SBMStructuralModelNodePseudoAtom Class Reference

This class describes a pseudo-atom in a structural model.

Constructors and destructors
	SBMStructuralModelNodePseudoAtom ()
	Builds a pseudo-atom (default position = (0,0,0))
	SBMStructuralModelNodePseudoAtom (const SBQuantity::length &x, const SBQuantity::length &y, const SBQuantity::length &z)
	Builds a pseudo-atom at position = (x,y,z)
	SBMStructuralModelNodePseudoAtom (SBPosition3 const &p)
	Builds a pseudo-atom at position p.
virtual	~SBMStructuralModelNodePseudoAtom ()

Serialization
bool	isSerializable () const
	Returns true.
virtual void	serialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0)) const
	Serializes the node.
virtual void	unserialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0))
	Unserializes the node.

Identity
virtual SBDDataGraphNode::Type	getType () const
	Returns the type of the data graph node.

Debugging
virtual void	print (unsigned int offset=0) const
	Prints debugging information.

Additional Inherited Members
Public Types inherited from SBDDataGraphNode
enum	RenderingPass {   RenderingPass::Setup,   RenderingPass::OpaqueGeometry,   RenderingPass::SelectableGeometry,   RenderingPass::ShadowingGeometry,   RenderingPass::TransparentGeometry,   RenderingPass::Interface,   RenderingPass::Text }
	The rendering pass. More...
enum	Type {   Undefined,   StructuralModel,   StructuralModelNode,   StructuralModelConformation,   Conformation,   StructuralModelPath,   Path,   StructuralModelNodeGroup,   StructuralGroup,   StructuralModelNodeRoot,   Root,   StructuralModelNodeParticle,   StructuralParticle,   StructuralModelNodeAtom,   Atom,   StructuralModelNodePseudoAtom,   PseudoAtom,   StructuralModelNodeBond,   Bond,   StructuralModelNodePseudoBond,   PseudoBond,   StructuralModelNodeHydrogenBond,   HydrogenBond,   StructuralModelNodeHydrogenBondGroup,   HydrogenBondGroup,   StructuralModelNodeResidue,   Residue,   StructuralModelNodeSegment,   Segment,   StructuralModelNodeProtein,   Protein,   StructuralModelNodeChain,   Chain,   StructuralModelNodeMolecule,   Molecule,   StructuralModelNodeBackbone,   Backbone,   StructuralModelNodeSideChain,   SideChain,   VisualModel,   VisualModelMesh,   Mesh,   DynamicalModel,   DynamicalModelParticleSystem,   ParticleSystem,   DynamicalModelRigidBodySystem,   RigidBodySystem,   DynamicalModelArticulatedBodySystem,   ArticulatedBodySystem,   DynamicalModelNode,   DynamicalNode,   DynamicalModelNodeGroup,   DynamicalGroup,   DynamicalModelNodeRoot,   DynamicalRoot,   DynamicalModelNodeParticle,   DynamicalParticle,   DynamicalModelNodeRigidBody,   RigidBody,   DynamicalModelNodeArticulatedBody,   ArticulatedBody,   InteractionModel,   InteractionModelParticleSystem,   InteractionModelRigidBodySystem,   InteractionModelArticulatedBodySystem,   PropertyModel,   PropertyModelFunction,   Simulator,   SimulatorParticleSystem,   SimulatorRigidBodySystem,   SimulatorArticulatedBodySystem,   StateUpdater,   StateUpdaterParticleSystem,   StateUpdaterRigidBodySystem,   StateUpdaterArticulatedBodySystem,   DocumentManager,   Document,   Folder,   Camera,   Label,   Note,   Animation,   Presentation,   DataGraphNodeGroup,   NodeGroup,   Controller,   ControllerNode,   Asset }
	The type of the data graph node. More...
Public Member Functions inherited from SBMStructuralModelNodeParticle
	SB_NODE_GETTER_0 (, SBQuantity::length, GetX)
	SB_NODE_GETTER_0 (, SBQuantity::length, GetY)
	SB_NODE_GETTER_0 (, SBQuantity::length, GetZ)
	SB_NODE_GETTER_0 (, SBPosition3, GetPosition)
	SB_DECLARE_DATA (SBMStructuralModelNodeParticle)
virtual	~SBMStructuralModelNodeParticle ()
SBQuantity::length const &	getX () const
	Returns the x coordinate.
void	setX (const SBQuantity::length &x)
	Sets the x coordinate.
SBQuantity::length const &	getY () const
	Returns the y coordinate.
void	setY (const SBQuantity::length &y)
	Sets the y coordinate.
SBQuantity::length const &	getZ () const
	Returns the z coordinate.
void	setZ (const SBQuantity::length &z)
	Sets the z coordinate.
SBPosition3 const &	getPosition () const
	Returns the particle's position.
void	setPosition (SBPosition3 const &newPosition)
	Sets the particle's position.
void	setPosition (SBPosition3 const &newPosition, SBPosition3 const &oldPosition)
	Sets the particle's position.
void	setPositionOnTetrahedron (SBPosition3 const &center, SBPosition3 const &vertex1, SBPosition3 const &vertex2, SBPosition3 const &vertex3, SBQuantity::length const &distanceFromCenter)
	Sets the particle's position on a tetrahedron vertex based on the center position, the distance from the center distanceFromCenter, and positions of other 3 vertices vertex1, vertex2, and vertex3.
Public Member Functions inherited from SBMStructuralModelNode
	SB_NODE_GETTER_0 (, bool, GetMobilityFlag)
	SB_DECLARE_DATA (SBMStructuralModelNode)
virtual	~SBMStructuralModelNode ()
virtual SBPointerList< SBMStructuralModelNode > const *	getChildren () const
SBMStructuralModelNode *	getNextStructuralNode () const
SBMStructuralModelNode *	getPreviousStructuralNode () const
virtual SBMStructuralModelNode *	clone ()
	Returns a copy of the node and its descendants.
virtual bool	isLocked () const
	Returns whether the node is locked (because of the model)
virtual bool	getLockedFlag () const
	Returns the locked flag of the model.
SBMStructuralModel *	getModel () const
bool	getMobilityFlag () const
	Returns the mobility flag.
void	setMobilityFlag (bool flag)
	Sets the mobility flag to flag.
virtual unsigned int	getOpacity () const
	Returns the opacity.
virtual unsigned int	getMinimumOpacity () const
	Returns the minimum opacity.
virtual unsigned int	getTransparency () const
	Returns the transparency.
virtual unsigned int	getMaximumTransparency () const
	Returns the maximum transparency.
void	connectStructuralSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *), SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBStructuralEvent *)=0)
bool	structuralSignalIsConnectedToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *)) const
void	disconnectStructuralSignalFromSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *))
virtual void	getNodes (SBNodeIndexer &nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const
	Collects nodes into nodeIndexer, based on a nodeType, a selection status and a visitPredicate, with our without dependencies.
virtual void	getNodes (SBNodeIndexer &nodeIndexer, const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const
	Returns some nodes.
void	getAllStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer)
void	getInternalStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer)
void	getLeafStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer)
void	getStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *))
void	getAllStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer)
void	getInternalStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer)
void	getLeafStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer)
void	getStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *))
void	getAllStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer)
void	getInternalStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer)
void	getLeafStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer)
void	getStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *))
void	getStructuralNodesBreadthFirst (std::vector< SBMStructuralModelNode *> &nodeVectorTopDown, std::vector< SBMStructuralModelNode *> &nodeVectorBottomUp, bool(*selectionRule)(SBMStructuralModelNode *))
virtual void	forEachNodeDepthFirst (void(*action)(SBDDataGraphNode *node))
	Performs an action on each node.
virtual void	forEachNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBDDataGraphNode *node))
	Performs an action on each node.
void	forEachStructuralNodeBreadthFirst (void(*action)(SBMStructuralModelNode *node))
void	forEachStructuralNodeDepthFirst (void(*action)(SBMStructuralModelNode *node))
void	forEachStructuralNodeBreadthFirst (SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node))
void	forEachStructuralNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node))
Public Member Functions inherited from SBMModelNode
	SB_DECLARE_DATA (SBMModelNode)
Public Member Functions inherited from SBDDataGraphNode
	SB_DECLARE_DATA (SBDDataGraphNode)
SBDDataGraphNode *	getParent () const
	Returns the parent of the node. More...
SBDDataGraphNode *	getThisNode () const
	Returns the pointer to this node. More...
SBDDataGraphNode *	getNextNode () const
	Returns the pointer to the next node in the children of the node's parent. More...
SBDDataGraphNode *	getPreviousNode () const
	Returns the pointer to the previous node in the children of the node's parent. More...
SBDDataGraphNode *	getNextNode (SBDDataGraphNode::Type nodeType) const
	Returns the pointer to the next node with type nodeType in the children of the node's parent. More...
SBDDataGraphNode *	getPreviousNode (SBDDataGraphNode::Type nodeType) const
	Returns the pointer to the previous node with type nodeType in the children of the node's parent. More...
SBDDocument *	getDocument () const
	Returns the document the node belongs to. More...
virtual bool	canAddChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=0) const
	Returns whether this node can add node as a child. More...
virtual bool	canAddChildType (SBDDataGraphNode::Type nodeType) const
	Returns whether this node can add a node with type nodeType as a child. More...
virtual bool	canHaveDescendantType (SBDDataGraphNode::Type nodeType) const
	Returns whether this node can have a node with type nodeType as a descendant. More...
virtual bool	addChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=0)
	Adds a child to the node. More...
virtual bool	removeChild (SBDDataGraphNode *node)
	Removes a child from the node. More...
bool	hasOneOf (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the nodeIndexer, or is the ancestor of one of them. More...
bool	descendsFrom (SBDDataGraphNode *node) const
	Returns true if and only if this node is node, or descends from it. More...
bool	descendsFrom (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the nodeIndexer, or descends from one of them. More...
bool	descendsFrom (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const
	Returns true if and only if this node is one of the nodes of the nodePointerIndexer, or descends from one of them. More...
bool	isIn (SBDDataGraphNode *node) const
	Returns true if and only if this node is node, or descends from it, or belongs to a group stored in node. More...
bool	isIn (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the nodeIndexer, or descends from one of them, or belongs to a group stored in one of the nodes of the nodeIndexer. More...
bool	isIn (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const
	Returns true if and only if this node is one of the nodes of the nodePointerIndexer, or descends from one of them, or belongs to a group stored in of the nodes of the nodePointerIndexer. More...
bool	isOneOf (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the nodeIndexer. More...
bool	isOneOf (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const
	Returns true if and only if this node is one of the nodes of the nodePointerIndexer. More...
SBDDataGraphNode *	getRoot () const
	Returns the root of the hierarchy the node belongs to. More...
unsigned int	getNodeIndex () const
	Returns the node index (unique in the whole data graph, but non-persistent) More...
std::string	getTypeString (bool humanReadable=false) const
	Returns a string describing the type of the data graph node. More...
virtual std::string const &	getName () const
	Returns the name of the node.
virtual void	setName (const std::string &name)
	Sets the name of the node. More...
bool	isType (Type type) const
	Returns true when the type of the node corresponds to type.
bool	isModel () const
	Returns true when the node is a model.
bool	isStructuralNode () const
	Returns true when the node is a structural node.
bool	isStructuralModel () const
	Returns true when the node is a structural model.
bool	isVisualModel () const
	Returns true when the node is a visual model.
bool	isDynamicalModel () const
	Returns true when the node is a dynamical model.
bool	isInteractionModel () const
	Returns true when the node is a interaction model.
bool	isPropertyModel () const
	Returns true when the node is a property model.
bool	isMesh () const
	Returns true when the node is a mesh.
bool	isSimulator () const
	Returns true when the node is a simulator.
bool	isStructuralParticle () const
	Returns true when the node is a structural particle (an atom or a pseudo-atom)
virtual void	setLockedFlag (bool flag)
	Sets the locked flag.
bool	isCreated () const
	Returns true if and only if the node is created. More...
void	create ()
	Creates the node. More...
bool	isErased () const
	Returns true if and only if the node is erased. More...
void	erase ()
	Erases the node. More...
unsigned int	getFlags () const
	Returns the flags. More...
unsigned int	getInheritedFlags () const
	Returns the inherited flags. More...
bool	isSelected () const
	Returns whether the node is selected. More...
bool	getSelected () const
	Returns whether the node is selected.
bool	getSelectionFlag () const
	Returns the selection flag. More...
void	setSelectionFlag (bool flag)
	Sets the selection flag. More...
bool	isVisible () const
	Returns whether the node is visible. More...
bool	getVisible () const
	Returns whether the node is visible.
bool	getVisibilityFlag () const
	Returns the visibility flag. More...
void	setVisibilityFlag (bool flag)
	Sets the visibility flag. More...
bool	isHighlighted () const
	Returns whether the node is highlighted. More...
bool	getHighlightingFlag () const
	Returns the highlighting flag. More...
void	setHighlightingFlag (bool flag)
	Sets the highlighting flag. More...
virtual void	display (RenderingPass renderingPass)
	Displays the node. More...
virtual void	display ()
	Displays the node (deprecated) More...
virtual void	displayForShadow ()
	Displays the node for shadowing purposes (deprecated) More...
virtual void	displayForSelection ()
	Displays the node for selection purposes (deprecated) More...
virtual void	setOpacity (unsigned int opacity)
	Sets the opacity.
virtual bool	hasOpacityRange () const
	Returns whether the node has the opacity range.
virtual unsigned int	getDefaultOpacity () const
	Returns the default opacity.
virtual unsigned int	getMaximumOpacity () const
	Returns the maximum opacity.
virtual unsigned int	getOpacitySingleStep () const
	Returns the opacity single step.
virtual std::string	getOpacitySuffix () const
	Returns the opacity suffix.
virtual void	setTransparency (unsigned int transparency)
	Sets the transparency.
virtual bool	hasTransparencyRange () const
	Returns whether the node has the transparency range.
virtual unsigned int	getDefaultTransparency () const
	Returns the default transparency.
virtual unsigned int	getMinimumTransparency () const
	Returns the minimum transparency.
virtual unsigned int	getTransparencySingleStep () const
	Returns the transparency single step.
virtual std::string	getTransparencySuffix () const
	Returns the transparency suffix.
float	getInheritedOpacity () const
	Returns the cumulative opacity, when taking into account the ascendants.
float	getInheritedTransparency () const
	Returns the cumulative transparency, when taking into account the ascendants.
bool	addMaterial (SBDDataGraphNodeMaterial *material)
	Adds a material. More...
bool	removeMaterial ()
	Removes the material. More...
SBDDataGraphNodeMaterial *	getMaterial () const
	Returns the material. More...
SBDDataGraphNode *	getMaterialOwner () const
	Returns the node whose material is inherited. More...
void	connectBaseSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *), SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBBaseEvent *)=0)
	Connects the base signal to a slot. More...
bool	baseSignalIsConnectedToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *)) const
	Returns true when the base signal is connected to a slot.
void	disconnectBaseSignalFromSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *))
	Disconnects the base signal from a slot.
unsigned int	countNodes (SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const
	Collects nodes into nodeIndexer, based on a nodeType, a selection status and a visitPredicate, with our without dependencies. More...
unsigned int	countNodes (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const
	Collects nodes into nodeIndexer, based on a selectionPredicate and a visitPredicate, with our without dependencies. More...
virtual std::string	getHierarchyString (const std::string &separator="/", bool includeNodeType=false) const
	Returns a string with hierarchical information on the node and its parents names. More...
Public Member Functions inherited from SBCReferenceTarget
	SBCReferenceTarget ()
virtual	~SBCReferenceTarget ()
unsigned int	getMemoryFootprint () const
void	printReferencesToOwners () const
Static Public Member Functions inherited from SBMStructuralModelNode
static void	forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode *> &selection, void(*action)(SBMStructuralModelNode *node))
static void	forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode *> &selection, SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node))
Static Public Member Functions inherited from SBDDataGraphNode
static void	clone (const SBNodeIndexer &sourceNodeIndexer, SBNodeIndexer &destinationNodeIndexer)
	Clones the nodes in sourceNodeIndexer (treated as a whole) and places the clones in destinationNodeIndexer. More...
static SBDDataGraphNode *	getNode (unsigned int nodeIndex)
	Returns the unique node corresponding to the node index nodeIndex. More...
static std::string	getTypeString (Type type, bool humanReadable=false)
	Returns a string describing the type of the data graph node. More...
static void	forEachNodeInSelection (SBNodeIndexer &nodeIndexer, void(*action)(SBDDataGraphNode *node))
	Performs an action for each node in a selection.
static void	forEachNodeInSelection (SBNodeIndexer &nodeIndexer, SBCClass *object, void(SBCClass::*action)(SBDDataGraphNode *node))
	Performs an action for each node in a selection.
Protected Member Functions inherited from SBMStructuralModelNodeParticle
	SBMStructuralModelNodeParticle (SBMStructuralModelNodeParticleData *dataPointer)
	Builds a particle at position p.
Protected Member Functions inherited from SBMStructuralModelNode
	SBMStructuralModelNode ()
	Builds a structural model node.
	SBMStructuralModelNode (SBMStructuralModelNodeData *dataPointer)
	Builds a structural model node.
Protected Member Functions inherited from SBMModelNode
	SBMModelNode ()
	Builds a base object.
	SBMModelNode (SBMModelNodeData *dataPointer)
	Builds a base object.
virtual	~SBMModelNode ()
Protected Member Functions inherited from SBDDataGraphNode
	SBDDataGraphNode ()
	Builds a data graph node. More...
	SBDDataGraphNode (SBDDataGraphNodeData *dataPointer)
	Builds a data graph node.
virtual	~SBDDataGraphNode ()
	Destroys the node. More...
Protected Member Functions inherited from SBCReferenceTarget
void	removeAllReferenceOwners ()
	SBCReferenceTarget (SBCReferenceTargetData *dataPointer)
Protected Attributes inherited from SBCReferenceTarget
SBCReferenceTargetData *	dataPointer