Class SBMDynamicalModel

ClassList > SBMDynamicalModel

This class is the base class of dynamical models. More...

• #include <SBMDynamicalModel.hpp>

Inherits the following classes: SBMModel

Inherited by the following classes: SBMDynamicalModelArticulatedBodySystem, SBMDynamicalModelParticleSystem, SBMDynamicalModelRigidBodySystem

Public Types inherited from SBDDataGraphNode

See SBDDataGraphNode

Type	Name
enum	RenderingPass The rendering pass.
enum	Type The type of the data graph node.

Public Functions

Type	Name
virtual SBMDynamicalModel *	clone () override Returns a copy of the node and its descendants.
void	connectDynamicalSignalToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBDynamicalEvent *) functionPointer, SBCReferenceTarget * nextReferenceTarget=0, void(SBCReferenceTarget::*)(SBDynamicalEvent *) nextFunctionPointer=0) Connects the dynamical signal to a slot.
void	disconnectDynamicalSignalFromSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBDynamicalEvent *) functionPointer) Disconnects the dynamical signal from a slot.
bool	dynamicalSignalIsConnectedToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBDynamicalEvent *) functionPointer) const Returns true if and only if the dynamical signal is connected to a given slot.
virtual bool	enforcePeriodicBoundaryConditions () Enforces the periodic boundary conditions.
virtual void	flushPositionBuffer () Flushes the position buffer.
virtual void	forEachNodeDepthFirst (void(*)(SBDDataGraphNode *node) action) override Performs the action on each node in the root of the dynamical model, depth-first.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) override Performs the object 'saction on each node in the root of the dynamical model, depth-first.
virtual unsigned int	getChangedPositionIndex (unsigned int i) const Returns the index of a changed position.
virtual SBDDataGraphNode::Type	getDynamicalModelType () const Returns the dynamical model type.
SBMDynamicalModelNodeRoot *	getDynamicalRoot () const Returns the root of the dynamical model.
virtual SBDDataGraphNode::Type	getModelType () override const Returns the model type.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Collects nodes into nodeIndexer , based on anodeType , a selection status and avisitPredicate , with or without dependencies.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Collects nodes into nodeIndexer , based on aselectionPredicate and avisitPredicate , with or without dependencies.
virtual unsigned int	getNumberOfChangedPositions () const Returns the number of changed positions.
SBIAPosition3 const &	getPeriodicBoundaryConditions () const Returns the periodic boundary conditions.
bool	getPeriodicBoundaryConditionsFlag () const Returns the periodic boundary conditions flag.
virtual bool	getPositionChanged (unsigned int i) const Returns whether position i has been changed since the last flush.
virtual SBDDataGraphNode::Type	getType () override const Returns the node type ( SBNode::DynamicalModel )
virtual bool	hasNode (SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Checks for nodes based on a nodeType , a selection status and avisitPredicate , with or without dependencies.
virtual bool	hasNode (const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Checks for nodes based on a selectionPredicate and avisitPredicate , with or without dependencies.
virtual bool	isSerializable () override const Returns true when the class is serializable.
virtual void	print (unsigned int offset=0) override const Prints debugging information.
virtual void	serialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override const Serializes the node.
void	setPeriodicBoundaryConditions (SBIAPosition3 const & box) Sets the periodic boundary conditions.
void	setPeriodicBoundaryConditionsFlag (bool flag) Sets the periodic boundary conditions flag.
virtual void	unserialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override Unserializes the node.
virtual void	updateStructuralNodes () Updates structural nodes based on the state of the dynamical model.

Public Functions inherited from SBMModel

See SBMModel

Type	Name
	SB_NODE_GETTER_0 (SB_SBMMODEL_EXPORT, SBDDataGraphNode::Type, GetModelType)
	SB_NODE_PREDICATE_1 (SB_SBMMODEL_EXPORT, IsModelType, SBDDataGraphNode::Type)
void	clearSourceFileName () Clears the name of the file associated to the model.
virtual SBMModel *	clone () override Returns a copy of the node and its descendants.
virtual SBDDataGraphNode::Type	getModelType () const Returns the model type.
SBMModel *	getNextModel () const Returns the next model in the parent.
virtual unsigned int	getOpacity () override const Returns the opacity.
SBMModel *	getPreviousModel () const Returns the previous model in the parent.
bool	getShadowingFlag () const Returns whether the model casts shadows.
const std::string &	getSourceFileName () const Returns the name of the file associated to the model.
virtual unsigned int	getTransparency () override const Returns the transparency.
virtual SBDDataGraphNode::Type	getType () override const Returns the type of the data graph node.
bool	hasSourceFileName () const Returns true when the model has the source file name set.
virtual bool	isSerializable () override const Returns true __
virtual void	print (unsigned int offset=0) override const Prints debugging information.
virtual void	serialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override const Serializes the node.
virtual void	setOpacity (unsigned int opacity) override Sets the opacity.
void	setShadowingFlag (bool shadowingFlag) Sets whether the model casts shadows.
void	setSourceFileName (const std::string & fileName) Sets the name of the file associated to the model.
virtual void	setTransparency (unsigned int transparency) override Sets the transparency.
virtual void	unserialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override Unserializes the node.
virtual	~SBMModel () Delete the model.

Public Functions inherited from SBDDataGraphNode

See SBDDataGraphNode

Type	Name
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBCClassProxy *, GetProxy)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, This)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetParent)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetThis)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetNextNode)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetPreviousNode)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDocument *, GetDocument)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetRoot)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, unsigned int, GetNodeIndex)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode::Type, GetType)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetSelectionFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetLockedFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetVisibilityFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetHighlightingFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, unsigned int, GetFlags)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, std::string, GetName)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, std::string, GetClass)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, std::string, GetElement)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBCContainerUUID, GetElementUUID)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, All)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, None)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsAtom)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsBond)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsStructuralNode)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsStructuralModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsVisualModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsMesh)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsLight)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsInteractionModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsDynamicalModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsPropertyModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSimulator)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsBallAndStick)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsLicorice)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsVanDerWaals)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsCartoon)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsRibbon)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsTube)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsGaussianSurface)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSolventAccessibleSurface)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSolventExcludedSurface)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, HasMaterial)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, OwnsMaterial)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsLocked)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSerializable)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsCreated)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsErased)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSelected)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsVisible)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsHighlighted)
	SB_NODE_PREDICATE_1 (SB_SBDDATAGRAPH_EXPORT, IsType, SBDDataGraphNode::Type)
	SB_NODE_PREDICATE_1 (SB_SBDDATAGRAPH_EXPORT, HasOneOf, SBNodeIndexer)
virtual bool	addChild (SBDDataGraphNode * node, SBDDataGraphNode * nextNode=nullptr) Adds a child to the node.
bool	addMaterial (SBDDataGraphNodeMaterial * material) Adds a material.
bool	baseSignalIsConnectedToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBBaseEvent *) functionPointer) const Returns true when the base signal is connected to a slot.
virtual bool	canAddChild (const SBDDataGraphNode * node, const SBDDataGraphNode * nextNode=nullptr) const Returns whether this node can add node as a child.
virtual bool	canAddChildType (SBDDataGraphNode::Type nodeType) const Returns whether this node can add a node with type nodeType as a child.
bool	canAddMaterial () const Returns whether can add a material to the node based on its type.
virtual bool	canHaveDescendantType (SBDDataGraphNode::Type nodeType) const Returns whether this node can have a node with type nodeType as a descendant.
virtual SBDDataGraphNode *	clone () Returns a copy of the node and its descendants.
void	connectBaseSignalToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBBaseEvent *) functionPointer, SBCReferenceTarget * nextReferenceTarget=0, void(SBCReferenceTarget::*)(SBBaseEvent *) nextFunctionPointer=0) Connects the base signal to a slot.
unsigned int	countNodes (SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Counts nodes based on a nodeType , a selection status and avisitPredicate , with or without dependencies.
unsigned int	countNodes (const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Counts nodes based on a selectionPredicate and avisitPredicate , with or without dependencies.
void	create () Creates the node.
bool	descendsFrom (const SBDDataGraphNode * node) const Returns true if and only if this node isnode , or descends from it.
bool	descendsFrom (const SBNodeIndexer & nodeIndexer) const Returns true if and only if this node is one of the nodes of thenodeIndexer , or descends from one of them.
bool	descendsFrom (SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer) const Returns true if and only if this node is one of the nodes of thenodePointerIndexer , or descends from one of them.
void	disconnectBaseSignalFromSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBBaseEvent *) functionPointer) Disconnects the base signal from a slot.
virtual void	display (RenderingPass renderingPass) Displays the node.
virtual void	display () Displays the node (deprecated)
virtual void	displayForSelection () Displays the node for selection purposes (deprecated)
virtual void	displayForShadow () Displays the node for shadowing purposes (deprecated)
void	erase () Erases the node.
virtual void	forEachNodeDepthFirst (void(*)(SBDDataGraphNode *node) action) Performs the action on this node.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) Performs the objects 'saction on this node.
unsigned int	getDefaultOpacity () const Returns the default opacity.
unsigned int	getDefaultTransparency () const Returns the default transparency.
SBDDocument *	getDocument () const Returns the document the node belongs to.
virtual unsigned int	getFlags () const Returns the flags.
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.
bool	getHighlightingFlag () const Returns the highlighting flag.
virtual unsigned int	getInheritedFlags () const Returns the inherited flags.
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.
virtual bool	getLockedFlag () const Returns the locked flag.
SBDDataGraphNodeMaterial *	getMaterial () const Returns the material.
SBDDataGraphNode *	getMaterialOwner () const Returns the node whose material is inherited.
unsigned int	getMaximumOpacity () const Returns the maximum opacity.
unsigned int	getMaximumTransparency () const Returns the maximum transparency.
unsigned int	getMinimumOpacity () const Returns the minimum opacity.
unsigned int	getMinimumTransparency () const Returns the minimum transparency.
virtual SBQuantity::mass	getMolecularWeight () Returns the molecular weight.
virtual std::string const &	getName () const Returns the name of the node.
SBDDataGraphNode *	getNextNode () const Returns the pointer to the next node in the children of the node's parent.
SBDDataGraphNode *	getNextNode (SBDDataGraphNode::Type nodeType) const Returns the pointer to the next node with type nodeType in the children of the node's parent.
unsigned int	getNodeIndex () const Returns the node index (unique in the whole data graph, but non-persistent)
SBUUID	getNodeUUID () const Returns the node UUID.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Collects nodes into nodeIndexer , based on anodeType , a selection status and avisitPredicate , with or without dependencies.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Collects nodes into nodeIndexer , based on aselectionPredicate and avisitPredicate , with or without dependencies.
virtual unsigned int	getNumberOfAtoms () Returns the number of atoms.
virtual unsigned int	getNumberOfCarbons () Returns the number of carbons.
virtual unsigned int	getNumberOfChains () Returns the number of chains.
virtual unsigned int	getNumberOfCoarseGrainedAtoms () Returns the number of coarse-grained atoms.
virtual unsigned int	getNumberOfHydrogens () Returns the number of hydrogens.
virtual unsigned int	getNumberOfMolecules () Returns the number of molecules.
virtual unsigned int	getNumberOfNitrogens () Returns the number of nitrogens.
virtual unsigned int	getNumberOfOtherAtoms () Returns the number of other atoms.
virtual unsigned int	getNumberOfOxygens () Returns the number of oxygens.
virtual unsigned int	getNumberOfResidues () Returns the number of residues.
virtual unsigned int	getNumberOfSegments () Returns the number of segments.
virtual unsigned int	getNumberOfStructuralGroups () Returns the number of structural groups.
virtual unsigned int	getNumberOfStructuralModels () Returns the number of structural models.
virtual unsigned int	getNumberOfSulfurs () Returns the number of sulfurs.
virtual unsigned int	getOpacity () const Returns the opacity.
unsigned int	getOpacitySingleStep () const Returns the opacity single step.
std::string	getOpacitySuffix () const Returns the opacity suffix.
SBDDataGraphNode *	getParent () const Returns the parent of the node.
SBDDataGraphNode *	getPreviousNode () const Returns the pointer to the previous node in the children of the node's parent.
SBDDataGraphNode *	getPreviousNode (SBDDataGraphNode::Type nodeType) const Returns the pointer to the previous node with type nodeType in the children of the node's parent.
SBDDataGraphNode *	getRoot () const Returns the root of the hierarchy the node belongs to.
bool	getSelected () const Returns whether the node is selected.
bool	getSelectionFlag () const Returns the selection flag.
virtual int	getSumOfFormalCharges () Returns the sum of formal charges.
virtual float	getSumOfPartialCharges () Returns the sum of partial charges.
SBDDataGraphNode *	getThisNode () const Returns the pointer to this node.
virtual unsigned int	getTransparency () const Returns the transparency.
unsigned int	getTransparencySingleStep () const Returns the transparency single step.
std::string	getTransparencySuffix () const Returns the transparency suffix.
virtual Type	getType () const Returns the type of the data graph node.
std::string	getTypeString (bool humanReadable=false) const Returns a string describing the type of the data graph node.
bool	getVisibilityFlag () const Returns the visibility flag.
bool	getVisible () const Returns whether the node is visible.
bool	hasMaterial () const Returns whether the node has a material (by itself, or inherited)
virtual bool	hasNode (SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Returns whether the node has nodes based on a nodeType , a selection status and avisitPredicate , with or without dependencies.
virtual bool	hasNode (const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Returns whether the node has nodes based on a selectionPredicate and avisitPredicate , with or without dependencies.
bool	hasOneOf (const SBNodeIndexer & nodeIndexer) const Returns true if and only if this node is one of the nodes of thenodeIndexer , or is the ancestor of one of them, or is a group that stores one of them.
bool	hasOpacityRange () const Returns whether the node has the opacity range.
bool	hasTransparencyRange () const Returns whether the node has the transparency range.
bool	isAtom () const Returns true when the node is an atom.
bool	isBallAndStick () const Returns true when the node is the default ball-and-stick visual model.
bool	isBond () const Returns true when the node is a bond.
bool	isCartoon () const Returns true when the node is the default cartoon visual model.
bool	isCreated () const Returns true if and only if the node is created.
bool	isDynamicalModel () const Returns true when the node is a dynamical model.
bool	isErased () const Returns true if and only if the node is erased.
bool	isGaussianSurface () const Returns true when the node is the default Gaussian surface visual model.
bool	isHighlighted () const Returns whether the node is highlighted.
bool	isIn (const SBDDataGraphNode * node) const Returns true if and only if this node isnode , or descends from it, or belongs to a group stored innode .
bool	isIn (const SBNodeIndexer & nodeIndexer) const Returns true if and only if this node is one of the nodes of thenodeIndexer , or descends from one of them, or belongs to a group stored in one of the nodes of thenodeIndexer .
bool	isIn (SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer) const Returns true if and only if this node is one of the nodes of thenodePointerIndexer , or descends from one of them, or belongs to a group stored in of the nodes of thenodePointerIndexer .
bool	isInteractionModel () const Returns true when the node is a interaction model.
bool	isLicorice () const Returns true when the node is the default licorice visual model.
bool	isLight () const Returns true when the node is a light.
virtual bool	isLocked () const Returns whether the node is locked.
bool	isMesh () const Returns true when the node is a mesh.
bool	isModel () const Returns true when the node is a model.
bool	isOneOf (const SBNodeIndexer & nodeIndexer) const Returns true if and only if this node is one of the nodes of thenodeIndexer .
bool	isOneOf (SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer) const Returns true if and only if this node is one of the nodes of thenodePointerIndexer .
bool	isPropertyModel () const Returns true when the node is a property model.
bool	isRibbon () const Returns true when the node is the default ribbon visual model.
bool	isSelected () const Returns whether the node is selected.
virtual bool	isSerializable () const Returns true when the class is serializable.
bool	isSimulator () const Returns true when the node is a simulator.
bool	isSolventAccessibleSurface () const Returns true when the node is the default solvent accessible surface visual model.
bool	isSolventExcludedSurface () const Returns true when the node is the default solvent excluded surface visual model.
bool	isStructuralModel () const Returns true when the node is a structural model.
bool	isStructuralNode () const Returns true when the node is a structural node.
bool	isTube () const Returns true when the node is the default tube visual model.
bool	isType (Type type) const Returns true when the type of the node corresponds totype .
bool	isVanDerWaals () const Returns true when the node is the default van der Waals visual model.
bool	isVisible () const Returns whether the node is visible.
bool	isVisualModel () const Returns true when the node is a visual model.
bool	ownsMaterial () const Returns whether the node owns a material.
virtual void	print (unsigned int offset=0) const Prints some debugging information.
virtual bool	removeChild (SBDDataGraphNode * node) Removes a child from the node.
bool	removeMaterial () Removes the material.
void	removeMaterialsFromDescendants () Removes materials from all nodes that descend from this node, but it does not remove the material from the node itself.
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.
void	setHighlightingFlag (bool flag) Sets the highlighting flag.
virtual void	setLockedFlag (bool flag) Sets the locked flag.
virtual void	setName (const std::string & name) Sets the name of the node.
virtual void	setOpacity (unsigned int opacity) Sets the opacity.
void	setSelectionFlag (bool flag) Sets the selection flag.
virtual void	setTransparency (unsigned int transparency) Sets the transparency.
void	setVisibilityFlag (bool flag) Sets the visibility flag.
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.

Public Functions inherited from SBCReferenceTarget

See SBCReferenceTarget

Type	Name
	SBCReferenceTarget () Builds the reference target.
unsigned int	getMemoryFootprint () const Returns the memory footprint.
void	printReferencesToOwners () const Prints the references to the owners of this reference target.
virtual	~SBCReferenceTarget () Destructor.

Public Static Functions inherited from SBDDataGraphNode

See SBDDataGraphNode

Type	Name
bool	canAddMaterial (SBDDataGraphNode::Type nodeType) Returns whether can add a material to a node of type nodeType .
void	clone (const SBNodeIndexer & sourceNodeIndexer, SBNodeIndexer & destinationNodeIndexer) Clones the nodes in sourceNodeIndexer (treated as a whole) and places the clones indestinationNodeIndexer .
void	forEachNodeInSelection (SBNodeIndexer & nodeIndexer, void(*)(SBDDataGraphNode *node) action) Performs the action for each node innodeIndexer __
void	forEachNodeInSelection (SBNodeIndexer & nodeIndexer, SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) Performs the objects 'saction for each node innodeIndexer __
SBDDataGraphNode *	getNode (unsigned int nodeIndex) Returns the unique node corresponding to the node index nodeIndex .
std::string	getTypeString (Type type, bool humanReadable=false) Returns a string describing the type of the data graph node.

Protected Attributes inherited from SBCReferenceTarget

See SBCReferenceTarget

Type	Name
SBCReferenceTargetData *	dataPointer A pointer to the private data.

Protected Functions

Type	Name
	SBMDynamicalModel () Builds a dynamical model.
	SBMDynamicalModel (SBMDynamicalModelData * dataPointer) Builds a dynamical model.
virtual	~SBMDynamicalModel () Deletes the dynamical model.

Protected Functions inherited from SBMModel

See SBMModel

Type	Name
	SBMModel () Builds a model.
	SBMModel (SBMModelData * dataPointer) Builds a model.

Protected Functions inherited from SBDDataGraphNode

See SBDDataGraphNode

Type	Name
	SBDDataGraphNode () Builds a data graph node.
	SBDDataGraphNode (SBDDataGraphNodeData * dataPointer) Builds a data graph node.
virtual	~SBDDataGraphNode () Destroys the node.

Protected Functions inherited from SBCReferenceTarget

See SBCReferenceTarget

Type	Name
	SBCReferenceTarget (SBCReferenceTargetData * dataPointer) Protected constructor.
void	removeAllReferenceOwners () Stops all the reference owners from referencing this reference target.

Detailed Description

Short name: SBDynamicalModel

Public Functions Documentation

function clone

Returns a copy of the node and its descendants.

virtual SBMDynamicalModel * SBMDynamicalModel::clone () override

Creates a copy of this dynamical model and its descendants.

Returns a newly allocated copy of the model.

Returns:

Pointer to the cloned SBMDynamicalModel.

Implements SBMModel::clone

---

function connectDynamicalSignalToSlot

Connects the dynamical signal to a slot.

void SBMDynamicalModel::connectDynamicalSignalToSlot (
    SBCReferenceTarget * referenceTarget,
    void(SBCReferenceTarget::*)( SBDynamicalEvent *) functionPointer,
    SBCReferenceTarget * nextReferenceTarget=0,
    void(SBCReferenceTarget::*)( SBDynamicalEvent *) nextFunctionPointer=0
) 

Connects a dynamical signal to a slot on a reference target.

Establishes a connection between the model's dynamical signal and the specified slot, optionally linking to a subsequent slot. The operation can be undone via the undo system if holding.

Parameters:

• referenceTarget Target object whose slot will be connected.
• functionPointer Pointer to the member function to be invoked when the signal is emitted.
• nextReferenceTarget Optional target for the next slot in the chain (may be null).
• nextFunctionPointer Optional pointer to the member function of the next target (may be null).

---

function disconnectDynamicalSignalFromSlot

Disconnects the dynamical signal from a slot.

void SBMDynamicalModel::disconnectDynamicalSignalFromSlot (
    SBCReferenceTarget * referenceTarget,
    void(SBCReferenceTarget::*)( SBDynamicalEvent *) functionPointer
) 

Disconnects a dynamical signal from a slot on a reference target.

Removes the connection between the model's dynamical signal and the specified slot. The operation can be undone via the undo system if holding.

Parameters:

• referenceTarget Target object whose slot will be disconnected.
• functionPointer Pointer to the member function to be disconnected.

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function dynamicalSignalIsConnectedToSlot

Returns true if and only if the dynamical signal is connected to a given slot.

bool SBMDynamicalModel::dynamicalSignalIsConnectedToSlot (
    SBCReferenceTarget * referenceTarget,
    void(SBCReferenceTarget::*)( SBDynamicalEvent *) functionPointer
) const

Checks whether a given slot is connected to the dynamical signal.

Determines if the specified reference target and member function are currently connected.

Parameters:

• referenceTarget Target object to check.
• functionPointer Pointer to the member function to check.

Returns:

true if the slot is connected, false otherwise.

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function enforcePeriodicBoundaryConditions

Enforces the periodic boundary conditions.

virtual bool SBMDynamicalModel::enforcePeriodicBoundaryConditions () 

Enforces the periodic boundary conditions on the model.

Adjusts positions to satisfy the periodic boundary constraints.

Returns:

true if the operation succeeded, false otherwise.

---

function flushPositionBuffer

Flushes the position buffer.

virtual void SBMDynamicalModel::flushPositionBuffer () 

Clears the buffer of changed positions.

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function forEachNodeDepthFirst [1/2]

Performs the action on each node in the root of the dynamical model, depth-first.

virtual void SBMDynamicalModel::forEachNodeDepthFirst (
    void(*)( SBDDataGraphNode *node) action
) override

Performs a depth‑first traversal of the dynamical model, invoking the provided action on each node.

The action is called for the model itself and then recursively for all descendant nodes.

Parameters:

• action Function pointer that will be invoked for each node. The function receives a pointer to the current node.

Implements SBDDataGraphNode::forEachNodeDepthFirst

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function forEachNodeDepthFirst [2/2]

Performs the object 'saction on each node in the root of the dynamical model, depth-first.

virtual void SBMDynamicalModel::forEachNodeDepthFirst (
    SBCClass * object,
    void(SBCClass::*)( SBDDataGraphNode *node) action
) override

Performs a depth‑first traversal of the dynamical model, invoking a member function on each node.

The specified member function of the given object is called for the model itself and then recursively for all descendant nodes.

Parameters:

• object Pointer to the object whose member function will be called.
• action Pointer to the member function to invoke for each node. The function receives a pointer to the current node.

Implements SBDDataGraphNode::forEachNodeDepthFirst

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function getChangedPositionIndex

Returns the index of a changed position.

virtual unsigned int SBMDynamicalModel::getChangedPositionIndex (
    unsigned int i
) const

Returns the global index of a changed position at the specified buffer index.

Parameters:

• i Buffer index (0-based) of the changed position.

Returns:

Global position index that changed.

---

function getDynamicalModelType

Returns the dynamical model type.

virtual SBDDataGraphNode::Type SBMDynamicalModel::getDynamicalModelType () const

Retrieves the dynamical model type identifier of this node.

Returns SBDDataGraphNode::DynamicalModel.

Returns:

The dynamical model type.

---

function getDynamicalRoot

Returns the root of the dynamical model.

SBMDynamicalModelNodeRoot * SBMDynamicalModel::getDynamicalRoot () const

Retrieves the root node of the dynamical model.

Returns a pointer to the root node, or nullptr if unavailable.

Returns:

Pointer to the root node.

---

function getModelType

Returns the model type.

virtual SBDDataGraphNode::Type SBMDynamicalModel::getModelType () override const

Retrieves the model type identifier of this node.

Returns SBDDataGraphNode::DynamicalModel.

Returns:

The model type.

Implements SBMModel::getModelType

---

function getNodes [1/2]

Collects nodes into nodeIndexer , based on anodeType , a selection status and avisitPredicate , with or without dependencies.

virtual void SBMDynamicalModel::getNodes (
    SBNodeIndexer & nodeIndexer,
    SBNode::Type nodeType,
    bool selectedNodesOnly=false,
    const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(),
    bool includeDependencies=false
) override const

Collects nodes of a specified type into an indexer, optionally filtered by selection and visitation criteria.

If the visit predicate returns true for this node, it may be added to the indexer. Then child nodes of the root are recursively processed.

Parameters:

• nodeIndexer Indexer to receive the collected nodes.
• nodeType Type of nodes to collect.
• selectedNodesOnly If true, only selected nodes are collected.
• visitPredicate Predicate to determine whether to visit a node.
• includeDependencies If true, dependent nodes are also included.

Implements SBDDataGraphNode::getNodes

---

function getNodes [2/2]

Collects nodes into nodeIndexer , based on aselectionPredicate and avisitPredicate , with or without dependencies.

virtual void SBMDynamicalModel::getNodes (
    SBNodeIndexer & nodeIndexer,
    const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(),
    const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(),
    bool includeDependencies=false
) override const

Collects nodes satisfying a selection predicate into an indexer, optionally filtered by visitation criteria.

If the visit predicate returns true for this node and the selection predicate matches, the node is added to the indexer. Then child nodes of the root are recursively processed.

Parameters:

• nodeIndexer Indexer to receive the collected nodes.
• selectionPredicate Predicate that selects nodes to include.
• visitPredicate Predicate to determine whether to visit a node.
• includeDependencies If true, dependent nodes are also included.

Implements SBDDataGraphNode::getNodes

---

function getNumberOfChangedPositions

Returns the number of changed positions.

virtual unsigned int SBMDynamicalModel::getNumberOfChangedPositions () const

Returns the number of positions that have changed since the last flush.

Returns:

Number of changed positions.

---

function getPeriodicBoundaryConditions

Returns the periodic boundary conditions.

SBIAPosition3 const & SBMDynamicalModel::getPeriodicBoundaryConditions () const

Retrieves the periodic boundary condition vector of the model.

Returns a reference to the current periodic boundary condition vector. If no data is available, returns a zero vector.

Returns:

Reference to the periodic boundary conditions.

---

function getPeriodicBoundaryConditionsFlag

Returns the periodic boundary conditions flag.

bool SBMDynamicalModel::getPeriodicBoundaryConditionsFlag () const

Checks whether periodic boundary conditions are enabled.

Returns the current state of the periodic boundary condition flag.

Returns:

true if periodic boundary conditions are enabled, false otherwise.

---

function getPositionChanged

Returns whether position i has been changed since the last flush.

virtual bool SBMDynamicalModel::getPositionChanged (
    unsigned int i
) const

Checks whether the position at the given index has changed since the last flush.

Parameters:

• i Position index to query.

Returns:

true if the position has changed, false otherwise.

---

function getType

Returns the node type ( SBNode::DynamicalModel )

virtual SBDDataGraphNode::Type SBMDynamicalModel::getType () override const

Retrieves the type identifier of this node.

Returns SBDDataGraphNode::DynamicalModel, indicating that this node is a dynamical model.

Returns:

The node type.

Implements SBMModel::getType

---

function hasNode [1/2]

Checks for nodes based on a nodeType , a selection status and avisitPredicate , with or without dependencies.

virtual bool SBMDynamicalModel::hasNode (
    SBNode::Type nodeType,
    bool selectedNodesOnly=false,
    const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(),
    bool includeDependencies=false
) override const

Checks whether the dynamical model contains a node of the specified type.

Traverses the model hierarchy and returns true if a matching node is found, optionally limited to selected nodes or filtered by a predicate. Dependencies can be included based on the provided flag.

Parameters:

• nodeType The type of node to search for.
• selectedNodesOnly If true, only selected nodes are considered.
• visitPredicate Predicate used to filter visited nodes.
• includeDependencies If true, dependencies are included in the search.

Returns:

true if a matching node exists; otherwise false.

Implements SBDDataGraphNode::hasNode

---

function hasNode [2/2]

Checks for nodes based on a selectionPredicate and avisitPredicate , with or without dependencies.

virtual bool SBMDynamicalModel::hasNode (
    const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(),
    const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(),
    bool includeDependencies=false
) override const

Checks whether the dynamical model contains a node matching the given selection predicate.

Traverses the model hierarchy and returns true if a node satisfying the selection predicate is found. The traversal can be filtered using a visit predicate and may include dependencies.

Parameters:

• selectionPredicate Predicate that selects nodes of interest.
• visitPredicate Predicate used to filter visited nodes.
• includeDependencies If true, dependencies are considered during the search.

Returns:

true if a matching node exists; otherwise false.

Implements SBDDataGraphNode::hasNode

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function isSerializable

Returns true when the class is serializable.

virtual bool SBMDynamicalModel::isSerializable () override const

Determines whether the model supports serialization.

Returns false, indicating that SBMDynamicalModel does not support serialization.

Returns:

true if the model can be serialized, false otherwise.

Implements SBMModel::isSerializable

---

function print

Prints debugging information.

virtual void SBMDynamicalModel::print (
    unsigned int offset=0
) override const

Prints debugging information for the dynamical model.

The function outputs the model name, source file name, and recursively prints information for all descendant nodes with the specified indentation offset.

Parameters:

• offset Number of tab characters to prepend to each line of output.

Implements SBMModel::print

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function serialize

Serializes the node.

virtual void SBMDynamicalModel::serialize (
    SBCSerializer * serializer,
    const SBNodeIndexer & nodeIndexer,
    const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER,
    const SBVersionNumber & classVersionNumber=SBVersionNumber (1, 0, 0)
) override const

Serializes the SBMDynamicalModel.

Calls the base class SBMModel::serialize to serialize common model data.

Parameters:

• serializer Pointer to the serializer object.
• nodeIndexer Indexer describing which nodes to serialize.
• sdkVersionNumber SDK version number used for serialization (default SB_SDK_VERSION_NUMBER).
• classVersionNumber Class version number (default 1.0.0).

Implements SBMModel::serialize

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function setPeriodicBoundaryConditions

Sets the periodic boundary conditions.

void SBMDynamicalModel::setPeriodicBoundaryConditions (
    SBIAPosition3 const & box
) 

Sets the periodic boundary condition vector for the model.

Updates the periodic boundary condition vector and its derived properties, then enforces the conditions.

Parameters:

• v New periodic boundary condition vector.

---

function setPeriodicBoundaryConditionsFlag

Sets the periodic boundary conditions flag.

void SBMDynamicalModel::setPeriodicBoundaryConditionsFlag (
    bool flag
) 

Enables or disables periodic boundary conditions.

Sets the flag controlling whether periodic boundary conditions are applied.

Parameters:

• flag true to enable, false to disable.

---

function unserialize

Unserializes the node.

virtual void SBMDynamicalModel::unserialize (
    SBCSerializer * serializer,
    const SBNodeIndexer & nodeIndexer,
    const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER,
    const SBVersionNumber & classVersionNumber=SBVersionNumber (1, 0, 0)
) override

Unserializes the SBMDynamicalModel.

Calls the base class SBMModel::unserialize to restore model data.

Parameters:

• serializer Pointer to the serializer object.
• nodeIndexer Indexer describing which nodes to unserialize.
• sdkVersionNumber SDK version number used for unserialization (default SB_SDK_VERSION_NUMBER).
• classVersionNumber Class version number (default 1.0.0).

Implements SBMModel::unserialize

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function updateStructuralNodes

Updates structural nodes based on the state of the dynamical model.

virtual void SBMDynamicalModel::updateStructuralNodes () 

Updates structural nodes based on the current state of the dynamical model.

---

Protected Functions Documentation

function SBMDynamicalModel [1/2]

Builds a dynamical model.

SBMDynamicalModel::SBMDynamicalModel () 

Constructs a default SBMDynamicalModel instance.

Initializes a new SBMDynamicalModel object with a default data structure. The root node is set up and linked to the model.

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function SBMDynamicalModel [2/2]

Builds a dynamical model.

SBMDynamicalModel::SBMDynamicalModel (
    SBMDynamicalModelData * dataPointer
) 

Constructs an SBMDynamicalModel with provided data.

Initializes the model using the given SBMDynamicalModelData pointer, linking the root node to the model.

Parameters:

• dataPointer Pointer to the model data to be used for initialization.

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function ~SBMDynamicalModel

Deletes the dynamical model.

virtual SBMDynamicalModel::~SBMDynamicalModel () 

Destroys the SBMDynamicalModel instance.

Emits a NodeDeleteBegin event and cleans up resources associated with the model.

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