This class describes a bond in a structural model.

Constructors and destructors
	SBMStructuralModelNodeBond ()
	Constructs a bond.

	SBMStructuralModelNodeBond (SBMStructuralModelNodeAtom leftAtom, SBMStructuralModelNodeAtom rightAtom, const SBQuantity::dimensionless &order=SBQuantity::dimensionless(1.0))
	Constructs a bond between atoms `leftAtom` and `rightAtom` and a specific bond `order`.

virtual	~SBMStructuralModelNodeBond ()
	Destructs the bond.

Serialization
bool	isSerializable () const
	Returns true.

virtual void	serialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0)) const
	Serializes the bond.

virtual void	unserialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0))
	Unserializes the bond.

Topology
enum	BondType { Undefined, Single, Double, Triple, Amide, Aromatic, Dummy }
	The bond type. More...

SBQuantity::dimensionless const &	getOrder () const
	Returns the bond order.

void	setOrder (const SBQuantity::dimensionless &order)
	Sets the bond order to `order`.

BondType	getBondType () const
	Returns the bond type.

void	setBondType (BondType bondType)
	Sets the bond type to `bondType`.

SBMStructuralModelNodeAtom *	getLeftAtom () const
	Returns a pointer to the left atom.

SBMStructuralModelNodeAtom *	getRightAtom () const
	Returns a pointer to the right atom.

SBMStructuralModelNodeAtom *	getOppositeAtom (SBMStructuralModelNodeAtom *atom) const
	Returns the pointer to the atom opposite `atom`, when `atom` is either the left atom or the right atom of the bond.

SBQuantity::length	getLength () const
	Compute the length of the bond.

SBPosition3	getMidPoint () const
	Compute the mid point of the bond.

bool	isLinking (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if either atom is in `nodeIndexer`, or descends from a node of `nodeIndexer`.

virtual SBMStructuralModelNodeBond *	clone ()
	Returns a copy of the node and its descendants.

static std::string	getBondTypeString (BondType bondType)
	Returns the string corresponding to the `bondType`.

Identity
SBDDataGraphNode::Type	getType () const
	Returns the node type (SBNode::Bond)

Selection functions
virtual void	getNodes (SBNodeIndexer &nodeIndexer, const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false)
	Returns some nodes. More...

Properties
bool	hasStatusBit () const
	Returns true when the bond's status bit is set.

std::string const &	getStatusBit () const
	Returns the bond's status bit.

void	setStatusBit (const std::string &statusBit)
	Sets the bond's status bit.

void	clearStatusBit ()
	Clears the bond's status bit.

bool	hasCustomType () const
	Returns true when the bond's custom type is set.

int const &	getCustomType () const
	Returns the bond's custom type.

void	setCustomType (const int &water)
	Sets the bond's custom type.

void	clearCustomType ()
	Clears the bond's custom type.

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

Additional Inherited Members
Public Types inherited from SBDDataGraphNode
enum	Type { Undefined, StructuralModel, StructuralModelNode, StructuralModelConformation, Conformation, StructuralModelPath, Path, StructuralModelNodeGroup, StructuralGroup, StructuralModelNodeRoot, Root, StructuralModelNodeParticle, StructuralParticle, StructuralModelNodeAtom, Atom, StructuralModelNodePseudoAtom, PseudoAtom, StructuralModelNodeBond, Bond, StructuralModelNodeResidue, Residue, StructuralModelNodeSegment, Segment, StructuralModelNodeProtein, Protein, StructuralModelNodeChain, Chain, StructuralModelNodeMolecule, Molecule, StructuralModelNodeBackbone, Backbone, StructuralModelNodeSideChain, SideChain, VisualModel, DynamicalModel, DynamicalModelParticleSystem, ParticleSystem, DynamicalModelRigidBodySystem, RigidBodySystem, DynamicalModelArticulatedBodySystem, ArticulatedBodySystem, DynamicalModelNode, DynamicalNode, DynamicalModelNodeGroup, DynamicalGroup, DynamicalModelNodeRoot, DynamicalRoot, DynamicalModelNodeParticle, DynamicalParticle, DynamicalModelNodeRigidBody, RigidBody, DynamicalModelNodeArticulatedBody, ArticulatedBody, InteractionModel, InteractionModelParticleSystem, InteractionModelRigidBodySystem, InteractionModelArticulatedBodySystem, PropertyModel, PropertyModelFunction, Simulator, SimulatorParticleSystem, SimulatorRigidBodySystem, SimulatorArticulatedBodySystem, StateUpdater, StateUpdaterParticleSystem, StateUpdaterRigidBodySystem, StateUpdaterArticulatedBodySystem, DocumentManager, Document, Folder, Camera, Label, DataGraphNodeGroup, NodeGroup, Controller, ControllerNode }
	The type of the data graph node. More...

Public Member Functions inherited from SBMStructuralModelNode
virtual	~SBMStructuralModelNode ()

virtual SBPointerList< SBMStructuralModelNode > const *	getChildren () const

SBMStructuralModelNode *	getNextStructuralNode () const

SBMStructuralModelNode *	getPreviousStructuralNode () const

SBMStructuralModel *	getModel () const

bool	getMobilityFlag () const
	Returns the mobility flag.

void	setMobilityFlag (bool flag)
	Sets the mobility flag to `flag`.

void	connectStructuralSignalToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBStructuralEvent ), SBCReferenceTarget nextReferenceTarget=0, void(SBCReferenceTarget::nextFunctionPointer)(SBStructuralEvent )=0)

bool	structuralSignalIsConnectedToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBStructuralEvent *)) const

void	disconnectStructuralSignalFromSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBStructuralEvent *))

void	getAllStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer)

void	getInternalStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer)

void	getLeafStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer)

void	getStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode > &nodeIndexer, bool(selectionRule)(SBMStructuralModelNode *))

void	getAllStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer)

void	getInternalStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer)

void	getLeafStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer)

void	getStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode > &nodeIndexer, bool(selectionRule)(SBMStructuralModelNode *))

void	getAllStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer)

void	getInternalStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer)

void	getLeafStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer)

void	getStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode > &nodeIndexer, bool(selectionRule)(SBMStructuralModelNode *))

void	getStructuralNodesBreadthFirst (std::vector< SBMStructuralModelNode > &nodeVectorTopDown, std::vector< SBMStructuralModelNode > &nodeVectorBottomUp, bool(selectionRule)(SBMStructuralModelNode ))

virtual void	forEachNodeDepthFirst (void(action)(SBDDataGraphNode node))
	Performs an action on each node.

virtual void	forEachNodeDepthFirst (SBCClass object, void(SBCClass::action)(SBDDataGraphNode *node))
	Performs an action on each node.

void	forEachStructuralNodeBreadthFirst (void(action)(SBMStructuralModelNode node))

void	forEachStructuralNodeDepthFirst (void(action)(SBMStructuralModelNode node))

void	forEachStructuralNodeBreadthFirst (SBCClass object, void(SBCClass::action)(SBMStructuralModelNode *node))

void	forEachStructuralNodeDepthFirst (SBCClass object, void(SBCClass::action)(SBMStructuralModelNode *node))

Public Member Functions inherited from SBMModelNode
Public Member Functions inherited from SBDDataGraphNode
SBDDataGraphNode *	getParent () const
	Returns the parent of the node. More...

SBDDataGraphNode *	getThisNode () const
	Returns the pointer to this node. More...

SBDDataGraphNode *	getNextNode () const
	Returns the pointer to the next node in the children of the node's parent. More...

SBDDataGraphNode *	getPreviousNode () const
	Returns the pointer to the previous node in the children of the node's parent. More...

SBDDataGraphNode *	getNextNode (SBDDataGraphNode::Type nodeType) const
	Returns the pointer to the next node with type `nodeType` in the children of the node's parent. More...

SBDDataGraphNode *	getPreviousNode (SBDDataGraphNode::Type nodeType) const
	Returns the pointer to the previous node with type `nodeType` in the children of the node's parent. More...

SBDDocument *	getDocument () const
	Returns the document the node belongs to. More...

virtual bool	canAddChild (SBDDataGraphNode node, SBDDataGraphNode nextNode=0) const
	Returns whether this node can add `node` as a child. More...

virtual bool	canAddChildType (SBDDataGraphNode::Type nodeType) const
	Returns whether this node can add a node with type `nodeType` as a child. More...

virtual bool	addChild (SBDDataGraphNode node, SBDDataGraphNode nextNode=0)
	Adds a child to the node. More...

virtual bool	removeChild (SBDDataGraphNode *node)
	Removes a child from the node. More...

bool	hasOneOf (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodeIndexer`, or is the ancestor of one of them. More...

bool	isIn (SBDDataGraphNode *node) const
	Returns true if and only if this node is `node`, or descends from it. More...

bool	isIn (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodeIndexer`, or descends from one of them. More...

bool	isIn (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodePointerIndexer`, or descends from one of them. More...

bool	isOneOf (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodeIndexer`. More...

bool	isOneOf (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodePointerIndexer`. More...

SBDDataGraphNode *	getRoot () const
	Returns the root of the hierarchy the node belongs to. More...

unsigned int	getNodeIndex () const
	Returns the node index (unique in the whole data graph, but non-persistent) More...

bool	isType (Type type) const
	Returns true when the type of the node corresponds to `type`.

bool	isModel () const
	Returns true when the node is a model.

bool	isStructuralModel () const
	Returns true when the node is a structural model.

bool	isVisualModel () const
	Returns true when the node is a visual model.

bool	isDynamicalModel () const
	Returns true when the node is a dynamical model.

bool	isInteractionModel () const
	Returns true when the node is a interaction model.

bool	isPropertyModel () const
	Returns true when the node is a property model.

bool	isSimulator () const
	Returns true when the node is a simulator.

bool	isStructuralParticle () const
	Returns true when the node is a structural particle (an atom or a pseudo-atom)

bool	isCreated () const
	Returns true if and only if the node is created. More...

void	create ()
	Creates the node. More...

bool	isErased () const
	Returns true if and only if the node is erased. More...

void	erase ()
	Erases the node. More...

unsigned int	getFlags () const
	Returns the flags. More...

unsigned int	getInheritedFlags () const
	Returns the inherited flags. More...

bool	isSelected () const
	Returns whether the node is selected. More...

bool	getSelected () const
	Returns whether the node is visible.

bool	getSelectionFlag () const
	Returns the selection flag. More...

void	setSelectionFlag (bool flag)
	Sets the selection flag. More...

bool	isVisible () const
	Returns whether the node is visible. More...

bool	getVisible () const
	Returns whether the node is visible.

bool	getVisibilityFlag () const
	Returns the visibility flag. More...

void	setVisibilityFlag (bool flag)
	Sets the visibility flag. More...

bool	isHighlighted () const
	Returns whether the node is highlighted. More...

bool	getHighlightingFlag () const
	Returns the highlighting flag. More...

void	setHighlightingFlag (bool flag)
	Sets the highlighting flag. More...

void	connectBaseSignalToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBBaseEvent ), SBCReferenceTarget nextReferenceTarget=0, void(SBCReferenceTarget::nextFunctionPointer)(SBBaseEvent )=0)
	Connects the base signal to a slot. More...

bool	baseSignalIsConnectedToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBBaseEvent *)) const
	Returns true when the base signal is connected to a slot.

void	disconnectBaseSignalFromSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBBaseEvent *))
	Disconnects the base signal from a slot.

unsigned int	countNodes (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false)
	Collects nodes into `nodeIndexer`, based on a `selectionPredicate` and a `visitPredicate`, with our without dependencies. More...

bool	addMaterial (SBDDataGraphNodeMaterial *material)
	Adds a material. More...

bool	removeMaterial ()
	Removes the material. More...

SBDDataGraphNodeMaterial *	getMaterial () const
	Returns the material. More...

SBDDataGraphNode *	getMaterialOwner () const
	Returns the node whose material is inherited. More...

Public Member Functions inherited from SBCReferenceTarget
	SBCReferenceTarget ()

virtual	~SBCReferenceTarget ()

unsigned int	getMemoryFootprint () const

void	printReferencesToOwners () const

Static Public Member Functions inherited from SBMStructuralModelNode
static void	forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode > &selection, void(action)(SBMStructuralModelNode *node))

static void	forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode > &selection, SBCClass object, void(SBCClass::action)(SBMStructuralModelNode node))

Static Public Member Functions inherited from SBDDataGraphNode
static SBDDataGraphNode *	getNode (unsigned int nodeIndex)
	Returns the unique node corresponding to the node index `nodeIndex`. More...

static std::string	getTypeString (Type type)
	Returns a string describing the type of the data graph node. More...

static void	forEachNodeInSelection (SBNodeIndexer &nodeIndexer, void(action)(SBDDataGraphNode node))
	Performs an action for each node in a selection.

static void	forEachNodeInSelection (SBNodeIndexer &nodeIndexer, SBCClass object, void(SBCClass::action)(SBDDataGraphNode *node))
	Performs an action for each node in a selection.

Protected Member Functions inherited from SBMStructuralModelNode
	SBMStructuralModelNode ()
	Builds a structural model node.

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

Protected Member Functions inherited from SBMModelNode
	SBMModelNode ()
	Builds a base object.

	SBMModelNode (SBMModelNodeData *dataPointer)
	Builds a base object.

virtual	~SBMModelNode ()

Protected Member Functions inherited from SBDDataGraphNode
	SBDDataGraphNode ()
	Builds a data graph node. More...

	SBDDataGraphNode (SBDDataGraphNodeData *dataPointer)
	Builds a data graph node.

virtual	~SBDDataGraphNode ()
	Destroys the node. More...

Member Enumeration Documentation

◆ BondType

enum SBMStructuralModelNodeBond::BondType

Enumerator
Undefined	The bond type.
Single	The single bond type.
Double	The double bond type.
Triple	The triple bond type.
Amide	The amide bond type.
Aromatic	The aromatic bond type.
Dummy	The dummy bond type.

Member Function Documentation

◆ getNodes()

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

virtual

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.

Reimplemented from SBMStructuralModelNode.

Constructors and destructors

Serialization

Topology

Identity

Selection functions

Properties

Debugging

Additional Inherited Members

Member Enumeration Documentation

◆ BondType

Member Function Documentation

◆ getNodes()