This class describes a structural model.

Constructors and destructors
	SBMStructuralModel ()
	Builds a base model.

virtual	~SBMStructuralModel ()
	Deletes the model.

Serialization
bool	isSerializable () const
	Returns true.

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

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.

Rendering
virtual void	expandBounds (SBIAPosition3 &bounds) const
	Expands the bounds to make sure the visual model fits inside them.

virtual void	collectAmbientOcclusion (const SBPosition3 &boxOrigin, const SBPosition3 &boxSize, unsigned int nCellsX, unsigned int nCellsY, unsigned int nCellsZ, float *ambientOcclusionData)
	To collect ambient occlusion data.

Geometry
void	centerTransform ()
	Centers the pivot of the transform on the center of mass of the particles contained in the structural model. More...

SBSpatialTransform const &	getTransform () const
	Returns the spatial transform of the structural model.

void	setTransform (const SBSpatialTransform &transform)
	Sets the `spatial` transform of the structural model.

void	setTransform (const SBSpatialTransform &transform, bool transformParticles)
	Sets the `spatial` transform of the structural model.

void	setTransform (SBSpatialTransform const &newTransform, SBSpatialTransform const &oldTransform, bool transformParticles=true)
	Sets the `newTransform` and the `oldTransform` of the structural model.

SBMatrix33 const &	getOrientation () const
	Returns the orientation of the structural model.

void	setOrientation (const SBMatrix33 &orientation)
	Sets the `orientation` of the structural model.

void	setOrientation (const SBMatrix33 &orientation, bool transformParticles)
	Sets the `orientation` of the structural model.

void	setOrientation (SBMatrix33 const &newOrientation, SBMatrix33 const &oldOrientation, bool transformParticles=true)
	Sets the `newOrientation` and the `oldOrientation` of the structural model.

SBPosition3 const &	getPosition () const
	Returns the position of the structural model.

void	setPosition (const SBPosition3 &position)
	Sets the `position` of the structural model.

void	setPosition (const SBPosition3 &position, bool transformParticles)
	Sets the `position` of the structural model.

void	setPosition (SBPosition3 const &newPosition, SBPosition3 const &oldPosition, bool transformParticles=true)
	Sets the `newPosition` and the `oldPosition` of the structural model.

void	transform (const SBSpatialTransform &transform)
	Applies a spatial transform to the structural model.

void	rotate (const SBVector3 &axis, const SBQuantity::dimensionless &angle)
	Rotates the structural model.

void	translate (const SBLength3 &translation)
	Translates the structural model.

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

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

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

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

virtual SBPointerList< SBMStructuralModelNode > const *	getChildren () const
	This function is a convenience function equivalent to `getStructuralRoot()->getChildren`

SBMStructuralModelNodeRoot *	getStructuralRoot () const

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

static bool	extractStructuralNodes (SBNodeIndexer &structuralModelIndexer, const SBNodeIndexer &structuralNodeIndexer)
	Adds in `structuralModelIndexer` the structural models resulting from extracting the structural nodes in `structuralNodeIndexer`.

static bool	cloneStructuralNodes (SBNodeIndexer &structuralModelIndexer, const SBNodeIndexer &structuralNodeIndexer)
	Adds in `structuralModelIndexer` the structural models resulting from cloning the structural nodes in `structuralNodeIndexer`.

static SBSpatialDomain	computeDomain (const SBNodeIndexer &nodeIndexer)
	Computes the domain containing the atoms and bond atoms in the node indexer.

Identity
virtual SBDDataGraphNode::Type	getType () const
	Returns the type of the data graph node.

virtual SBDDataGraphNode::Type	getModelType () const
	Returns the model type.

Atoms
static void	replaceAtom (SBMStructuralModelNodeAtom oldAtom, SBMStructuralModelNodeAtom newAtom, bool preserveOldAtomPosition=false)
	Replaces atom `oldAtom` with atom `newAtom`. All bonds from the old atom are transferred to the new atom.

Bonds
void	createCovalentBonds ()
	Builds covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances.

int	createCovalentBondsByResidueType ()
	Builds covalent bonds for the atoms belonging to the structural model according to the residue types, regardless of inter-atomic distances. If the bonds are already present, it sets the order of covalent bonds for the atoms belonging to the structural model according to the residue types.

int	createCovalentBondsByResidueType (const SBNodeIndexer &nodeIndexer)
	Builds covalent bonds for the atoms belonging to the given residues of the structural model according to the residue types, regardless of inter-atomic distances. If the bonds are already present, it sets the order of covalent bonds for the atoms belonging to the structural model according to the residue types.

static void	replaceBond (SBMStructuralModelNodeBond oldBond, SBMStructuralModelNodeBond newBond, bool flipBond=false, bool preserveOldBondPosition=false)
	Replaces bond `oldBond` with bond `newBond`. All neighboring bonds from the old bond are transferred to the new bond.

Secondary structure
bool	computeSecondaryStructure (bool &updated, bool forceUpdate=false)
	Computes the secondary structure for all residues in the structural model. More...

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

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

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

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

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

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

Properties
bool	hasTitleInformation () const
	Returns true when the model's title information is set.

std::string const &	getTitleInformation () const
	Returns the model's title information.

void	setTitleInformation (const std::string &info)
	Sets the model's title information.

void	clearTitleInformation ()
	Clears the model's title information.

bool	hasPrimaryStructureInformation () const
	Returns true when the model's primary structure information is set.

std::string const &	getPrimaryStructureInformation () const
	Returns the model's primary structure information.

void	setPrimaryStructureInformation (const std::string &info)
	Sets the model's primary structure information.

void	clearPrimaryStructureInformation ()
	Clears the model's primary structure information.

bool	hasHeterogenInformation () const
	Returns true when the model's heterogen information is set.

std::string const &	getHeterogenInformation () const
	Returns the model's heterogen information.

void	setHeterogenInformation (const std::string &info)
	Sets the model's heterogen information.

void	clearHeterogenInformation ()
	Clears the model's heterogen information.

bool	hasSecondaryStructureInformation () const
	Returns true when the model's secondary structure information is set.

std::string const &	getSecondaryStructureInformation () const
	Returns the model's secondary structure information.

void	setSecondaryStructureInformation (const std::string &info)
	Sets the model's secondary structure information.

void	clearSecondaryStructureInformation ()
	Clears the model's secondary structure information.

bool	hasConnectivityAnnotationInformation () const
	Returns true when the model's connectivity annotation information is set.

std::string const &	getConnectivityAnnotationInformation () const
	Returns the model's connectivity annotation information.

void	setConnectivityAnnotationInformation (const std::string &info)
	Sets the model's connectivity annotation information.

void	clearConnectivityAnnotationInformation ()
	Clears the model's connectivity annotation information.

bool	hasMiscellaneousInformation () const
	Returns true when the model's miscellaneous information is set.

std::string const &	getMiscellaneousInformation () const
	Returns the model's miscellaneous information.

void	setMiscellaneousInformation (const std::string &info)
	Sets the model's miscellaneous information.

void	clearMiscellaneousInformation ()
	Clears the model's miscellaneous information.

bool	hasCrystallographicAndTransformationInformation () const
	Returns true when the model's crystallographic and transformation information is set.

std::string const &	getCrystallographicAndTransformationInformation () const
	Returns the model's crystallographic and transformation information.

void	setCrystallographicAndTransformationInformation (const std::string &info)
	Sets the model's crystallographic and transformation information.

void	clearCrystallographicAndTransformationInformation ()
	Clears the model's crystallographic and transformation information.

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

Additional Inherited Members
Public Types inherited from SBDDataGraphNode
enum	RenderingPass { RenderingPass::OpaqueGeometry, RenderingPass::SelectableGeometry, RenderingPass::ShadowingGeometry, RenderingPass::TransparentGeometry, RenderingPass::Interface, RenderingPass::Text }
	The rendering pass. More...

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

Public Member Functions inherited from SBMModel
virtual	~SBMModel ()
	Delete the model.

SBMModel *	getNextModel () const
	Returns the next model in the parent.

SBMModel *	getPreviousModel () const
	Returns the previous model in the parent.

std::string const &	getName () const
	Returns the name of the model.

void	setName (const std::string &name)
	Sets the name of the model.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

virtual void	display (RenderingPass renderingPass)
	Displays the node. More...

virtual void	display ()
	Displays the node (deprecated) More...

virtual void	displayForShadow ()
	Displays the node for shadowing purposes (deprecated) More...

virtual void	displayForSelection ()
	Displays the node for selection purposes (deprecated) More...

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

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

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

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

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

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

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

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

Public Member Functions inherited from SBCReferenceTarget
	SBCReferenceTarget ()

virtual	~SBCReferenceTarget ()

unsigned int	getMemoryFootprint () const

void	printReferencesToOwners () const

Static Public Member Functions inherited from SBDDataGraphNode
static void	clone (const SBNodeIndexer &sourceNodeIndexer, SBNodeIndexer &destinationNodeIndexer)
	Clones the nodes in `sourceNodeIndexer` (treated as a whole) and places the clones in `destinationNodeIndexer`. More...

static SBDDataGraphNode *	getNode (unsigned int nodeIndex)
	Returns the unique node corresponding to the node index `nodeIndex`. More...

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

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

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

Protected Member Functions inherited from SBMModel
	SBMModel ()
	Builds a model.

	SBMModel (SBMModelData *dataPointer)
	Builds a model.

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

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

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

Member Function Documentation

◆ addChild()

bool SBMStructuralModel::addChild	(	SBNode *	node,
		SBNode *	nextNode = `0`
	)

virtual

This function is a convenience function equivalent to getStructuralRoot()->addChild(node, nextNode)

◆ canAddChild()

bool SBMStructuralModel::canAddChild	(	SBNode *	node,
		SBNode *	nextNode = `0`
	)		const

virtual

This function is a convenience function equivalent to getStructuralRoot()->canAddChild(node, nextNode)

◆ canAddChildType()

bool SBMStructuralModel::canAddChildType ( SBNode::Type nodeType ) const

virtual

This function is a convenience function equivalent to getStructuralRoot()->canAddChildType(nodeType)

Reimplemented from SBDDataGraphNode.

◆ centerTransform()

void SBMStructuralModel::centerTransform ( )

Centers the pivot of the transform on the center of mass of the particles contained in the structural model. This changes the transform only, and does not move particles (atoms or pseudo-atoms) belonging to the structural model.

◆ computeSecondaryStructure()

bool SBMStructuralModel::computeSecondaryStructure	(	bool &	secondaryStructureChanged,
		bool	forceUpdate = `false`
	)

This functions incrementally computes the secondary structure of the structural model, i.e. both the secondary structure types of residues and geometric descriptors. The function returns true if and only if everything went well. The boolean secondaryStructureChanged is modified by the function and is true if and only if the secondary structure was changed compared to the previous call. Since several objects may call this function, a SecondaryStructureChanged event is also sent when this is the case, so that all objects may be warned.

◆ getStructuralRoot()

SBMStructuralModelNodeRoot * SBMStructuralModel::getStructuralRoot ( ) const

This function returns a pointer to the structural root of the structural model. This root is a structural node, and can be used as a convenience root for e.g. recursive algorithms that operate on structural nodes (such algorithms could not work on the structural model itself, since the SBMStructuralModel class does not derive from SBMStructuralModelNode).

◆ removeChild()

bool SBMStructuralModel::removeChild ( SBNode * node )

virtual

This function is a convenience function equivalent to getStructuralRoot()->removeChild(node)

Constructors and destructors

Serialization

Rendering

Geometry

Topology

Identity

Atoms

Bonds

Secondary structure

Messaging

Selection functions

Visitor functions

Properties

Debugging

Additional Inherited Members

Member Function Documentation

◆ addChild()

◆ canAddChild()

◆ canAddChildType()

◆ centerTransform()

◆ computeSecondaryStructure()

◆ getStructuralRoot()

◆ removeChild()