Class SBMStructuralModelNodeBond

ClassList > SBMStructuralModelNodeBond

This class describes a bond in a structural model. More...

• #include <SBMStructuralModelNodeBond.hpp>

Inherits the following classes: SBMStructuralModelNode

Inherited by the following classes: SBMStructuralModelNodeHydrogenBond

Classes

Type	Name
class	IsLinking

Public Types

Type	Name
enum	BondType The bond type.

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
	SBMStructuralModelNodeBond () Constructs a bond.
	SBMStructuralModelNodeBond (SBMStructuralModelNodeAtom * leftAtom, SBMStructuralModelNodeAtom * rightAtom, const SBQuantity::dimensionless & order=SBQuantity::dimensionless(1.0)) Constructs a bond between atoms leftAtom andrightAtom and a specific bondorder .
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::dimensionless, GetOrder)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBMStructuralModelNodeBond::BondType, GetBondType)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBMStructuralModelNodeAtom *, GetLeftAtom)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBMStructuralModelNodeAtom *, GetRightAtom)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::length, GetLength)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBPosition3, GetMidPoint)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetStatusBit)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, int, GetCustomType)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasStatusBit)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasCustomType)
	SB_NODE_PREDICATE_1 (SB_SBMSTRUCTURALMODEL_EXPORT, IsLinkingElementType, SBMElement::Type)
void	clearCustomType () Clears the bond's custom type.
void	clearStatusBit () Clears the bond's status bit.
virtual SBMStructuralModelNodeBond *	clone () override Returns a copy of the node and its descendants.
BondType	getBondType () const Returns the bond type.
int const &	getCustomType () const Returns the bond's custom type.
const SBVector3 &	getDisplacement () const Returns the displacement used for display when multiple bond rendering is turned on.
SBMStructuralModelNodeAtom *	getLeftAtom () const Returns a pointer to the left atom.
SBQuantity::length	getLength () const Compute the length of the bond.
SBQuantity::dimensionless const &	getMaximumOrder () const Returns the maximum bond order for the inspector.
SBPosition3	getMidPoint () const Compute the mid point of the bond.
SBQuantity::dimensionless const &	getMinimumOrder () const Returns the minimum bond order for the inspector.
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.
SBMStructuralModelNodeAtom *	getOppositeAtom (const SBMStructuralModelNodeAtom * atom) const Returns the pointer to the atom opposite atom , whenatom is either the left atom or the right atom of the bond.
SBQuantity::dimensionless const &	getOrder () const Returns the bond order.
SBQuantity::dimensionless const &	getOrderSingleStep () const Returns the bond order single step for the inspector.
std::string	getOrderSuffix () const Returns the bond order suffix for the inspector.
SBMStructuralModelNodeAtom *	getRightAtom () const Returns a pointer to the right atom.
std::string const &	getStatusBit () const Returns the bond's status bit.
virtual SBDDataGraphNode::Type	getType () override const Returns the node type ( SBNode::Bond )
bool	hasCustomType () const Returns true when the bond's custom type is set.
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.
bool	hasStatusBit () const Returns true when the bond's status bit is set.
bool	isAmideBond () const Returns true if the bond is an amide bond, i.e. between a Nitrogen and a carbonyl Carbon: N-C=O.
bool	isCarbonylBond () const Returns true if the bond is a carbonyl bond (C=O)
bool	isEsterBond () const Returns true if the bond is an ester bond, i.e. between an Oxygen and a carbonyl Carbon: O-C=O.
bool	isLinking (SBMElement::Type elementType) const Returns true if and only if at least one of the atoms that the bond links is of element typeelementType .
bool	isLinking (const SBNodeIndexer & nodeIndexer) const Returns true if and only if either atom is innodeIndexer , or descends from a node ofnodeIndexer .
bool	isPrimaryAmideBond () const Returns true if the bond is a primary amide bond, i.e. an amid bond where the Nitrogen atom has exactly one non-Hydrogen bond.
bool	isSecondaryAmideBond () const Returns true if the bond is a secondary amide bond, i.e. an amid bond where the Nitrogen atom has exactly two non-Hydrogen bonds.
virtual bool	isSerializable () override const Returns true __
bool	isTertiaryAmideBond () const Returns true if the bond is a tertiary amide bond, i.e. an amid bond where the Nitrogen atom has exactly three non-Hydrogen bonds.
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 bond.
void	setBondType (BondType bondType) Sets the bond type to bondType .
void	setCustomType (const int & water) Sets the bond's custom type.
void	setOrder (const SBQuantity::dimensionless & order) Sets the bond order to order .
void	setStatusBit (const std::string & statusBit) Sets the bond's status bit.
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 bond.
virtual	~SBMStructuralModelNodeBond () Destructs the bond.

Public Functions inherited from SBMStructuralModelNode

See SBMStructuralModelNode

Type	Name
virtual SBMStructuralModelNode *	clone () override Returns a copy of the node and its descendants.
void	connectStructuralSignalToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBStructuralEvent *) functionPointer, SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any, SBCReferenceTarget * nextReferenceTarget=nullptr, void(SBCReferenceTarget::*)(SBStructuralEvent *) nextFunctionPointer=nullptr) Connects the structural signal to a slot.
void	disconnectStructuralSignalFromSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBStructuralEvent *) functionPointer, SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any) Disconnects the structural signal from a slot.
virtual void	forEachNodeDepthFirst (void(*)(SBDDataGraphNode *node) action) override Performs the action on this node.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) override Performs the object 'saction on this node.
void	forEachStructuralNodeBreadthFirst (void(*)(SBMStructuralModelNode *node) action) Performs the action on this node and all its structural node children in the breadth-first way.
void	forEachStructuralNodeBreadthFirst (SBCClass * object, void(SBCClass::*)(SBMStructuralModelNode *node) action) Performs the object 'saction on this node and all its structural node children in the breadth-first way.
void	forEachStructuralNodeDepthFirst (void(*)(SBMStructuralModelNode *node) action) Performs the action on this node and all its structural node children in the depth-first way.
void	forEachStructuralNodeDepthFirst (SBCClass * object, void(SBCClass::*)(SBMStructuralModelNode *node) action) Performs the object 'saction on this node and all its structural node children in the depth-first way.
void	getAllStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates nodeIndexer with all structural nodes (the node itself and all its structural node children), breadth-first, bottom-up.
void	getAllStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates nodeIndexer with all structural nodes (the node itself and all its structural node children), breadth-first, top-down.
void	getAllStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates nodeIndexer with all structural nodes (the node itself and all its structural node children), depth-first.
virtual SBPointerList< SBMStructuralModelNode > const *	getChildren () const Returns the list of child nodes.
void	getInternalStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates nodeIndexer with internal structural nodes (the node's structural node children), breadth-first, bottom-up.
void	getInternalStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates nodeIndexer with internal structural nodes (the node's structural node children), breadth-first, top-down.
void	getInternalStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates nodeIndexer with internal structural nodes (the node's structural node children), depth-first.
void	getLeafStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates nodeIndexer with leaf structural nodes (i.e., only with the nodes that have no shildren), breadth-first, bottom-up.
void	getLeafStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates nodeIndexer with leaf structural nodes (i.e., only with the nodes that have no shildren), breadth-first, top-down.
void	getLeafStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates nodeIndexer with leaf structural nodes (i.e., only with the nodes that have no shildren), depth-first.
virtual bool	getLockedFlag () override const Returns the locked flag of the model.
SBMStructuralModel *	getModel () const Returns a pointer to the structural model this structural node belongs to.
SBMStructuralModelNode *	getNextStructuralNode () const Returns the next structural node in the node's parent.
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	getOpacity () override const Returns the opacity.
SBMStructuralModelNode *	getPreviousStructuralNode () const Returns the previous structural node in the node's parent.
void	getStructuralNodesBreadthFirst (std::vector< SBMStructuralModelNode * > & nodeVectorTopDown, std::vector< SBMStructuralModelNode * > & nodeVectorBottomUp, bool(*)(SBMStructuralModelNode *) selectionRule) Selects some structural nodes, breadth-first, both top-down and bottom-up.
void	getStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool(*)(SBMStructuralModelNode *) selectionRule) Populates nodeIndexer with some structural nodes based on theselectionRule , breadth-first, bottom-up.
void	getStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool(*)(SBMStructuralModelNode *) selectionRule) Populates nodeIndexer with some structural nodes based on theselectionRule , breadth-first, top-down.
void	getStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool(*)(SBMStructuralModelNode *) selectionRule) Populates nodeIndexer with some structural nodes based on theselectionRule , depth-first.
bool	getStructuralSignalFlag () const Returns true when the node can send structural signals.
virtual unsigned int	getTransparency () override const Returns the transparency.
virtual SBDDataGraphNode::Type	getType () override const Returns the node type.
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	isLocked () override const Returns whether the node is locked (because of the model)
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.
void	setStructuralSignalFlag (bool structuralSignalFlag) Sets whether the node can send structural signals.
bool	structuralSignalIsConnectedToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBStructuralEvent *) functionPointer, SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any) const Returns true if and only if the structural signal is connected to a given slot.
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	~SBMStructuralModelNode () Destructor.

Public Functions inherited from SBMModelNode

See SBMModelNode

Type	Name
virtual SBMModelNode *	clone () override Returns a copy of the node and its descendants.
virtual SBDDataGraphNode::Type	getType () override const Returns the type of the data graph node.
virtual bool	isSerializable () override 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)) override 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)) override Unserializes the node.

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

Type	Name
std::string	getBondTypeString (BondType bondType) Returns the string corresponding to the bondType .

Public Static Functions inherited from SBMStructuralModelNode

See SBMStructuralModelNode

Type	Name
void	forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode * > & selection, void(*)(SBMStructuralModelNode *node) action) Performs the action on nodes in theselection __
void	forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode * > & selection, SBCClass * object, void(SBCClass::*)(SBMStructuralModelNode *node) action) Performs the object 'saction on nodes in theselection __

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
	SBMStructuralModelNodeBond (SBMStructuralModelNodeBondData * dataPointer) Builds a bond.

Protected Functions inherited from SBMStructuralModelNode

See SBMStructuralModelNode

Type	Name
	SBMStructuralModelNode () Builds a structural model node.
	SBMStructuralModelNode (SBMStructuralModelNodeData * dataPointer) Builds a structural model node.

Protected Functions inherited from SBMModelNode

See SBMModelNode

Type	Name
	SBMModelNode () Builds a base object.
	SBMModelNode (SBMModelNodeData * dataPointer) Builds a base object.
virtual	~SBMModelNode () Destructor.

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: SBBond

Public Types Documentation

enum BondType

The bond type.

enum SBMStructuralModelNodeBond::BondType {
    Undefined = 0,
    Single = 1,
    Double = 2,
    Triple = 3,
    Amide = 4,
    Aromatic = 5,
    Dummy = 6
};

---

Public Functions Documentation

function SBMStructuralModelNodeBond [1/3]

Constructs a bond.

SBMStructuralModelNodeBond::SBMStructuralModelNodeBond () 

Constructs a bond node with default parameters.

This constructor creates a new bond node with an empty data object. The bond has no atoms and uses the default order.

---

function SBMStructuralModelNodeBond [2/3]

Constructs a bond between atoms leftAtom andrightAtom and a specific bondorder .

SBMStructuralModelNodeBond::SBMStructuralModelNodeBond (
    SBMStructuralModelNodeAtom * leftAtom,
    SBMStructuralModelNodeAtom * rightAtom,
    const SBQuantity::dimensionless & order=SBQuantity::dimensionless (1.0)
) 

Constructs a bond between two atoms with a specified order.

This constructor creates a bond node linking the given left and right atoms and sets the bond order to the specified value.

Parameters:

• l Pointer to the left atom, or nullptr if not specified.
• r Pointer to the right atom, or nullptr if not specified.
• o The bond order to assign.

---

function SB_NODE_GETTER_0 [1/8]

SBMStructuralModelNodeBond::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::dimensionless,
    GetOrder
) 

---

function SB_NODE_GETTER_0 [2/8]

SBMStructuralModelNodeBond::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBMStructuralModelNodeBond::BondType,
    GetBondType
) 

---

function SB_NODE_GETTER_0 [3/8]

SBMStructuralModelNodeBond::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBMStructuralModelNodeAtom *,
    GetLeftAtom
) 

---

function SB_NODE_GETTER_0 [4/8]

SBMStructuralModelNodeBond::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBMStructuralModelNodeAtom *,
    GetRightAtom
) 

---

function SB_NODE_GETTER_0 [5/8]

SBMStructuralModelNodeBond::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::length,
    GetLength
) 

---

function SB_NODE_GETTER_0 [6/8]

SBMStructuralModelNodeBond::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBPosition3,
    GetMidPoint
) 

---

function SB_NODE_GETTER_0 [7/8]

SBMStructuralModelNodeBond::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetStatusBit
) 

---

function SB_NODE_GETTER_0 [8/8]

SBMStructuralModelNodeBond::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    int,
    GetCustomType
) 

---

function SB_NODE_PREDICATE_0 [1/2]

SBMStructuralModelNodeBond::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasStatusBit
) 

---

function SB_NODE_PREDICATE_0 [2/2]

SBMStructuralModelNodeBond::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasCustomType
) 

---

function SB_NODE_PREDICATE_1

SBMStructuralModelNodeBond::SB_NODE_PREDICATE_1 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsLinkingElementType,
    SBMElement::Type
) 

---

function clearCustomType

Clears the bond's custom type.

void SBMStructuralModelNodeBond::clearCustomType () 

---

function clearStatusBit

Clears the bond's status bit.

void SBMStructuralModelNodeBond::clearStatusBit () 

---

function clone

Returns a copy of the node and its descendants.

virtual SBMStructuralModelNodeBond * SBMStructuralModelNodeBond::clone () override

Creates a copy of the bond node.

Returns:

Pointer to the cloned bond.

Implements SBMStructuralModelNode::clone

---

function getBondType

Returns the bond type.

BondType SBMStructuralModelNodeBond::getBondType () const

Returns the type of the bond.

Returns:

The bond type.

---

function getCustomType

Returns the bond's custom type.

int const & SBMStructuralModelNodeBond::getCustomType () const

---

function getDisplacement

Returns the displacement used for display when multiple bond rendering is turned on.

const SBVector3 & SBMStructuralModelNodeBond::getDisplacement () const

Returns the displacement vector used for display when multiple bond rendering is enabled.

Returns:

Reference to the displacement vector.

---

function getLeftAtom

Returns a pointer to the left atom.

SBMStructuralModelNodeAtom * SBMStructuralModelNodeBond::getLeftAtom () const

Returns a pointer to the left atom of the bond.

Returns:

Pointer to the left atom.

---

function getLength

Compute the length of the bond.

SBQuantity::length SBMStructuralModelNodeBond::getLength () const

Computes the length of the bond.

Returns:

The length of the bond.

---

function getMaximumOrder

Returns the maximum bond order for the inspector.

SBQuantity::dimensionless const & SBMStructuralModelNodeBond::getMaximumOrder () const

Returns:

Reference to the maximum bond order.

---

function getMidPoint

Compute the mid point of the bond.

SBPosition3 SBMStructuralModelNodeBond::getMidPoint () const

Computes the midpoint of the bond.

Returns:

The midpoint position.

---

function getMinimumOrder

Returns the minimum bond order for the inspector.

SBQuantity::dimensionless const & SBMStructuralModelNodeBond::getMinimumOrder () const

Returns:

Reference to the minimum bond order.

---

function getNodes [1/2]

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

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

Adds the bond and optionally its atoms to a node indexer.

This function adds to nodeIndexer the bond itself (if the predicates are valid) and, if includeDependencies is true, attempts to add the bonded atoms as well.

Parameters:

• nodeIndexer The node indexer to which nodes are added.
• nodeType The type of node to add.
• selectedNodesOnly If true, only selected nodes are considered.
• visitPredicate Predicate that determines whether a node should be visited.
• includeDependencies If true, also adds the bonded atoms as well.

Implements SBMStructuralModelNode::getNodes

---

function getNodes [2/2]

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

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

Adds the bond and optionally its atoms to a node indexer.

This function adds to nodeIndexer the bond itself (if the predicates are valid) and, if includeDependencies is true, attempts to add the bonded atoms as well.

Parameters:

• nodeIndexer The node indexer to which nodes are added.
• selectionPredicate Predicate that selects nodes to be added.
• visitPredicate Predicate that determines whether a node should be visited.
• includeDependencies If true, also adds the bonded atoms.

Implements SBMStructuralModelNode::getNodes

---

function getOppositeAtom

Returns the pointer to the atom opposite atom , whenatom is either the left atom or the right atom of the bond.

SBMStructuralModelNodeAtom * SBMStructuralModelNodeBond::getOppositeAtom (
    const SBMStructuralModelNodeAtom * atom
) const

Returns the atom opposite the specified atom in the bond.

Parameters:

• atom Pointer to one of the bond's atoms.

Returns:

Pointer to the opposite atom, or nullptr if the input atom is not part of the bond.

---

function getOrder

Returns the bond order.

SBQuantity::dimensionless const & SBMStructuralModelNodeBond::getOrder () const

Returns:

The bond order as a dimensionless quantity.

---

function getOrderSingleStep

Returns the bond order single step for the inspector.

SBQuantity::dimensionless const & SBMStructuralModelNodeBond::getOrderSingleStep () const

Returns the step size for bond order increments in the inspector.

Returns:

Reference to the bond order single step.

---

function getOrderSuffix

Returns the bond order suffix for the inspector.

std::string SBMStructuralModelNodeBond::getOrderSuffix () const

Returns the suffix string used for the bond order in the inspector.

Returns:

The bond order suffix.

---

function getRightAtom

Returns a pointer to the right atom.

SBMStructuralModelNodeAtom * SBMStructuralModelNodeBond::getRightAtom () const

Returns a pointer to the right atom of the bond.

Returns:

Pointer to the right atom.

---

function getStatusBit

Returns the bond's status bit.

std::string const & SBMStructuralModelNodeBond::getStatusBit () const

---

function getType

Returns the node type ( SBNode::Bond )

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

Returns the node type identifier for a bond.

Returns:

The type SBDDataGraphNode::StructuralModelNodeBond.

Implements SBMStructuralModelNode::getType

---

function hasCustomType

Returns true when the bond's custom type is set.

bool SBMStructuralModelNodeBond::hasCustomType () const

---

function hasNode [1/2]

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

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

Checks whether the bond or its atoms satisfy the given criteria.

This function checks the bond itself (if the predicates are valid) and, if includeDependencies is true, checks the bonded atoms as well.

Parameters:

• nodeType The type of node to check.
• selectedNodesOnly If true, only selected nodes are considered.
• visitPredicate Predicate that determines whether a node should be visited.
• includeDependencies If true, also checks the bonded atoms.

Returns:

true if the bond or one of its atoms matches the criteria; otherwise false.

Implements SBMStructuralModelNode::hasNode

---

function hasNode [2/2]

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

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

Checks whether the bond or its atoms satisfy the given predicates.

This function checks the bond itself (if the predicates are valid) and, if includeDependencies is true, checks the bonded atoms as well.

Parameters:

• selectionPredicate Predicate that selects nodes to be checked.
• visitPredicate Predicate that determines whether a node should be visited.
• includeDependencies If true, also checks the bonded atoms.

Returns:

true if the bond or one of its atoms matches the criteria; otherwise false.

Implements SBMStructuralModelNode::hasNode

---

function hasStatusBit

Returns true when the bond's status bit is set.

bool SBMStructuralModelNodeBond::hasStatusBit () const

---

function isAmideBond

Returns true if the bond is an amide bond, i.e. between a Nitrogen and a carbonyl Carbon: N-C=O.

bool SBMStructuralModelNodeBond::isAmideBond () const

Returns true if the bond is an amide bond (a bond between a nitrogen and a carbonyl carbon).

The amide has a general formula RC(=O)NR'R'', where R, R', and R'' represent organic groups or hydrogen atoms. This function checks for a single C-N bond in which the nitrogen has three bonds and the carbon is part of a carbonyl group (C=O).

Returns:

true if the bond is an amide bond; otherwise false.

---

function isCarbonylBond

Returns true if the bond is a carbonyl bond (C=O)

bool SBMStructuralModelNodeBond::isCarbonylBond () const

Returns true if the bond is a carbonyl bond (a double bond between carbon and oxygen).

Returns:

true if the bond is a carbonyl bond; otherwise false.

---

function isEsterBond

Returns true if the bond is an ester bond, i.e. between an Oxygen and a carbonyl Carbon: O-C=O.

bool SBMStructuralModelNodeBond::isEsterBond () const

Returns true if the bond is an ester bond (a single bond between an oxygen and a carbonyl carbon, with the carbon also forming a carbonyl bond elsewhere).

Returns:

true if the bond is an ester bond; otherwise false.

---

function isLinking [1/2]

Returns true if and only if at least one of the atoms that the bond links is of element typeelementType .

bool SBMStructuralModelNodeBond::isLinking (
    SBMElement::Type elementType
) const

Determines whether the bond links an atom of the specified element type.

Parameters:

• elementType The element type to check.

Returns:

true if at least one of the bonded atoms matches the element type; otherwise false.

---

function isLinking [2/2]

Returns true if and only if either atom is innodeIndexer , or descends from a node ofnodeIndexer .

bool SBMStructuralModelNodeBond::isLinking (
    const SBNodeIndexer & nodeIndexer
) const

Determines whether the bond links any atom contained in the given node indexer.

Parameters:

• nodeIndexer The node indexer to check.

Returns:

true if either atom is in the nodeIndexer or descends from a node in the nodeIndexer; otherwise false.

---

function isPrimaryAmideBond

Returns true if the bond is a primary amide bond, i.e. an amid bond where the Nitrogen atom has exactly one non-Hydrogen bond.

bool SBMStructuralModelNodeBond::isPrimaryAmideBond () const

Returns true if the bond is an amide bond and the nitrogen has exactly one non-hydrogen bond.

Returns:

true if the bond is a primary amide bond; otherwise false.

---

function isSecondaryAmideBond

Returns true if the bond is a secondary amide bond, i.e. an amid bond where the Nitrogen atom has exactly two non-Hydrogen bonds.

bool SBMStructuralModelNodeBond::isSecondaryAmideBond () const

Returns true if the bond is an amide bond and the nitrogen has exactly two non-hydrogen bonds.

Returns:

true if the bond is a secondary amide bond; otherwise false.

---

function isSerializable

Returns true __

virtual bool SBMStructuralModelNodeBond::isSerializable () override const

Indicates whether the bond node can be serialized.

Returns:

true because bond nodes are serializable.

Implements SBMStructuralModelNode::isSerializable

---

function isTertiaryAmideBond

Returns true if the bond is a tertiary amide bond, i.e. an amid bond where the Nitrogen atom has exactly three non-Hydrogen bonds.

bool SBMStructuralModelNodeBond::isTertiaryAmideBond () const

Returns true if the bond is an amide bond and the nitrogen has exactly three non-hydrogen bonds.

Returns:

true if the bond is a tertiary amide bond; otherwise false.

---

function print

Prints debugging information.

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

Prints debugging information for the bond.

Parameters:

• offset Number of tabs to indent the output.

Implements SBMStructuralModelNode::print

---

function serialize

Serializes the bond.

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

Serializes the bond node to a serializer.

This function writes the bond type, order, atom references (by index or address), and optional properties such as status bit and custom type to the provided serializer.

Parameters:

• serializer The serializer used to write the data.
• nodeIndexer Indexer that maps nodes to indices for serialization.
• sdkVersionNumber The SDK version number.
• classVersionNumber The class version number.

Implements SBMStructuralModelNode::serialize

---

function setBondType

Sets the bond type to bondType .

void SBMStructuralModelNodeBond::setBondType (
    BondType bondType
) 

Sets the bond type.

Parameters:

• bt The new bond type to assign.

---

function setCustomType

Sets the bond's custom type.

void SBMStructuralModelNodeBond::setCustomType (
    const int & water
) 

---

function setOrder

Sets the bond order to order .

void SBMStructuralModelNodeBond::setOrder (
    const SBQuantity::dimensionless & order
) 

Sets the bond order to a new value.

The bond order is updated only if the node is not locked and the new order is non-negative. This operation clears the hybridization of the bonded atoms and emits a structural event indicating the bond order change.

Parameters:

• o The new bond order to set.

Note: If an undo command is being recorded, the change is undoable.

---

function setStatusBit

Sets the bond's status bit.

void SBMStructuralModelNodeBond::setStatusBit (
    const std::string & statusBit
) 

---

function unserialize

Unserializes the bond.

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

Deserializes the bond node from a serializer.

This function reads the bond type, order, atom references (by index or address), and optional properties such as status bit and custom type from the provided serializer, and restores the bond node state.

Parameters:

• serializer The serializer used to read the data.
• nodeIndexer Indexer that maps indices to nodes for deserialization.
• sdkVersionNumber The SDK version number.
• classVersionNumber The class version number.

Implements SBMStructuralModelNode::unserialize

---

function ~SBMStructuralModelNodeBond

Destructs the bond.

virtual SBMStructuralModelNodeBond::~SBMStructuralModelNodeBond () 

Destroys the bond node and emits a deletion event.

---

Public Static Functions Documentation

function getBondTypeString

Returns the string corresponding to the bondType .

static std::string SBMStructuralModelNodeBond::getBondTypeString (
    BondType bondType
) 

Returns a string representation of the given bond type.

Parameters:

• bondType The bond type to convert.

Returns:

The string corresponding to the bond type.

---

Protected Functions Documentation

function SBMStructuralModelNodeBond [3/3]

Builds a bond.

SBMStructuralModelNodeBond::SBMStructuralModelNodeBond (
    SBMStructuralModelNodeBondData * dataPointer
) 

Constructs a bond from an existing data pointer (internal use).

Parameters:

• dataPointer Pointer to the internal data structure representing the bond.

---