanceHelix is true
static int	LINES
harmonic.mz.data.fields.IntField	lineWidth Line width if lines are used
harmonic.mz.data.fields.IntField	polygonization Number of smoothing (splining) samples per residue
harmonic.mz.data.fields.ScalarField	resColorBlend Amount of residue color vs front/back color
harmonic.mz.data.TableNode	resProps Per element residue props.
static int	SHADED
static int	SHADED_AND_LINES
harmonic.mz.data.fields.BooleanField	sharpColors Whether to do a sharp color break half way between residues.
harmonic.mz.data.fields.ColorField	strandBottomColor Color for strand top bottom, blended with residue color, if fanceStrand is true
harmonic.mz.data.fields.ColorField	strandSideColor Color for strand side, blended with residue color, if fanceStrand is true
harmonic.mz.data.fields.ColorField	strandTopColor Color for strand top flat, blended with residue color, if fanceStrand is true
harmonic.mz.data.fields.ExclusiveIntField	surface Shading or lines or both
harmonic.mz.data.fields.IntField	tubeDis Number of faces around a tube
harmonic.mz.data.fields.BooleanField	vertexColors May be used to defeat vertex coloring

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

RibbonBackboneShape()
Constructs an RibbonBackboneShape, without adding it to database.

RibbonBackboneShape(Molecule mol)
Constructs an RibbonBackboneShape, 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.
int	getSSType(Residue res)
boolean	isElementShowing(java.lang.Object res)
harmonic.mz.data.ModelNode	makePrototype()
void	nodeChanged(harmonic.mz.event.NodeEvent event)
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 ribbon for given set
void	setColor(TreeNodeSet set, Scheme scheme) Set ribbon colors shown by this ribbon for given set
void	setHelixThickness(TreeNodeSet set, float t) Sets helix thickness shown by this ribbon for given set
void	setHelixThickness(TreeNodeSet set, Scheme scheme) Sets helix thickness shown by this ribbon for given set
void	setHelixWidth(TreeNodeSet set, float t) Sets helix width shown by this ribbon for given set
void	setHelixWidth(TreeNodeSet set, Scheme scheme) Sets helix width shown by this ribbon for given set
void	setSSType(TreeNodeSet set, int type) Sets the secondary structure type shown by this ribbon for given set
void	setSSType(TreeNodeSet set, Scheme scheme) Sets the secondary structure type shown by this ribbon for given set
void	setStrandThickness(TreeNodeSet set, float t) Sets strand thickness shown by this ribbon for given set
void	setStrandThickness(TreeNodeSet set, Scheme scheme) Sets strand thickness shown by this ribbon for given set
void	setStrandWidth(TreeNodeSet set, Scheme scheme) Sets strand width shown by this ribbon for 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

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 props. Properties are:
ResidueColorProp: color of residue. it is smoothed with the adjacent residue colors ResidueSSProp: secondary structure type of residue TraceThicknessProp("Helix Width"): width of helix if is a helix, smoothed with adjacent residues TraceThicknessProp("Helix Thickness"): thickness of helix if is a helix, smoothed with adjacent residues TraceThicknessProp("Strand Width"): width of sheet strand if is strand , smoothed with adjacent residues TraceThicknessProp("Strand Thickness"): width of sheet strand if is a strand, smoothed with adjacent residues TraceThicknessProp("Tube Thickness"): thickness of tube if is a turn or loop, smoothed with adjacent residues

polygonization

public harmonic.mz.data.fields.IntField polygonization

Number of smoothing (splining) samples per residue

tubeDis

public harmonic.mz.data.fields.IntField tubeDis

Number of faces around a tube

vertexColors

public harmonic.mz.data.fields.BooleanField vertexColors

May be used to defeat vertex coloring

fancyHelix

public harmonic.mz.data.fields.BooleanField fancyHelix

If true helix is colored differently on its sides and inner and outer flat

fancyStrand

public harmonic.mz.data.fields.BooleanField fancyStrand

If true strand is colored differently on its sides and inner and outer flat

helixInsideColor

public harmonic.mz.data.fields.ColorField helixInsideColor

Color for helix inside flat, blended with residue color, if fanceHelix is true

helixOutsideColor

public harmonic.mz.data.fields.ColorField helixOutsideColor

Color for helix outside flat, blended with residue color, if fanceHelix is true

helixSideColor

public harmonic.mz.data.fields.ColorField helixSideColor

Color for helix side, blended with residue color, if fanceHelix is true

strandTopColor

public harmonic.mz.data.fields.ColorField strandTopColor

Color for strand top flat, blended with residue color, if fanceStrand is true

strandBottomColor

public harmonic.mz.data.fields.ColorField strandBottomColor

Color for strand top bottom, blended with residue color, if fanceStrand is true

strandSideColor

public harmonic.mz.data.fields.ColorField strandSideColor

Color for strand side, blended with residue color, if fanceStrand is true

arrows

public harmonic.mz.data.fields.BooleanField arrows

Whether to add arrows to strands or not

circularTurns

public harmonic.mz.data.fields.BooleanField circularTurns

Whether turns and loops are square

arrowMajorSize

public harmonic.mz.data.fields.ScalarField arrowMajorSize

Thickest arrow width

resColorBlend

public harmonic.mz.data.fields.ScalarField resColorBlend

Amount of residue color vs front/back color

sharpColors

public harmonic.mz.data.fields.BooleanField sharpColors

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

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

RibbonBackboneShape

public RibbonBackboneShape(Molecule mol)

Constructs an RibbonBackboneShape, without adding it to database.

RibbonBackboneShape

public RibbonBackboneShape()

Constructs an RibbonBackboneShape, without adding it to database. No residues are shown by default.

Method Detail

setColor

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

Set ribbon colors shown by this ribbon for given set

setColor

public void setColor(TreeNodeSet set,
                     Scheme scheme)

Set ribbon colors shown by this ribbon for given set

setSSType

public void setSSType(TreeNodeSet set,
                      int type)

Sets the secondary structure type shown by this ribbon for given set

setSSType

public void setSSType(TreeNodeSet set,
                      Scheme scheme)

Sets the secondary structure type shown by this ribbon for given set

setHelixWidth

public void setHelixWidth(TreeNodeSet set,
                          float t)

Sets helix width shown by this ribbon for given set

setHelixWidth

public void setHelixWidth(TreeNodeSet set,
                          Scheme scheme)

Sets helix width shown by this ribbon for given set

setHelixThickness

public void setHelixThickness(TreeNodeSet set,
                              float t)

Sets helix thickness shown by this ribbon for given set

setHelixThickness

public void setHelixThickness(TreeNodeSet set,
                              Scheme scheme)

Sets helix thickness shown by this ribbon for given set

setStrandWidth

public void setStrandWidth(TreeNodeSet set,
                           Scheme scheme)

Sets strand width shown by this ribbon for given set

setStrandThickness

public void setStrandThickness(TreeNodeSet set,
                               float t)

Sets strand thickness shown by this ribbon for given set

setStrandThickness

public void setStrandThickness(TreeNodeSet set,
                               Scheme scheme)

Sets strand thickness shown by this ribbon for given set

areFieldsValid

public java.lang.String areFieldsValid()

Overrides:

areFieldsValid 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

makePrototype

public harmonic.mz.data.ModelNode makePrototype()

Overrides:

makePrototype in class harmonic.mz.data.ModelNode

getSSType

public int getSSType(Residue res)

fullInvalidate

public void fullInvalidate()

Overrides:

fullInvalidate in class VVM_RepShape

validateGeometry

public void validateGeometry()

Overrides:

validateGeometry in class harmonic.mz.data.ShapeNode

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

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

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