Class SBDDataGraphNode#

This class is the base class to describe a node in the data graph.More...

#include <SBDDataGraphNode.hpp>

Inherits the following classes: SBCReferenceTarget

Inherited by the following classes: SBDAsset, SBDController, SBDControllerNode, SBDDataGraphNodeGroup, SBDDocumentAnimation, SBDDocumentCamera, SBDDocumentFile, SBDDocumentFolder, SBDDocumentLabel, SBDDocumentLight, SBDDocumentNote, SBDDocumentPresentation, SBDDocumentRenderPreset, SBMModel, SBMModelNode, SBMStructuralModelConformation, SBMStructuralModelPath, SBSSimulator, SBSStateUpdater

Classes#

Type	Name
class	All This node predicate returns true for all nodes.
class	DescendsFrom This node predicate returns true if the node descends from a given node or node indexer.
class	GetClass This node getter returns the class name of the node.
class	GetDocument This node getter returns the document the node belongs to.
class	GetElement This node getter returns the SAMSON Extension defining the node.
class	GetElementUUID This node getter returns the UUID of the SAMSON Extension defining the node.
class	GetFlags This node getter returns the flags of the node.
class	GetHighlightingFlag This node getter returns the highlighting flag of the node.
class	GetLockedFlag This node getter returns the locked flag of the node.
class	GetName This node getter returns the name of the node.
class	GetNextNode This node getter returns the next node in the parent's children.
class	GetNodeIndex This node getter returns the index of the node.
class	GetParent This node getter returns the parent of the node.
class	GetPreviousNode This node getter returns the previous node in the parent's children.
class	GetProxy This node getter returns the pointer to the class proxy of the node.
class	GetRoot This node getter returns the root of the node.
class	GetSelectionFlag This node getter returns the selection flag of the node.
class	GetThis This node getter returns the pointer to the node.
class	GetType This node getter returns the type of the node.
class	GetVisibilityFlag This node getter returns the visibility flag of the node.
class	HasMaterial This node predicate is true when the node has a material.
class	HasOneOf This node predicate returns true if the node is an ancestor of a node in a given node indexer.
class	IsAtom This node predicate is true when the node is an atom.
class	IsBallAndStick This node predicate is true when the node is a ball-and-stick visual model.
class	IsBond This node predicate is true when the node is a bond.
class	IsCartoon This node predicate is true when the node is a cartoon visual model.
class	IsCreated This node predicate returns true for created nodes.
class	IsDynamicalModel This node predicate is true when the node is a dynamical model.
class	IsErased This node predicate returns true for erased nodes.
class	IsGaussianSurface This node predicate is true when the node is a gaussian surface visual model.
class	IsHighlighted This node predicate returns true for highlighted nodes.
class	IsIn This node predicate returns true if the node descends from a given node or node indexer, or if the node belongs to a group stored in the given node or node indexer.
class	IsInteractionModel This node predicate is true when the node is an interaction model.
class	IsLicorice This node predicate is true when the node is a licorice visual model.
class	IsLight This node predicate is true when the node is a light.
class	IsLocked This node predicate is true when the node is locked.
class	IsMesh This node predicate is true when the node is a mesh.
class	IsModel This node predicate is true when the node is a model, i.e. is a structural, visual, dynamical, interaction or property model.
class	IsOneOf This node predicate returns true for nodes in a given node indexer.
class	IsPropertyModel This node predicate is true when the node is a property model.
class	IsRibbon This node predicate is true when the node is a ribbon visual model.
class	IsSelected This node predicate returns true for selected nodes.
class	IsSerializable This node predicate returns true for serializable nodes.
class	IsSimulator This node predicate is true when the node is a simulator.
class	IsSolventAccessibleSurface This node predicate is true when the node is a solvent accessible surface visual model.
class	IsSolventExcludedSurface This node predicate is true when the node is a solvent excluded surface visual model.
class	IsStructuralModel This node predicate is true when the node is a structural model.
class	IsStructuralNode This node predicate is true when the node is a structural node.
class	IsTube This node predicate is true when the node is a tube visual model.
class	IsType This node predicate compares the node type with a given type.
class	IsVanDerWaals This node predicate is true when the node is a van der Waals visual model.
class	IsVisible This node predicate returns true for visible nodes.
class	IsVisualModel This node predicate is true when the node is a visual model.
class	None This node predicate returns false for all nodes.
class	OwnsMaterial This node predicate is true when the node owns a material.
class	This This node getter returns the node itself.

Public Types#

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

Public Functions#

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
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#

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#

The data graph contains everything directly or indirectly added by the user through SAMSON's user interface, plugins, etc. A data graph node has basic pre-defined data and functionalities to manage the data (models, apps, etc.).

All nodes in SAMSON's data graph, e.g. atoms (SBAtom), bonds (SBBond), etc., derive from SBDDataGraphNode. The figure below shows the document view, which is a view of SAMSON's data graph structure.

Short name: SBNode

Topology#

SAMSON's data graph is a directed graph, where each node has one and only one parent (with the exception of documents, which have no parent), and possibly some children. The parent of a node can never be directly set, but can be retrieved using the getParent function. Children are managed using the addChild and removeChild functions.

Node lifecycle#

In SAMSON, a data graph node may go through four lifecycle stages:

C++ object creation (e.g. with a new operator)
Node creation (using the create function)
Node destruction (using the erase function)
C++ object destruction (usually automatically, or forced with a call to deleteReferenceTarget)

As reference targets, data graph nodes should not be destructed using the delete operator, because objects that are referencing them need to stop doing so before the node is deleted. Thus, when a node needs to be deleted (in the C++ sense), a SAMSON pointer (see References) must be used:

SBPointer<SBAtom> nodePointer = new SBAtom();

// ...

// remove all references to the atom, and delete it
nodePointer.deleteReferenceTarget();

See also: References, MemoryManagement

Node identity#

Each node in the data graph has a type, which may be retrieved using the getType function. For example, the type returned by the SBAtom class, which derives from the SBDDataGraphNode class, is SBNode::Atom, while the type returned by the SBStructuralModel class is SBNode::StructuralModel. The getTypeString function is a convenience function that may be used to obtain a type as a string.

Types may be used, for example, to rapidly search the data graph:

// Find all atoms
SBNodeIndexer nodeIndexer;
SAMSON::getActiveDocument()->getNodes(nodeIndexer, SBNode::Atom);

Each data graph node also has a unique index, that is managed internally by SAMSON. All indices are contiguous unsigned integers between 0 and n-1, where n is the number of data graph nodes. As a result, the node index is not permanent: when node i is deleted (and i is different from n-1), then node n-1 becomes node i. Node indices are used for example when picking objects in a viewport, by writing integers into the framebuffer instead of colors. The unique node index can be retrieved using getNodeIndex.

Flags#

Each data graph node has four flags:

The created flag indicates whether the node is created or not (see Node lifecycle)
The visibility flag indicates whether the renderer should display the node in the viewport
The highlighting indicates whether the renderer should highlight the node in the viewport
The selection flag indicates whether the node is selected or not

These flags are accessed through functions of SBDDataGraphNode and, except for the highlighting flag which has temporary purposes, changing these flags' values is undoable.

The getFlags function returns an unsigned int that combines the highlighting and selection flags.

Materials and color schemes#

Each data graph node may have a material, which may affect its rendering in the viewport. A material may be applied to a node with the addMaterial function. When a material is added to a node, it affects the node itself and all its descendants (unless they have a material themselves, which then has priority). Precisely, the getMaterial function returns the material directly applied to the node (if the addMaterial function was called), or determines the deepest ancestor that has a material applied (by examining the node's parent, then its parent's parent, etc.). If no material is found, the getMaterial function returns 0.

Each material has a color scheme which may be modified and used to associate a color to a node or a spatial position.

See also: Materials, Color schemes

Node predicates#

The SBDDataGraphNode class defines a series of \nps, i.e. functors that may be used to e.g. collect nodes in the data graph. For example, the SBNode::IsType predicate may be used to collect nodes by type:

// Find all atoms
SBNodeIndexer nodeIndexer;
SAMSON::getActiveDocument()->getNodes(nodeIndexer, 
    SBNode:IsType(SBNode::Atom));

and the SBNode::IsSelected predicate may be used to collect all nodes that are selected (directly, because their selection flag is true, or because one of their ancestors is selected):

// Find all selected nodes
SBNodeIndexer nodeIndexer;
SAMSON::getActiveDocument()->getNodes(nodeIndexer, 
    SBNode:IsSelected());

Predicates may be combined through logical operations. For example, collecting selected atoms may be achieved with:

// Find all selected nodes
SBNodeIndexer nodeIndexer;
SAMSON::getActiveDocument()->getNodes(nodeIndexer, 
    SBNode::IsAtom() && SBNode:IsSelected());

Please refer to Functors for more information.

See also: getNodes

See also: Functors

Node getters#

The SBDDataGraphNode class also defines a series of \ngs, i.e. functors that may be used to collect nodes in the data graph. For example, the SBNode::GetType getter may be used to retrieve the type of a node instead of through the getType function:

// Get the type of a node
SBPointer<SBAtom> nodePointer = new SBAtom();
SBNode::GetType()(nodePointer()); // returns SBNode::Atom

\Ngs may be used to construct \nps through comparison operators, so that collecting all atoms may also be achieved with:

// Find all atoms
SBNodeIndexer nodeIndexer;
SAMSON::getActiveDocument()->getNodes(nodeIndexer, 
    SBNode::GetType() == SBNode::Atom);

since the statement SBNode::GetType() == SBNode::Atom constructs a node predicate that is passed to the getNodes function.

In general, node getters have the same name as the corresponding getter function, but the first letter of their name is capitalized, since they are classes. For example, just like the SBNode::GetType getter corresponds to the SBNode::getType function, the SBAtom::GetTemperatureFactor getter corresponds to the SBAtom::getTemperatureFactor function.

\Nps and \ngs may be used to collect nodes from potentially complex rules:

// Find all selected atoms with a large enough temperature factor
SBNodeIndexer nodeIndexer;
SAMSON::getActiveDocument()->getNodes(nodeIndexer, 
    SBNode::IsSelected() &&
    SBNode::IsAtom() &&
    (SBAtom::GetTemperatureFactor() > 2.0));

\Nps and \ngs constitute the foundation of SAMSON's NSL.

See also: getNodes

See also: Functors, NSL

Serialization#

Data graph nodes support serialization through the serialize and unserialize functions. Serialization is used in SAMSON to e.g. copy, paste, save, load, etc. data graph nodes. Please refer to Serialization for more information.

Public Types Documentation#

enum RenderingPass#

The rendering pass.

enum SBDDataGraphNode::RenderingPass {
    Setup = 10,
    OpaqueGeometry = 20,
    SelectableGeometry = 30,
    ShadowingGeometry = 40,
    TransparentGeometry = 50,
    Interface = 60,
    Text = 70
};

enum Type#

The type of the data graph node.

href="#__codelineno-9-1">enum SBDDataGraphNode::Type { Undefined = 0, StructuralModel = 1, StructuralModelNode = 2, StructuralModelConformation = 28, Conformation = 28, StructuralModelPath = 29, Path = 29, StructuralModelNodeGroup = 200, StructuralGroup = 200, StructuralModelNodeRoot = 20000, Root = 20000, StructuralModelNodeAtom = 20100, Atom = 20100, StructuralModelNodeBond = 202, Bond = 202, StructuralModelNodeHydrogenBond = 20202, HydrogenBond = 20202, StructuralModelNodeHydrogenBondGroup = 20203, HydrogenBondGroup = 20203, StructuralModelNodeResidue = 204, Residue = 204, StructuralModelNodeSegment = 205, Segment = 205, StructuralModelNodeChain = 207, Chain = 207, StructuralModelNodeMolecule = 208, Molecule = 208, StructuralModelNodeBackbone = 209, Backbone = 209, StructuralModelNodeSideChain = 210, SideChain = 210, VisualModel = 3, VisualModelMesh = 300, Mesh = 300, DynamicalModel = 5, DynamicalModelParticleSystem = 500, ParticleSystem = 500, DynamicalModelRigidBodySystem = 501, RigidBodySystem = 501, DynamicalModelArticulatedBodySystem = 502, ArticulatedBodySystem = 502, DynamicalModelNode = 6, DynamicalNode = 6, DynamicalModelNodeGroup = 600, DynamicalGroup = 600, DynamicalModelNodeRoot = 60000, DynamicalRoot = 60000, DynamicalModelNodeParticle = 601, Particle = 601, DynamicalModelNodeRigidBody = 602, RigidBody = 602, DynamicalModelNodeArticulatedBody = 603, ArticulatedBody = 603, InteractionModel = 7, InteractionModelParticleSystem = 700, InteractionModelRigidBodySystem = 701, InteractionModelArticulatedBodySystem = 702, PropertyModel = 9, PropertyModelFunction = 900, Simulator = 11, SimulatorParticleSystem = 1100, SimulatorRigidBodySystem = 1101, SimulatorArticulatedBodySystem = 1102, StateUpdater = 15, StateUpdaterParticleSystem = 1501, StateUpdaterRigidBodySystem = 1502, StateUpdaterArticulatedBodySystem = 1503, Animation = 800, Camera = 801, Document = 802, DocumentManager = 803, File = 804, Folder = 805, Label = 806, Light = 807, Note = 808, Presentation = 809, RenderPreset = 810, DataGraphNodeGroup = 30, NodeGroup = 30, Controller = 40, ControllerNode = 41, Asset = 50 };

Public Functions Documentation#

function SB_DECLARE_DATA#

SBDDataGraphNode::SB_DECLARE_DATA (
    SBDDataGraphNode
)

function addChild#

Adds a child to the node.

virtual bool SBDDataGraphNode::addChild (
    SBDDataGraphNode * node,
    SBDDataGraphNode * nextNode=nullptr
)

Parameters:

node A pointer to the child that should be added
nextNode A pointer to the node before which the child should be added

This functions adds node as a child of this node, immediately before node nextNode. By default, nextNode is 0 and the child is added at the end of the list of this node's children. This function is reimplemented in derived classes. When developing new data graph nodes types, with custom children management, this convention should be respected if it makes sense for the custom node, and the reimplemented function should be undoable. The function returns true if the child was added successfully.

This function is undoable.

See also: removeChild

function addMaterial#

Adds a material.

bool SBDDataGraphNode::addMaterial (
    SBDDataGraphNodeMaterial * material
)

This functions adds a material to the node. A node may have at most one material, and a material may be applied to at most one node. The function returns true when the material is successfully added.

Please see Materials for more information

This function is undoable.

See also: Materials

function baseSignalIsConnectedToSlot#

Returns true when the base signal is connected to a slot.

bool SBDDataGraphNode::baseSignalIsConnectedToSlot (
    SBCReferenceTarget * referenceTarget,
    void(SBCReferenceTarget::*)( SBBaseEvent *) functionPointer
) const

function canAddChild#

Returns whether this node can add node as a child.

virtual bool SBDDataGraphNode::canAddChild (
    const SBDDataGraphNode * node,
    const SBDDataGraphNode * nextNode=nullptr
) const

Parameters:

node A pointer to a potential child
nextNode A pointer to the node before which the child should be added

This functions returns a boolean that indicates whether node can be added as a child of this node, immediately before node nextNode.

function canAddChildType#

Returns whether this node can add a node with type nodeType as a child.

virtual bool SBDDataGraphNode::canAddChildType (
    SBDDataGraphNode::Type nodeType
) const

Parameters:

nodeType A node type

This functions returns a boolean that indicates whether a node with type nodeType can be added as a child of this node.

function canAddMaterial [1/2]#

Returns whether can add a material to the node based on its type.

bool SBDDataGraphNode::canAddMaterial () const

This functions returns whether it is possible to add a material to this node based on its node type. Not all nodes can have materials, i.e. can be colorized, - this is the case for e.g. SBNode::Animation, SBNode::Camera, SBNode::Path, etc.

See also: Materials

function canHaveDescendantType#

Returns whether this node can have a node with type nodeType as a descendant.

virtual bool SBDDataGraphNode::canHaveDescendantType (
    SBDDataGraphNode::Type nodeType
) const

Parameters:

nodeType A node type

This functions returns a boolean that indicates whether a node with type nodeType can be added as a descendant of this node.

See also: canAddChild, addChild

function clone [1/2]#

Returns a copy of the node and its descendants.

virtual SBDDataGraphNode * SBDDataGraphNode::clone ()

This function returns a copy of the node and its descendants. In case the copy cannot be performed (for example if some nodes in the hierarchy have not been exposed through SAMSON's Introspection), the function returns nullptr. Note that the highlighting flag, the selection flag, and the created flag are not cloned. As a result, a clone must be created before insertion in the document:

SBNode* clone = node->clone();

if (clone) {

    SAMSON::beginHolding("Add clone");
    SAMSON::hold(clone); // hold the clone in memory
    clone->create(); // mark the clone as created
    node->getParent()->addChild(clone); // add the clone as a sibling
    SAMSON::endHolding();

}

Finally, note that cloning assumes that the serialize and unserialize functions have been implemented for each cloned node.

See also: Serialization

function connectBaseSignalToSlot#

Connects the base signal to a slot.

void SBDDataGraphNode::connectBaseSignalToSlot (
    SBCReferenceTarget * referenceTarget,
    void(SBCReferenceTarget::*)( SBBaseEvent *) functionPointer,
    SBCReferenceTarget * nextReferenceTarget=0,
    void(SBCReferenceTarget::*)( SBBaseEvent *) nextFunctionPointer=0
)

Parameters:

referenceTarget A pointer to the reference target that will receives the signal
functionPointer A pointer to the reference target's member function that will be called when the node's base signal is emitted
nextReferenceTarget A pointer to the next reference target; null by default
nextFunctionPointer A pointer to the next reference target's member function; null by default

This function connects the node's base signal to a slot.

Please refer to Signals and slots for more information.

This function is undoable.

function countNodes [1/2]#

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

unsigned int SBDDataGraphNode::countNodes (
    SBDDataGraphNode::Type nodeType,
    bool selectedNodesOnly=false,
    const SBNodePredicate & visitPredicate=SBDDataGraphNode::All (),
    bool includeDependencies=false
) const

This function traverses the sub-tree for which visitPredicate is true (depth-first), and counts the nodes for which the selectionPredicate is true. Precisely, if the visitPredicate returns false, a node is not visited, and neither are its descendants. If the visitPredicate returns true, the node is visited, and the visitPredicate will be used to decide whether its children are visited or not.

When includeDependencies is true, the function also counts nodes that are not descendants of this node, but are dependencies nonetheless. For example, in a bond, the two atoms connected by the bond are not children of the bond, but are still dependencies of the bond. Hence, provided they satisfy the nodeType, selectedNodesOnly, and visitPredicate, they are counted if includeDependencies is true.

Among the node types defined in the SAMSON SDK, four have dependencies that are not children:

Bonds: the left and right atom
Conformations: the atoms whose positions are stored in the conformation
Groups: the nodes belonging to the group
Paths: the atoms whose positions are stored in the path

Some SAMSON Extensions may define nodes that have non-child dependencies. For example, a visual model that references atoms should reimplement the getNodes function to add these dependencies to the nodeIndexer. See getNodes for more information and examples.

This function is a convenience function that internally calls getNodes.

See also: getNodes, hasNode

function countNodes [2/2]#

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

unsigned int SBDDataGraphNode::countNodes (
    const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All (),
    const SBNodePredicate & visitPredicate=SBDDataGraphNode::All (),
    bool includeDependencies=false
) const

This function traverses the sub-tree for which visitPredicate is true (depth-first), and counts the nodes for which the selectionPredicate is true. Precisely, if the visitPredicate returns false, a node is not visited, and neither are its descendants. If the visitPredicate returns true, the node is visited, and the visitPredicate will be used to decide whether its children are visited or not.

When includeDependencies is true, the function also counts nodes that are not descendants of this node, but are dependencies nonetheless. For example, in a bond, the two atoms connected by the bond are not children of the bond, but are still dependencies of the bond. Hence, provided they satisfy the selectionPredicate and visitPredicate, they are counted if includeDependencies is true.

Among the node types defined in the SAMSON SDK, four have dependencies that are not children:

Bonds: the left and right atom
Conformations: the atoms whose positions are stored in the conformation
Groups: the nodes belonging to the group
Paths: the atoms whose positions are stored in the path

Some SAMSON Extensions may define nodes that have non-child dependencies. For example, a visual model that references atoms should reimplement the getNodes function to add these dependencies to the nodeIndexer. See getNodes for more information and examples.

This function is a convenience function that internally calls getNodes.

See also: getNodes, hasNode

function create#

Creates the node.

void SBDDataGraphNode::create ()

This function creates the node and all its descendants, i.e. sets their created flag to true. Nodes which were not already created send the event SBEvent::NodeCreated. The created flag indicates whether the node is created or not, from SAMSON's point of view (as opposed to C++ object creation and destruction).

For more information, please refer to section Node lifecycle.

See also: isCreated, isErased, create, erase

See also: Node lifecycle

See also: Signals and slots This function is undoable.

function descendsFrom [1/3]#

Returns true if and only if this node is node , or descends from it.

bool SBDDataGraphNode::descendsFrom (
    const SBDDataGraphNode * node
) const

See also: data graph

function descendsFrom [2/3]#

Returns true if and only if this node is one of the nodes of the nodeIndexer , or descends from one of them.

bool SBDDataGraphNode::descendsFrom (
    const SBNodeIndexer & nodeIndexer
) const

This function returns true if and only if this node is one of the nodes of the nodeIndexer, or descends from one of them.

See also: data graph

function descendsFrom [3/3]#

Returns true if and only if this node is one of the nodes of the nodePointerIndexer , or descends from one of them.

bool SBDDataGraphNode::descendsFrom (
    SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer
) const

This function returns true if and only if this node is one of the nodes of the nodePointerIndexer, or descends from one of them.

See also: data graph

function disconnectBaseSignalFromSlot#

Disconnects the base signal from a slot.

void SBDDataGraphNode::disconnectBaseSignalFromSlot (
    SBCReferenceTarget * referenceTarget,
    void(SBCReferenceTarget::*)( SBBaseEvent *) functionPointer
)

function display [1/2]#

Displays the node.

virtual void SBDDataGraphNode::display (
    RenderingPass renderingPass
)

This function displays the node. It receives from the SAMSON renderer the current renderingPass which indicates what the function should display.

Setup: the setup pass where you can perform initialization that may be used in other passes, without rendering anything
OpaqueGeometry: the main pass where you should render opaque geometry
SelectableGeometry: the pass where you should render selectable geometry
ShadowingGeometry: the pass where you should render shadowing geometry
TransparentGeometry: the pass where you should render transparent geometry
Interface: the pass where you should render 2D and 3D interface components
Text: the pass where you should render text

Please refer to tutorials for more information.

Starting with SAMSON 0.9.0, this is the main and only function to display nodes in the viewport. Previous display functions (SBDDataGraphNode::display(), SBDDataGraphNode::displayForSelection() and SBDDataGraphNode::displayForShadow()) are marked as deprecated and will be removed in a future SAMSON version.

To facilitate porting to SAMSON 0.9.0, the default implementation of this function calls the now deprecated functions SBDDataGraphNode::display(), SBDDataGraphNode::displayForSelection() and SBDDataGraphNode::displayForShadow().

function display [2/2]#

Displays the node (deprecated)

virtual void SBDDataGraphNode::display ()

This function is deprecated and will be removed in a future version. Implement SBDDataGraphNode::display(RenderingPass renderingPass) instead.

function displayForSelection#

Displays the node for selection purposes (deprecated)

virtual void SBDDataGraphNode::displayForSelection ()

This function is deprecated and will be removed in a future version. Implement SBDDataGraphNode::display(RenderingPass renderingPass) instead.

function displayForShadow#

Displays the node for shadowing purposes (deprecated)

virtual void SBDDataGraphNode::displayForShadow ()

This function is deprecated and will be removed in a future version. Implement SBDDataGraphNode::display(RenderingPass renderingPass) instead.

function erase#

Erases the node.

void SBDDataGraphNode::erase ()

This function erases the node and all its descendants. To perform custom erase operations (for example, a bond being erased will remove itself from its parent and disconnect from the base signal of its left and right atom), derived class may reimplement onErase, which is a private virtual function of SBDDataGraphNode. Because the objects that are connected to this node's base signal might want to perform some tasks before the node is erased, nodes being erased send three events: SBBaseEvent::NodeEraseBegin immediately before erasing begins, SBBaseEvent::NodeEraseEnd after erasing is complete, and finally SBBaseEvent::NodeErased. Precisely, the erase function sends the SBBaseEvent::NodeEraseBegin event, sets the selection flag of the node to false, calls the virtual onErase function, removes the node from its parent, then sends the SBBaseEvent::NodeEraseEnd and the SBBaseEvent::NodeErased events. In the case of a bond, for example, the operations mentioned above are thus performed between the SBBaseEvent::NodeEraseBegin and SBBaseEvent::NodeEraseEnd events.

For more information, please refer to section Node lifecycle.

See also: Node lifecycle

function forEachNodeDepthFirst [1/2]#

Performs an action on each node.

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

function forEachNodeDepthFirst [2/2]#

Performs an action on each node.

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

function getDefaultOpacity#

Returns the default opacity.

virtual unsigned int SBDDataGraphNode::getDefaultOpacity () const

function getDefaultTransparency#

Returns the default transparency.

virtual unsigned int SBDDataGraphNode::getDefaultTransparency () const

function getDocument#

Returns the document the node belongs to.

SBDDocument * SBDDataGraphNode::getDocument () const

This function returns a pointer to the document the node belongs to. It goes up the ascendants of the node, and attempts to find a document node. If it doesn't find one, it returns 0.

function getFlags#

Returns the flags.

virtual unsigned int SBDDataGraphNode::getFlags () const

This function returns an unsigned int that contains the flags of the node:

the first bit is the selection flag
the second bit is the highlighting flag

Returns:

the flags

function getHierarchyString#

Returns a string with hierarchical information on the node and its parents names.

virtual std::string SBDDataGraphNode::getHierarchyString (
    const std::string & separator=" / ",
    bool includeNodeType=false
) const

This functions returns a string with information on the node's hierarchy. This information can be used for logging and debugging.

function getHighlightingFlag#

Returns the highlighting flag.

bool SBDDataGraphNode::getHighlightingFlag () const

This function returns the highlighting flag of the node. Setting this flag to true instructs the renderer to highlight the node in the viewport.

See also: setHighlightingFlag

function getInheritedFlags#

Returns the inherited flags.

virtual unsigned int SBDDataGraphNode::getInheritedFlags () const

This function returns an unsigned int that contains the inherited flags of the node:

the first bit is true if the node is selected
the second bit is true if the node is highlighted

Returns:

the flags

See also: isSelected, isHighlighted

function getInheritedOpacity#

Returns the cumulative opacity, when taking into account the ascendants.

float SBDDataGraphNode::getInheritedOpacity () const

This function returns the product of the opacities of all the ascendant nodes.

function getInheritedTransparency#

Returns the cumulative transparency, when taking into account the ascendants.

float SBDDataGraphNode::getInheritedTransparency () const

function getLockedFlag#

Returns the locked flag.

virtual bool SBDDataGraphNode::getLockedFlag () const

function getMaterial#

Returns the material.

SBDDataGraphNodeMaterial * SBDDataGraphNode::getMaterial () const

This function returns the material associated to this node, if a material was added to the node itself or to one of its ancestors (in which case it returns the deepest ancestor with a material applied).

See also: Materials

function getMaterialOwner#

Returns the node whose material is inherited.

SBDDataGraphNode * SBDDataGraphNode::getMaterialOwner () const

This function returns the node which owns the material associated to this node, i.e. the deepest ancestor with a material applied. The function returns 0 if no (direct or inherited) material is applied.

See also: Materials

function getMaximumOpacity#

Returns the maximum opacity.

virtual unsigned int SBDDataGraphNode::getMaximumOpacity () const

function getMaximumTransparency#

Returns the maximum transparency.

virtual unsigned int SBDDataGraphNode::getMaximumTransparency () const

function getMinimumOpacity#

Returns the minimum opacity.

virtual unsigned int SBDDataGraphNode::getMinimumOpacity () const

function getMinimumTransparency#

Returns the minimum transparency.

virtual unsigned int SBDDataGraphNode::getMinimumTransparency () const

function getMolecularWeight#

Returns the molecular weight.

virtual SBQuantity::mass SBDDataGraphNode::getMolecularWeight ()

function getName#

Returns the name of the node.

virtual std::string const & SBDDataGraphNode::getName () const

function getNextNode [1/2]#

Returns the pointer to the next node in the children of the node's parent.

SBDDataGraphNode * SBDDataGraphNode::getNextNode () const

This function returns a pointer to the next node in the children of the node's parent.

function getNextNode [2/2]#

Returns the pointer to the next node with type nodeType in the children of the node's parent.

SBDDataGraphNode * SBDDataGraphNode::getNextNode (
    SBDDataGraphNode::Type nodeType
) const

This function returns a pointer to the next node with type nodeType in the children of the node's parent.

function getNodeIndex#

Returns the node index (unique in the whole data graph, but non-persistent)

unsigned int SBDDataGraphNode::getNodeIndex () const

This function returns the unique index of the data graph node. At any time, each data graph node has a unique index, that is managed internally by SAMSON. All indices are contiguous unsigned integers between 0 and n-1, where n is the number of data graph nodes. As a result, the node index is not permanent: when node i is deleted (and i is different from n-1), then node n-1 becomes node i. Node indices are used for example when picking objects in a viewport, by writing integers into the framebuffer instead of colors.

function getNodeUUID#

Returns the node UUID.

SBUUID SBDDataGraphNode::getNodeUUID () const

function getNodes [1/2]#

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

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

This function traverses the node's sub-tree for which visitPredicate is true (depth-first), and stores in nodeIndexer the nodes whose type is nodeType. Precisely, if the visitPredicate returns false, the node is not visited, and neither are its descendants. If the visitPredicate returns true, the node is visited, and the visitPredicate will be used to decide whether its children are visited or not. Note that the node itself must satisfy the visitPredicate else nothing is visited.

If selectedNodesOnly is set to true, then only nodes that are selected, directly or via their parents, will be traversed.

When includeDependencies is true, the function also adds to nodeIndexer nodes that are not descendants of this node, but are dependencies nonetheless. For example, in a bond, the two atoms connected by the bond are not children of the bond, but are still dependencies of the bond. Hence, provided the node type is nodeType and they satisfy they satisfy visitPredicate, they are added to the nodeIndexer if includeDependencies is true.

Among the node types defined in the SAMSON SDK, four have dependencies that are not children:

Bonds: the left and right atom
Conformations: the atoms whose positions are stored in the conformation
Groups: the nodes belonging to the group
Paths: the atoms whose positions are stored in the path

Some SAMSON Extensions may define nodes that have non-child dependencies. For example, a visual model that references atoms should reimplement the getNodes function to add these dependencies to the nodeIndexer:

void SEMyVisualModel::getNodes(SBNodeIndexer& nodeIndexer, 
    SBNode::Type nodeType, 
    bool selectedNodesOnly, 
    const SBNodePredicate& visitPredicate, 
    bool includeDependencies) {

    if (!visitPredicate(this)) return;

    if ((getType() == nodeType) && (!selectedNodesOnly || isSelected())) nodeIndexer.push_back(this);

    if (includeDependencies) {

        SB_FOR(SBNode* node, atomIndexer) {

            node->getNodes(nodeIndexer, 
                nodeType, 
                selectedNodesOnly, 
                visitPredicate, 
                includeDependencies);

        }

    }

}

Note that the nodeIndexer is not cleared when entering this function.

See also: SBNodeIndexer, SBNodePredicate

See also: hasNode, countNodes

function getNodes [2/2]#

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

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

This function traverses the node's sub-tree for which visitPredicate is true (depth-first), and stores in nodeIndexer the nodes for which the selectionPredicate is true. Precisely, if the visitPredicate returns false, the node is not visited, and neither are its descendants. If the visitPredicate returns true, the node is visited, and the visitPredicate will be used to decide whether its children are visited or not. Note that the node itself must satisfy the visitPredicate else nothing is visited.

When includeDependencies is true, the function also adds to nodeIndexer nodes that are not descendants of this node, but are dependencies nonetheless. For example, in a bond, the two atoms connected by the bond are not children of the bond, but are still dependencies of the bond. Hence, provided they satisfy the selectionPredicate and visitPredicate, they are added to the nodeIndexer if includeDependencies is true.

Among the node types defined in the SAMSON SDK, four have dependencies that are not children:

Bonds: the left and right atom
Conformations: the atoms whose positions are stored in the conformation
Groups: the nodes belonging to the group
Paths: the atoms whose positions are stored in the path

Some SAMSON Extensions may define nodes that have non-child dependencies. For example, a visual model that references atoms should reimplement the getNodes function to add these dependencies to the nodeIndexer:

void SEMyVisualModel::getNodes(SBNodeIndexer& nodeIndexer, 
    const SBNodePredicate& selectionPredicate, 
    const SBNodePredicate& visitPredicate, 
    bool includeDependencies) {

    if (!visitPredicate(this)) return;
    if (selectionPredicate(this)) nodeIndexer.push_back(this);

    if (includeDependencies) {

        SB_FOR(SBNode* node, atomIndexer) {

            node->getNodes(nodeIndexer, 
                selectionPredicate, 
                visitPredicate, 
                includeDependencies);

        }

    }

}

Note that the nodeIndexer is not cleared when entering this function.

See also: SBNodeIndexer, SBNodePredicate

See also: hasNode, countNodes

function getNumberOfAtoms#

Returns the number of atoms.

virtual unsigned int SBDDataGraphNode::getNumberOfAtoms ()

function getNumberOfCarbons#

Returns the number of carbons.

virtual unsigned int SBDDataGraphNode::getNumberOfCarbons ()

function getNumberOfChains#

Returns the number of chains.

virtual unsigned int SBDDataGraphNode::getNumberOfChains ()

function getNumberOfCoarseGrainedAtoms#

Returns the number of coarse-grained atoms.

virtual unsigned int SBDDataGraphNode::getNumberOfCoarseGrainedAtoms ()

function getNumberOfHydrogens#

Returns the number of hydrogens.

virtual unsigned int SBDDataGraphNode::getNumberOfHydrogens ()

function getNumberOfMolecules#

Returns the number of molecules.

virtual unsigned int SBDDataGraphNode::getNumberOfMolecules ()

function getNumberOfNitrogens#

Returns the number of nitrogens.

virtual unsigned int SBDDataGraphNode::getNumberOfNitrogens ()

function getNumberOfOtherAtoms#

Returns the number of other atoms.

virtual unsigned int SBDDataGraphNode::getNumberOfOtherAtoms ()

function getNumberOfOxygens#

Returns the number of oxygens.

virtual unsigned int SBDDataGraphNode::getNumberOfOxygens ()

function getNumberOfResidues#

Returns the number of residues.

virtual unsigned int SBDDataGraphNode::getNumberOfResidues ()

function getNumberOfSegments#

Returns the number of segments.

virtual unsigned int SBDDataGraphNode::getNumberOfSegments ()

function getNumberOfStructuralGroups#

Returns the number of structural groups.

virtual unsigned int SBDDataGraphNode::getNumberOfStructuralGroups ()

function getNumberOfStructuralModels#

Returns the number of structural models.

virtual unsigned int SBDDataGraphNode::getNumberOfStructuralModels ()

function getNumberOfSulfurs#

Returns the number of sulfurs.

virtual unsigned int SBDDataGraphNode::getNumberOfSulfurs ()

function getOpacity#

Returns the opacity.

virtual unsigned int SBDDataGraphNode::getOpacity () const

function getOpacitySingleStep#

Returns the opacity single step.

virtual unsigned int SBDDataGraphNode::getOpacitySingleStep () const

function getOpacitySuffix#

Returns the opacity suffix.

virtual std::string SBDDataGraphNode::getOpacitySuffix () const

function getParent#

Returns the parent of the node.

SBDDataGraphNode * SBDDataGraphNode::getParent () const

The data graph node has a hierarchical structure, in which each node has zero or one parent.

function getPreviousNode [1/2]#

Returns the pointer to the previous node in the children of the node's parent.

SBDDataGraphNode * SBDDataGraphNode::getPreviousNode () const

This function returns a pointer to the previous node in the children of the node's parent.

function getPreviousNode [2/2]#

Returns the pointer to the previous node with type nodeType in the children of the node's parent.

SBDDataGraphNode * SBDDataGraphNode::getPreviousNode (
    SBDDataGraphNode::Type nodeType
) const

This function returns a pointer to the previous node with type nodeType in the children of the node's parent.

function getRoot#

Returns the root of the hierarchy the node belongs to.

SBDDataGraphNode * SBDDataGraphNode::getRoot () const

This function returns the root of the hierarchy the node belongs to. In general, this returns a pointer to the document that contains the node. However, if the node is not yet inserted in a document, this may return a node with a different type. In case the node has not been added as a child to another node, this function returns a pointer to the node itself.

See also: data graph

function getSelected#

Returns whether the node is selected.

bool SBDDataGraphNode::getSelected () const

function getSelectionFlag#

Returns the selection flag.

bool SBDDataGraphNode::getSelectionFlag () const

This function returns the selection flag of the data graph node. The selection flag is true if and only if the node is currently selected. Please refer to SBDDocument for more information about the way selection works in SAMSON.

See also: setSelectionFlag

function getSumOfFormalCharges#

Returns the sum of formal charges.

virtual int SBDDataGraphNode::getSumOfFormalCharges ()

function getSumOfPartialCharges#

Returns the sum of partial charges.

virtual float SBDDataGraphNode::getSumOfPartialCharges ()

function getThisNode#

Returns the pointer to this node.

SBDDataGraphNode * SBDDataGraphNode::getThisNode () const

This function returns a pointer to this node. This is mostly useful for inspectors, in order to make it easy for users to select the inspected node.

function getTransparency#

Returns the transparency.

virtual unsigned int SBDDataGraphNode::getTransparency () const

function getTransparencySingleStep#

Returns the transparency single step.

virtual unsigned int SBDDataGraphNode::getTransparencySingleStep () const

function getTransparencySuffix#

Returns the transparency suffix.

virtual std::string SBDDataGraphNode::getTransparencySuffix () const

function getType#

Returns the type of the data graph node.

virtual Type SBDDataGraphNode::getType () const

Each node in the data graph has a type, which can be used, for example, to rapidly search the data graph:

// Find all atoms
SBNodeIndexer nodeIndexer;
SAMSON::getActiveDocument()->getNodes(nodeIndexer, SBNode::Atom);

function getTypeString [1/2]#

Returns a string describing the type of the data graph node.

std::string SBDDataGraphNode::getTypeString (
    bool humanReadable=false
) const

This function is a convenience function used to produce a string corresponding to the node's type.

function getVisibilityFlag#

Returns the visibility flag.

bool SBDDataGraphNode::getVisibilityFlag () const

This function returns the visibility flag of the node. The visibility flag is true if and only if the node is visible in viewports. In other words, setting this flag to false instructs the renderer to not display the node (in case it has a visual representation).

See also: setVisibilityFlag

function getVisible#

Returns whether the node is visible.

bool SBDDataGraphNode::getVisible () const

function hasMaterial#

Returns whether the node has a material (by itself, or inherited)

bool SBDDataGraphNode::hasMaterial () const

This functions returns whether the node has a material by itself, or inherited

See also: Materials

function hasNode [1/2]#

Returns whether the node has nodes based on a nodeType , a selection status and avisitPredicate , with or without dependencies.

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

This function traverses the sub-tree for which visitPredicate is true (depth-first), and checks for the nodes for which the selectionPredicate is true. Precisely, if the visitPredicate returns false, a node is not visited, and neither are its descendants. If the visitPredicate returns true, the node is visited, and the visitPredicate will be used to decide whether its children are visited or not.

When includeDependencies is true, the function also checks for nodes that are not descendants of this node, but are dependencies nonetheless. For example, in a bond, the two atoms connected by the bond are not children of the bond, but are still dependencies of the bond. Hence, provided they satisfy the nodeType, selectedNodesOnly, and visitPredicate, they are checked for if includeDependencies is true.

Among the node types defined in the SAMSON SDK, four have dependencies that are not children:

Bonds: the left and right atom
Conformations: the atoms whose positions are stored in the conformation
Groups: the nodes belonging to the group
Paths: the atoms whose positions are stored in the path

Some SAMSON Extensions may define nodes that have non-child dependencies. For example, a visual model that references atoms should reimplement the getNodes function to add these dependencies to the nodeIndexer. See getNodes for more information and examples.

See also: getNodes, countNodes

function hasNode [2/2]#

Returns whether the node has nodes based on a selectionPredicate and avisitPredicate , with or without dependencies.

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

This function traverses the sub-tree for which visitPredicate is true (depth-first), and checks for the nodes for which the selectionPredicate is true. Precisely, if the visitPredicate returns false, a node is not visited, and neither are its descendants. If the visitPredicate returns true, the node is visited, and the visitPredicate will be used to decide whether its children are visited or not.

When includeDependencies is true, the function also checks for nodes that are not descendants of this node, but are dependencies nonetheless. For example, in a bond, the two atoms connected by the bond are not children of the bond, but are still dependencies of the bond. Hence, provided they satisfy the selectionPredicate and visitPredicate, they are checked for if includeDependencies is true.

Among the node types defined in the SAMSON SDK, four have dependencies that are not children:

Bonds: the left and right atom
Conformations: the atoms whose positions are stored in the conformation
Groups: the nodes belonging to the group
Paths: the atoms whose positions are stored in the path

Some SAMSON Extensions may define nodes that have non-child dependencies. For example, a visual model that references atoms should reimplement the getNodes function to add these dependencies to the nodeIndexer. See getNodes for more information and examples.

See also: getNodes, countNodes

function hasOneOf#

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.

bool SBDDataGraphNode::hasOneOf (
    const SBNodeIndexer & nodeIndexer
) const

This function 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

See also: data graph

function hasOpacityRange#

Returns whether the node has the opacity range.

virtual bool SBDDataGraphNode::hasOpacityRange () const

function hasTransparencyRange#

Returns whether the node has the transparency range.

virtual bool SBDDataGraphNode::hasTransparencyRange () const

function isAtom#

Returns true when the node is an atom.

bool SBDDataGraphNode::isAtom () const

function isBallAndStick#

Returns true when the node is the default ball-and-stick visual model.

bool SBDDataGraphNode::isBallAndStick () const

function isBond#

Returns true when the node is a bond.

bool SBDDataGraphNode::isBond () const

function isCartoon#

Returns true when the node is the default cartoon visual model.

bool SBDDataGraphNode::isCartoon () const

function isCreated#

Returns true if and only if the node is created.

bool SBDDataGraphNode::isCreated () const

For more information, please refer to section Node lifecycle.

See also: isErased, create, erase

See also: Node lifecycle

function isDynamicalModel#

Returns true when the node is a dynamical model.

bool SBDDataGraphNode::isDynamicalModel () const

function isErased#

Returns true if and only if the node is erased.

bool SBDDataGraphNode::isErased () const

This function returns true when the node is erased (i.e. when the node is not created). For more information, please refer to section Node lifecycle.

See also: isCreated, create, erase

See also: Node lifecycle

function isGaussianSurface#

Returns true when the node is the default Gaussian surface visual model.

bool SBDDataGraphNode::isGaussianSurface () const

function isHighlighted#

Returns whether the node is highlighted.

bool SBDDataGraphNode::isHighlighted () const

This function returns whether the node is highlighted directly (because its highlighting flag is true) or indirectly (because the highlighting flag of one of its ancestors is true).

See also: getHighlightingFlag

function isIn [1/3]#

Returns true if and only if this node is node , or descends from it, or belongs to a group stored innode .

bool SBDDataGraphNode::isIn (
    const SBDDataGraphNode * node
) const

This function returns true if and only if this node is node, or descends from it. If node contains groups, then the function returns true if this node belongs to them.

See also: data graph

function isIn [2/3]#

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 thenodeIndexer .

bool SBDDataGraphNode::isIn (
    const SBNodeIndexer & nodeIndexer
) const

This function returns true if and only if this node is one of the nodes of the nodeIndexer, or descends from one of them. If a node of the nodeIndexer contains groups, then the function returns true if this node belongs to them.

See also: data graph

function isIn [3/3]#

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 thenodePointerIndexer .

bool SBDDataGraphNode::isIn (
    SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer
) const

This function returns true if and only if this node is one of the nodes of the nodePointerIndexer, or descends from one of them. If a node of the nodePointerIndexer contains groups, then the function returns true if this node belongs to them.

See also: data graph

function isInteractionModel#

Returns true when the node is a interaction model.

bool SBDDataGraphNode::isInteractionModel () const

function isLicorice#

Returns true when the node is the default licorice visual model.

bool SBDDataGraphNode::isLicorice () const

function isLight#

Returns true when the node is a light.

bool SBDDataGraphNode::isLight () const

function isLocked#

Returns whether the node is locked.

virtual bool SBDDataGraphNode::isLocked () const

function isMesh#

Returns true when the node is a mesh.

bool SBDDataGraphNode::isMesh () const

function isModel#

Returns true when the node is a model.

bool SBDDataGraphNode::isModel () const

function isOneOf [1/2]#

Returns true if and only if this node is one of the nodes of the nodeIndexer .

bool SBDDataGraphNode::isOneOf (
    const SBNodeIndexer & nodeIndexer
) const

This function returns true if and only if this node is one of the nodes of the nodeIndexer

See also: data graph

function isOneOf [2/2]#

Returns true if and only if this node is one of the nodes of the nodePointerIndexer .

bool SBDDataGraphNode::isOneOf (
    SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer
) const

This function returns true if and only if this node is one of the nodes of the nodePointerIndexer

See also: data graph

function isPropertyModel#

Returns true when the node is a property model.

bool SBDDataGraphNode::isPropertyModel () const

function isRibbon#

Returns true when the node is the default ribbon visual model.

bool SBDDataGraphNode::isRibbon () const

function isSelected#

Returns whether the node is selected.

bool SBDDataGraphNode::isSelected () const

This function returns whether the node is selected directly (because its selection flag is true) or indirectly (because the selection flag of one of its ancestors is true). Please refer to SBDDocument for more information about the way selection works in SAMSON.

See also: getSelectionFlag

function isSerializable#

Returns true when the class is serializable.

virtual bool SBDDataGraphNode::isSerializable () const

This function returns true when the node is serializable. By default, custom nodes are not serializable (i.e. the function returns false). If the node should be serializable (for example to make it possible to copy and paste the node, and save and load it), this function should be overloaded to return true.

See also: Serialization

See also: serialize, unserialize

function isSimulator#

Returns true when the node is a simulator.

bool SBDDataGraphNode::isSimulator () const

function isSolventAccessibleSurface#

Returns true when the node is the default solvent accessible surface visual model.

bool SBDDataGraphNode::isSolventAccessibleSurface () const

function isSolventExcludedSurface#

Returns true when the node is the default solvent excluded surface visual model.

bool SBDDataGraphNode::isSolventExcludedSurface () const

function isStructuralModel#

Returns true when the node is a structural model.

bool SBDDataGraphNode::isStructuralModel () const

function isStructuralNode#

Returns true when the node is a structural node.

bool SBDDataGraphNode::isStructuralNode () const

function isTube#

Returns true when the node is the default tube visual model.

bool SBDDataGraphNode::isTube () const

function isType#

Returns true when the type of the node corresponds to type .

bool SBDDataGraphNode::isType (
    Type type
) const

function isVanDerWaals#

Returns true when the node is the default van der Waals visual model.

bool SBDDataGraphNode::isVanDerWaals () const

function isVisible#

Returns whether the node is visible.

bool SBDDataGraphNode::isVisible () const

This function returns whether the node is visible, which happens when the node and all its ancestors have their visibility flag set to true.

See also: getVisibilityFlag

function isVisualModel#

Returns true when the node is a visual model.

bool SBDDataGraphNode::isVisualModel () const

function ownsMaterial#

Returns whether the node owns a material.

bool SBDDataGraphNode::ownsMaterial () const

This functions returns whether the node owns a material

See also: Materials

function print#

Prints some debugging information.

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

function removeChild#

Removes a child from the node.

virtual bool SBDDataGraphNode::removeChild (
    SBDDataGraphNode * node
)

Parameters:

node A pointer to the child that should be removed

This functions removes node from the children of this node. This function is reimplemented in derived classes. When developing new data graph nodes types, with custom children management, the reimplemented function should be undoable. The function returns true if the child was removed successfully.

This function is undoable.

See also: addChild

function removeMaterial#

Removes the material.

bool SBDDataGraphNode::removeMaterial ()

This functions removes a material from the node. Please see Materials for more information

This function is undoable.

See also: Materials

function removeMaterialsFromDescendants#

Removes materials from all nodes that descend from this node, but it does not remove the material from the node itself.

void SBDDataGraphNode::removeMaterialsFromDescendants ()

This functions removes materials from all nodes that descend from this node, but it does not remove the material from the node itself. Please see Materials for more information

This function is undoable.

See also: Materials

function serialize#

Serializes the node.

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

Parameters:

serializer A pointer to a serializer
nodeIndexer A node indexer used to retrieve indices associated to nodes
sdkVersionNumber A version number of the SDK
classVersionNumber A version number of the class

This function serializes the node. Please refer to the page about Serialization for more information.

See also: Serialization

See also: isSerializable, unserialize

function setHighlightingFlag#

Sets the highlighting flag.

void SBDDataGraphNode::setHighlightingFlag (
    bool flag
)

This function sets the highlighting flag of the node. Setting this flag to true instructs the renderer to highlight the node in the viewport.

This function is undoable.

See also: getHighlightingFlag

function setLockedFlag#

Sets the locked flag.

virtual void SBDDataGraphNode::setLockedFlag (
    bool flag
)

function setName#

Sets the name of the node.

virtual void SBDDataGraphNode::setName (
    const std::string & name
)

Set the name of the node:

SBCamera* activeCamera = SAMSON::getActiveCamera();
activeCamera->setName("Overview camera");

This function is undoable.

function setOpacity#

Sets the opacity.

virtual void SBDDataGraphNode::setOpacity (
    unsigned int opacity
)

function setSelectionFlag#

Sets the selection flag.

void SBDDataGraphNode::setSelectionFlag (
    bool flag
)

This function sets the selection flag of the data graph node. The selection flag is true if and only if the node is currently selected. Please refer to SBDDocument for more information about the way selection works in SAMSON.

This function is undoable.

See also: getSelectionFlag

function setTransparency#

Sets the transparency.

virtual void SBDDataGraphNode::setTransparency (
    unsigned int transparency
)

function setVisibilityFlag#

Sets the visibility flag.

void SBDDataGraphNode::setVisibilityFlag (
    bool flag
)

This function sets the visibility flag of the node.

This function is undoable.

See also: getVisibilityFlag

function unserialize#

Unserializes the node.

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

Parameters:

serializer A pointer to a serializer
nodeIndexer A node indexer used to retrieve indices associated to nodes
sdkVersionNumber A version number of the SDK
classVersionNumber A version number of the class

This function unserializes the node. Please refer to the page about Serialization for more information.

See also: Serialization

See also: isSerializable, serialize

Public Static Functions Documentation#

function canAddMaterial [2/2]#

Returns whether can add a material to a node of type nodeType .

static bool SBDDataGraphNode::canAddMaterial (
    SBDDataGraphNode::Type nodeType
)

This functions returns whether it is possible to add a material to a node of type nodeType. Not all nodes can have materials, i.e. can be colorized, - this is the case for e.g. SBNode::Animation, SBNode::Camera, SBNode::Path, etc.

See also: Materials

function clone [2/2]#

Clones the nodes in sourceNodeIndexer (treated as a whole) and places the clones indestinationNodeIndexer .

static void SBDDataGraphNode::clone (
    const SBNodeIndexer & sourceNodeIndexer,
    SBNodeIndexer & destinationNodeIndexer
)

This function clones the nodes in sourceNodeIndexer and places the roots of the clones in destinationNodeIndexer. This variant is useful when multiple nodes must be cloned simultaneously. For example, cloning a bond would not clone the two referenced atoms, and the clone would still reference the original atoms. With this variant, placing the bond and the two referenced atoms in sourceNodeIndexer will result in three nodes in destinationNodeIndexer (the cloned bond and the two cloned atoms), and the cloned bond will reference the two bond atoms.

Note that all restrictions applying to clone cloning individual nodes still apply. In particular, if one of the nodes cannot be cloned, the function may return without modifying destinationNodeIndexer.

See also: Serialization

See also: clone()

function forEachNodeInSelection [1/2]#

Performs an action for each node in a selection.

static void SBDDataGraphNode::forEachNodeInSelection (
    SBNodeIndexer & nodeIndexer,
    void(*)( SBDDataGraphNode *node) action
)

function forEachNodeInSelection [2/2]#

Performs an action for each node in a selection.

static void SBDDataGraphNode::forEachNodeInSelection (
    SBNodeIndexer & nodeIndexer,
    SBCClass * object,
    void(SBCClass::*)( SBDDataGraphNode *node) action
)

function getNode#

Returns the unique node corresponding to the node index nodeIndex .

static SBDDataGraphNode * SBDDataGraphNode::getNode (
    unsigned int nodeIndex
)

This function returns the unique node of the data graph node corresponding to the nodeIndex.

See also: getNodeIndex

function getTypeString [2/2]#

Returns a string describing the type of the data graph node.

static std::string SBDDataGraphNode::getTypeString (
    Type type,
    bool humanReadable=false
)

This function is a convenience function used to produce a string corresponding to a given type.

Protected Functions Documentation#

function SBDDataGraphNode [1/2]#

Builds a data graph node.

SBDDataGraphNode::SBDDataGraphNode ()

This (protected) constructor is indirectly called when constructing instances of derived classes, and assigns a unique index to the new node. By default, the created flag, the selection flag and the highlighting flag are set to false, whereas the visibility flag is set to true.

See also: Node identity, Flags

function SBDDataGraphNode [2/2]#

Builds a data graph node.

SBDDataGraphNode::SBDDataGraphNode (
    SBDDataGraphNodeData * dataPointer
)

function ~SBDDataGraphNode#

Destroys the node.

virtual SBDDataGraphNode::~SBDDataGraphNode ()

This (protected) destructor is indirectly called when deleting instances of derived classes. The destructor releases the node's unique index. When this destructor completes, the SBBaseEvent::NodeDeleted event is emitted.

See also: Node identity