Class SBMStructuralModelNodeHydrogenBond#

ClassList > SBMStructuralModelNodeHydrogenBond

#include <SBMStructuralModelNodeHydrogenBond.hpp>

Inherits the following classes: SBMStructuralModelNodeBond

Classes#

Type	Name
class	IsLinking

Public Types inherited from SBMStructuralModelNodeBond#

See SBMStructuralModelNodeBond

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
	SBMStructuralModelNodeHydrogenBond () Constructs a H-bond.
	SBMStructuralModelNodeHydrogenBond (SBMStructuralModelNodeAtom * acceptor, SBMStructuralModelNodeAtom * donor, SBMStructuralModelNodeAtom * hydrogen=nullptr) Constructs a H-bond.
	SB_DECLARE_DATA (SBMStructuralModelNodeHydrogenBond)
	SB_NODE_GETTER_0 (SBMStructuralModelNodeAtom *, GetAcceptor)
	SB_NODE_GETTER_0 (SBMStructuralModelNodeAtom *, GetDonor)
	SB_NODE_GETTER_0 (SBMStructuralModelNodeAtom *, GetHydrogen)
	SB_NODE_GETTER_0 (SBQuantity::length, GetDonorAcceptorDistance)
	SB_NODE_GETTER_0 (SBQuantity::length, GetHydrogenAcceptorDistance)
	SB_NODE_GETTER_0 (SBQuantity::length, GetDonorHydrogenDistance)
	SB_NODE_GETTER_0 (SBQuantity::degree, GetAngle)
virtual SBMStructuralModelNodeHydrogenBond *	clone () override Returns a copy of the node and its descendants.
SBMStructuralModelNodeAtom *	getAcceptor () const Returns a pointer to the acceptor atom.
SBQuantity::degree	getAngle () const Returns the donor-hydrogen-acceptor angle.
SBMStructuralModelNodeAtom *	getDonor () const Returns a pointer to the donor atom.
SBQuantity::length	getDonorAcceptorDistance () const Returns the donor-acceptor distance.
SBQuantity::length	getDonorHydrogenDistance () const Returns the donor-hydrogen distance.
SBMStructuralModelNodeAtom *	getHydrogen () const Returns a pointer to the hydrogen atom.
SBQuantity::length	getHydrogenAcceptorDistance () const Returns the hydrogen-acceptor distance.
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 a`nodeType` , a selection status and a`visitPredicate` , 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 a`selectionPredicate` and a`visitPredicate` , with or without dependencies.
virtual SBDDataGraphNode::Type	getType () override const Returns the node type ( SBNode::HydrogenBond )
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 a`visitPredicate` , 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 a`visitPredicate` , with or without dependencies.
bool	isLinking (const SBNodeIndexer & nodeIndexer) const Returns true if and only if donor and acceptor atoms are in `nodeIndexer` , or descends from a node of`nodeIndexer` .
virtual bool	isSerializable () override const Returns false.
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	setSelectionFlag (bool flag) Sets the selection flag and selects corresponding atoms.
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	~SBMStructuralModelNodeHydrogenBond () Destructs the H-bond.

Public Functions inherited from SBMStructuralModelNodeBond#

See SBMStructuralModelNodeBond

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` and`rightAtom` and a specific bond`order` .
	SB_DECLARE_DATA (SBMStructuralModelNodeBond)
	SB_NODE_GETTER_0 (SBQuantity::dimensionless, GetOrder)
	SB_NODE_GETTER_0 (SBMStructuralModelNodeBond::BondType, GetBondType)
	SB_NODE_GETTER_0 (SBMStructuralModelNodeAtom *, GetLeftAtom)
	SB_NODE_GETTER_0 (SBMStructuralModelNodeAtom *, GetRightAtom)
	SB_NODE_GETTER_0 (SBQuantity::length, GetLength)
	SB_NODE_GETTER_0 (SBPosition3, GetMidPoint)
	SB_NODE_GETTER_0 (std::string, GetStatusBit)
	SB_NODE_GETTER_0 (int, GetCustomType)
	SB_NODE_PREDICATE_0 (HasStatusBit)
	SB_NODE_PREDICATE_0 (HasCustomType)
	SB_NODE_PREDICATE_1 (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 a`nodeType` , a selection status and a`visitPredicate` , 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 a`selectionPredicate` and a`visitPredicate` , with or without dependencies.
SBMStructuralModelNodeAtom *	getOppositeAtom (const 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::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 a`visitPredicate` , 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 a`visitPredicate` , 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 type `elementType` .
bool	isLinking (const SBNodeIndexer & nodeIndexer) const Returns true if and only if either atom is in `nodeIndexer` , or descends from a node of`nodeIndexer` .
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
	SB_DECLARE_DATA (SBMStructuralModelNode)
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=0, void(SBCReferenceTarget::)(SBStructuralEvent* *) nextFunctionPointer=0)
void	disconnectStructuralSignalFromSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::)(SBStructuralEvent* ) functionPointer, SBStructuralEvent::Type* eventType=SBStructuralEvent::Type::Any)
virtual void	forEachNodeDepthFirst (void()(SBDDataGraphNode* node) action) override Performs an action on each node.*
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) override Performs an action on each node.*
void	forEachStructuralNodeBreadthFirst (void()(SBMStructuralModelNode* *node) action)
void	forEachStructuralNodeBreadthFirst (SBCClass * object, void(SBCClass::)(SBMStructuralModelNode* *node) action)
void	forEachStructuralNodeDepthFirst (void()(SBMStructuralModelNode* *node) action)
void	forEachStructuralNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBMStructuralModelNode* *node) action)
void	getAllStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer)
void	getAllStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer)
void	getAllStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer)
virtual SBPointerList< SBMStructuralModelNode > const *	getChildren () const Returns the list of child nodes.
void	getInternalStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer)
void	getInternalStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer)
void	getInternalStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer)
void	getLeafStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer)
void	getLeafStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer)
void	getLeafStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer)
virtual bool	getLockedFlag () override const Returns the locked flag of the model.
virtual unsigned int	getMaximumTransparency () override const Returns the maximum transparency.
virtual unsigned int	getMinimumOpacity () override const Returns the minimum opacity.
SBMStructuralModel *	getModel () const
SBMStructuralModelNode *	getNextStructuralNode () const
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 a`nodeType` , a selection status and a`visitPredicate` , 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 a`selectionPredicate` and a`visitPredicate` , with or without dependencies.
virtual unsigned int	getOpacity () override const Returns the opacity.
SBMStructuralModelNode *	getPreviousStructuralNode () const
void	getStructuralNodesBreadthFirst (std::vector< SBMStructuralModelNode * > & nodeVectorTopDown, std::vector< SBMStructuralModelNode * > & nodeVectorBottomUp, bool()(SBMStructuralModelNode* *) selectionRule)
void	getStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool()(SBMStructuralModelNode* *) selectionRule)
void	getStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool()(SBMStructuralModelNode* *) selectionRule)
void	getStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool()(SBMStructuralModelNode* *) selectionRule)
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 type of the data graph node.
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 a`visitPredicate` , 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 a`visitPredicate` , 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
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 ()

Public Functions inherited from SBMModelNode#

See SBMModelNode

Type	Name
	SB_DECLARE_DATA (SBMModelNode)
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_DECLARE_DATA (SBDDataGraphNode)
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 a`visitPredicate` , 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 a`visitPredicate` , with or without dependencies.
void	create () Creates the node.
bool	descendsFrom (const SBDDataGraphNode * node) const Returns true if and only if this node is `node` , or descends from it.
bool	descendsFrom (const SBNodeIndexer & nodeIndexer) const Returns true if and only if this node is one of the nodes of the `nodeIndexer` , or descends from one of them.
bool	descendsFrom (SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer) const Returns true if and only if this node is one of the nodes of the `nodePointerIndexer` , or descends from one of them.
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 an action on each node.*
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) Performs an action on each node.*
virtual unsigned int	getDefaultOpacity () const Returns the default opacity.
virtual 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.
virtual unsigned int	getMaximumOpacity () const Returns the maximum opacity.
virtual unsigned int	getMaximumTransparency () const Returns the maximum transparency.
virtual unsigned int	getMinimumOpacity () const Returns the minimum opacity.
virtual 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 a`nodeType` , a selection status and a`visitPredicate` , 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 a`selectionPredicate` and a`visitPredicate` , 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.
virtual unsigned int	getOpacitySingleStep () const Returns the opacity single step.
virtual 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.
virtual unsigned int	getTransparencySingleStep () const Returns the transparency single step.
virtual 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 a`visitPredicate` , 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 a`visitPredicate` , with or without dependencies.
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, or is a group that stores one of them.
virtual bool	hasOpacityRange () const Returns whether the node has the opacity range.
virtual 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 is `node` , or descends from it, or belongs to a group stored in`node` .
bool	isIn (const SBNodeIndexer & nodeIndexer) const Returns true if and only if this node is one of the nodes of the `nodeIndexer` , or descends from one of them, or belongs to a group stored in one of the nodes of the`nodeIndexer` .
bool	isIn (SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer) const Returns true if and only if this node is one of the nodes of the `nodePointerIndexer` , or descends from one of them, or belongs to a group stored in of the nodes of the`nodePointerIndexer` .
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 the `nodeIndexer` .
bool	isOneOf (SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer) const Returns true if and only if this node is one of the nodes of the `nodePointerIndexer` .
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 to `type` .
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 ()
unsigned int	getMemoryFootprint () const
void	printReferencesToOwners () const
virtual	~SBCReferenceTarget ()

Public Static Functions#

Type	Name
SBQuantity::degree	getAngle (SBMStructuralModelNodeAtom * donor, SBMStructuralModelNodeAtom * hydrogen, SBMStructuralModelNodeAtom * acceptor) Returns the donor-hydrogen-acceptor angle.

Public Static Functions inherited from SBMStructuralModelNodeBond#

See SBMStructuralModelNodeBond

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

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

Protected Functions inherited from SBMStructuralModelNodeBond#

See SBMStructuralModelNodeBond

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 ()

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)
void	removeAllReferenceOwners ()

Detailed Description#

This class describes a bond in a structural model.

Short name: SBHydrogenBond

Public Functions Documentation#

function SBMStructuralModelNodeHydrogenBond [1/2]#

Constructs a H-bond.

SBMStructuralModelNodeHydrogenBond::SBMStructuralModelNodeHydrogenBond ()

function SBMStructuralModelNodeHydrogenBond [2/2]#

Constructs a H-bond.

SBMStructuralModelNodeHydrogenBond::SBMStructuralModelNodeHydrogenBond (
    SBMStructuralModelNodeAtom * acceptor,
    SBMStructuralModelNodeAtom * donor,
    SBMStructuralModelNodeAtom * hydrogen=nullptr
)

function SB_DECLARE_DATA#

SBMStructuralModelNodeHydrogenBond::SB_DECLARE_DATA (
    SBMStructuralModelNodeHydrogenBond
)

function SB_NODE_GETTER_0 [1/7]#

SBMStructuralModelNodeHydrogenBond::SB_NODE_GETTER_0 (
    SBMStructuralModelNodeAtom *,
    GetAcceptor
)

function SB_NODE_GETTER_0 [2/7]#

SBMStructuralModelNodeHydrogenBond::SB_NODE_GETTER_0 (
    SBMStructuralModelNodeAtom *,
    GetDonor
)

function SB_NODE_GETTER_0 [3/7]#

SBMStructuralModelNodeHydrogenBond::SB_NODE_GETTER_0 (
    SBMStructuralModelNodeAtom *,
    GetHydrogen
)

function SB_NODE_GETTER_0 [4/7]#

SBMStructuralModelNodeHydrogenBond::SB_NODE_GETTER_0 (
    SBQuantity::length,
    GetDonorAcceptorDistance
)

function SB_NODE_GETTER_0 [5/7]#

SBMStructuralModelNodeHydrogenBond::SB_NODE_GETTER_0 (
    SBQuantity::length,
    GetHydrogenAcceptorDistance
)

function SB_NODE_GETTER_0 [6/7]#

SBMStructuralModelNodeHydrogenBond::SB_NODE_GETTER_0 (
    SBQuantity::length,
    GetDonorHydrogenDistance
)

function SB_NODE_GETTER_0 [7/7]#

SBMStructuralModelNodeHydrogenBond::SB_NODE_GETTER_0 (
    SBQuantity::degree,
    GetAngle
)

function clone#

Returns a copy of the node and its descendants.

virtual SBMStructuralModelNodeHydrogenBond * SBMStructuralModelNodeHydrogenBond::clone () override

Implements SBMStructuralModelNodeBond::clone

function getAcceptor#

Returns a pointer to the acceptor atom.

SBMStructuralModelNodeAtom * SBMStructuralModelNodeHydrogenBond::getAcceptor () const

function getAngle [1/2]#

Returns the donor-hydrogen-acceptor angle.

SBQuantity::degree SBMStructuralModelNodeHydrogenBond::getAngle () const

function getDonor#

Returns a pointer to the donor atom.

SBMStructuralModelNodeAtom * SBMStructuralModelNodeHydrogenBond::getDonor () const

function getDonorAcceptorDistance#

Returns the donor-acceptor distance.

SBQuantity::length SBMStructuralModelNodeHydrogenBond::getDonorAcceptorDistance () const

function getDonorHydrogenDistance#

Returns the donor-hydrogen distance.

SBQuantity::length SBMStructuralModelNodeHydrogenBond::getDonorHydrogenDistance () const

function getHydrogen#

Returns a pointer to the hydrogen atom.

SBMStructuralModelNodeAtom * SBMStructuralModelNodeHydrogenBond::getHydrogen () const

function getHydrogenAcceptorDistance#

Returns the hydrogen-acceptor distance.

SBQuantity::length SBMStructuralModelNodeHydrogenBond::getHydrogenAcceptorDistance () const

function getNodes [1/2]#

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

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

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

Implements SBMStructuralModelNodeBond::getNodes

function getNodes [2/2]#

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

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

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

Implements SBMStructuralModelNodeBond::getNodes

function getType#

Returns the node type ( SBNode::HydrogenBond )

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

Implements SBMStructuralModelNodeBond::getType

function hasNode [1/2]#

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

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

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

Implements SBMStructuralModelNodeBond::hasNode

function hasNode [2/2]#

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

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

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

Implements SBMStructuralModelNodeBond::hasNode

function isLinking#

Returns true if and only if donor and acceptor atoms are in nodeIndexer , or descends from a node ofnodeIndexer .

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

function isSerializable#

Returns false.

virtual bool SBMStructuralModelNodeHydrogenBond::isSerializable () override const

Implements SBMStructuralModelNodeBond::isSerializable

function print#

Prints debugging information.

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

Implements SBMStructuralModelNodeBond::print

function serialize#

Serializes the bond.

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

Implements SBMStructuralModelNodeBond::serialize

function setSelectionFlag#

Sets the selection flag and selects corresponding atoms.

void SBMStructuralModelNodeHydrogenBond::setSelectionFlag (
    bool flag
)

function unserialize#

Unserializes the bond.

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

Implements SBMStructuralModelNodeBond::unserialize

function ~SBMStructuralModelNodeHydrogenBond#

Destructs the H-bond.

virtual SBMStructuralModelNodeHydrogenBond::~SBMStructuralModelNodeHydrogenBond ()

Public Static Functions Documentation#

function getAngle [2/2]#

Returns the donor-hydrogen-acceptor angle.

static SBQuantity::degree SBMStructuralModelNodeHydrogenBond::getAngle (
    SBMStructuralModelNodeAtom * donor,
    SBMStructuralModelNodeAtom * hydrogen,
    SBMStructuralModelNodeAtom * acceptor
)