This class describes a structural model.

Public Member Functions
	SB_NODE_GETTER_0 (, std::string, GetTitleInformation)

	SB_NODE_GETTER_0 (, std::string, GetPrimaryStructureInformation)

	SB_NODE_GETTER_0 (, std::string, GetHeterogenInformation)

	SB_NODE_GETTER_0 (, std::string, GetSecondaryStructureInformation)

	SB_NODE_GETTER_0 (, std::string, GetConnectivityAnnotationInformation)

	SB_NODE_GETTER_0 (, std::string, GetMiscellaneousInformation)

	SB_NODE_GETTER_0 (, std::string, GetCrystallographicAndTransformationInformation)

	SB_NODE_PREDICATE_0 (, HasTitleInformation)

	SB_NODE_PREDICATE_0 (, HasPrimaryStructureInformation)

	SB_NODE_PREDICATE_0 (, HasHeterogenInformation)

	SB_NODE_PREDICATE_0 (, HasSecondaryStructureInformation)

	SB_NODE_PREDICATE_0 (, HasConnectivityAnnotationInformation)

	SB_NODE_PREDICATE_0 (, HasMiscellaneousInformation)

	SB_NODE_PREDICATE_0 (, HasCrystallographicAndTransformationInformation)

	SB_DECLARE_DATA (SBMStructuralModel)

Public Member Functions inherited from SBMModel
	SB_NODE_GETTER_0 (, SBDDataGraphNode::Type, GetModelType)

	SB_NODE_PREDICATE_1 (, IsModelType, SBDDataGraphNode::Type)

	SB_DECLARE_DATA (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.

virtual unsigned int	getOpacity () const
	Returns the opacity.

virtual void	setOpacity (unsigned int opacity)
	Sets the opacity.

virtual unsigned int	getMinimumOpacity () const
	Returns the minimum opacity.

virtual unsigned int	getTransparency () const
	Returns the transparency.

virtual void	setTransparency (unsigned int transparency)
	Sets the transparency.

virtual unsigned int	getMaximumTransparency () const
	Returns the maximum transparency.

Public Member Functions inherited from SBDDataGraphNode
	SB_DECLARE_DATA (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	descendsFrom (SBDDataGraphNode *node) const
	Returns true if and only if this node is `node`, or descends from it. More...

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. More...

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. More...

bool	isIn (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`. 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, or belongs to a group stored in one of the nodes of the `nodeIndexer`. 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, or belongs to a group stored in of the nodes of the `nodePointerIndexer`. 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...

std::string	getTypeString (bool humanReadable=false) const
	Returns a string describing the type of the data graph node. More...

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

virtual void	setName (const std::string &name)
	Sets the name of the node. 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	isMesh () const
	Returns true when the node is a mesh.

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 selected.

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...

virtual bool	hasOpacityRange () const
	Returns whether the node has the opacity range.

virtual unsigned int	getDefaultOpacity () const
	Returns the default opacity.

virtual unsigned int	getMaximumOpacity () const
	Returns the maximum opacity.

virtual unsigned int	getOpacitySingleStep () const
	Returns the opacity single step.

virtual std::string	getOpacitySuffix () const
	Returns the opacity suffix.

virtual bool	hasTransparencyRange () const
	Returns whether the node has the transparency range.

virtual unsigned int	getDefaultTransparency () const
	Returns the default transparency.

virtual unsigned int	getMinimumTransparency () const
	Returns the minimum transparency.

virtual unsigned int	getTransparencySingleStep () const
	Returns the transparency single step.

virtual std::string	getTransparencySuffix () const
	Returns the transparency suffix.

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.

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

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

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

bool	ownsMaterial () const
	Returns whether the node owns a material.

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 (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 our without dependencies. More...

unsigned int	countNodes (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 our without dependencies. More...

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. More...

Public Member Functions inherited from SBCReferenceTarget
	SBCReferenceTarget ()

virtual	~SBCReferenceTarget ()

unsigned int	getMemoryFootprint () const

void	printReferencesToOwners () const

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	canHaveDescendantType (SBNode::Type nodeType) const
	Returns whether this node can have a node with type `nodeType` as a descendant. 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.

Locking
virtual bool	isLocked () const
	Returns whether the model is locked. More...

virtual bool	getLockedFlag () const
	Returns the locked flag. More...

virtual void	setLockedFlag (bool flag)
	Sets the locked flag. More...

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.

static std::set< char >	getAltLocations (const SBNodeIndexer &nodeIndexer)
	Returns a set of all alternate locations for atoms that belong to nodes present in `nodeIndexer`.

static std::set< char >	getAltLocations (const SBIndexer< SBMStructuralModelNodeAtom *> &atomIndexer)
	Returns a set of all alternate locations of atoms present in the `atomIndexer`.

static SBMStructuralModelNodeAtom *	findAtom (const SBNodeIndexer &nodeIndexer, SBElement::Type type, const std::string &name)
	Returns, if found, an atom from a node indexer `nodeIndexer` with the type `type` and name `name`; else returns 0.

static SBMStructuralModelNodeAtom *	findAtom (const SBIndexer< SBMStructuralModelNodeAtom *> &atomIndexer, SBElement::Type type, const std::string &name)
	Returns, if found, an atom from an atom node indexer `atomIndexer` with the type `type` and name `name`; else returns 0.

static SBMStructuralModelNodeAtom *	findAtom (const SBNodeIndexer &nodeIndexer, SBElement::Type type, const std::string &name, char altLoc)
	Returns, if found, an atom from a node indexer `nodeIndexer` with the type `type`, name `name`, and an alternate location `altLoc` (if the atom has an alternate location); else returns 0.

static SBMStructuralModelNodeAtom *	findAtom (const SBIndexer< SBMStructuralModelNodeAtom *> &atomIndexer, SBElement::Type type, const std::string &name, char altLoc)
	Returns, if found, an atom from an atom node indexer `atomIndexer` with the type `type`, name `name`, and an alternate location `altLoc` (if the atom has an alternate location); else returns 0.

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.

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.

static bool	createBond (SBMStructuralModelNodeAtom atom1, SBMStructuralModelNodeAtom atom2, double bondOrder=1.0, SBBond::BondType bondType=SBBond::BondType::Undefined)
	Creates a bond between `atom1` and `atom2` if there is none; sets the bond order to `bondOrder` and the bond type to `bondType`.

static bool	bondExists (SBMStructuralModelNodeAtom atom1, SBMStructuralModelNodeAtom atom2)
	Checks whether the bond between atoms `atom1` and `atom2` exists. More...

static 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.

Chains
bool	populateChainIDs (bool forceRenumbering=false)
	Populates the chain IDs for all chains in the structural model. More...

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, SBNode::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 our without dependencies.

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

Utility functions
void	getWater (SBNodeIndexer &resultNodeIndexer) const
	Finds water nodes in the structural model. More...

static void	getWater (SBNodeIndexer &resultNodeIndexer, const SBNodeIndexer &nodeIndexer)
	Finds water nodes in the `nodeIndexer`. More...

static SBQuantity::mass	getMolecularWeight (const SBNodeIndexer &nodeIndexer)
	Returns the cumulative molecular weight of atoms in `nodeIndexer`. More...

static SBPosition3	getCentroid (const SBNodeIndexer &nodeIndexer)
	Returns the centroid (the geometric center) of atoms in `nodeIndexer`. More...

static SBPosition3	getCenterOfMass (const SBNodeIndexer &nodeIndexer)
	Returns the center of mass of atoms in `nodeIndexer`. More...

static double	getAsphericity (const SBNodeIndexer &nodeIndexer)
	Returns the asphericity parameter of the system of atoms (based on their positions and masses) in `nodeIndexer`. The asphericity parameter changes in the [0, 1] interval: 0 - a sphere, 1 - a rod. More...

static double	getShapeParameter (const SBNodeIndexer &nodeIndexer)
	Returns the shape parameter of the system of atoms (based on their positions and masses) in `nodeIndexer`. The shape parameter, S, changes in the [-0.25, 2] interval, where 0 corresponds to a sphere, negative values correspond to oblate ellipsoid, possitive values correspond to prolate ellipsoid. More...

static SBQuantity::length	getRadiusOfGyration (const SBNodeIndexer &nodeIndexer)
	Returns the radius of gyration of the system of atoms (based on their positions and masses) in `nodeIndexer`. More...

static SBInertiaTensor33	getInertiaTensor (const SBNodeIndexer &nodeIndexer)
	Returns the inertia tensor of the system of atoms (based on their positions and masses) in `nodeIndexer`. More...

static SBMatrix33	getPrincipalAxes (const SBNodeIndexer &nodeIndexer)
	Returns the principal axes of the inertia tensor of the system of atoms (based on their positions and masses) in `nodeIndexer`. More...

static SBDTypeSpatialTransform	getSpatialTransform (const SBNodeIndexer &nodeIndexer)
	Returns the spatial transform based on the inertia tensor of the system of atoms (based on their positions and masses) in `nodeIndexer`. More...

static SBQuantity::squareLength	getSolventAccessibleSurfaceArea (const SBNodeIndexer &nodeIndexer, const SBQuantity::length &probeRadius, const unsigned int numberOfPointsOnSphere)
	Returns the solvent-accessible surface area (SASA) of the system of atoms in `nodeIndexer` with the probe radius `probeRadius`, and the number of points on a sphere `numberOfPointsOnSphere`. More...

static bool	isPlanar (const SBNodeIndexer &nodeIndexer)
	Returns true if all atoms in `nodeIndexer` are in the same plane. More...

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.

Statistics
unsigned int	getNumberOfChains ()
	Returns the number of chains.

unsigned int	getNumberOfMolecules ()
	Returns the number of molecules.

unsigned int	getNumberOfResidues ()
	Returns the number of residues.

unsigned int	getNumberOfSegments ()
	Returns the number of segments.

unsigned int	getNumberOfStructuralGroups ()
	Returns the number of structural groups.

unsigned int	getNumberOfStructuralModels ()
	Returns the number of structural models.

unsigned int	getNumberOfAtoms ()
	Returns the number of atoms.

unsigned int	getNumberOfCarbons ()
	Returns the number of carbons.

unsigned int	getNumberOfHydrogens ()
	Returns the number of hydrogens.

unsigned int	getNumberOfNitrogens ()
	Returns the number of nitrogens.

unsigned int	getNumberOfOxygens ()
	Returns the number of oxygens.

unsigned int	getNumberOfSulfurs ()
	Returns the number of sulfurs.

unsigned int	getNumberOfOtherAtoms ()
	Returns the number of other atoms.

int	getSumOfFormalCharges ()
	Returns the sum of formal charges.

float	getSumOfPartialCharges ()
	Returns the sum of partial charges.

SBQuantity::mass	getMolecularWeight ()
	Returns the molecular weight. More...

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

Additional Inherited Members
Public Types inherited from SBDDataGraphNode
enum	RenderingPass { RenderingPass::Setup, 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, StructuralModelNodePseudoBond, PseudoBond, StructuralModelNodeHydrogenBond, HydrogenBond, StructuralModelNodeHydrogenBondGroup, HydrogenBondGroup, StructuralModelNodeResidue, Residue, StructuralModelNodeSegment, Segment, StructuralModelNodeProtein, Protein, StructuralModelNodeChain, Chain, StructuralModelNodeMolecule, Molecule, StructuralModelNodeBackbone, Backbone, StructuralModelNodeSideChain, SideChain, VisualModel, VisualModelMesh, Mesh, 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, Note, Animation, Presentation, DataGraphNodeGroup, NodeGroup, Controller, ControllerNode, Asset }
	The type of the data graph node. More...

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, bool humanReadable=false)
	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...

Protected Member Functions inherited from SBCReferenceTarget
void	removeAllReferenceOwners ()

	SBCReferenceTarget (SBCReferenceTargetData *dataPointer)

Protected Attributes inherited from SBCReferenceTarget
SBCReferenceTargetData *	dataPointer

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)

◆ bondExists()

bool SBMStructuralModel::bondExists	(	SBMStructuralModelNodeAtom *	atom1,
		SBMStructuralModelNodeAtom *	atom2
	)

static

This function checks whether the bond between atoms atom1 and atom2 exists: it returns true if the bond exists and false otherwise.

◆ 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.

◆ canHaveDescendantType()

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

virtual

This function is a convenience function equivalent to getStructuralRoot()->canHaveDescendantType(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.

◆ getAsphericity()

double SBMStructuralModel::getAsphericity ( const SBNodeIndexer & nodeIndexer )

static

This function returns the asphericity parameter of the system of atoms (based on their positions and masses) in nodeIndexer. The asphericity parameter changes in the [0, 1] range, where 0 corresponds to a sphere and 1 corresponds to a rod.

If the nodeIndexer doesn't contain any atoms or their parents then the function returns zero.

◆ getCenterOfMass()

SBPosition3 SBMStructuralModel::getCenterOfMass ( const SBNodeIndexer & nodeIndexer )

static

This function returns the center of mass of atoms from nodeIndexer The center of mass is computed as follows: R = sqrt(sum(m_i * r_i, i=1..N)/ M) where N is the number of atoms, m_i is the i-th atom's mass, r_i is the i-th atom's position, and M is the total mass of all of the N atoms.

If the nodeIndexer doesn't contain any atoms or their parents then the function returns the center of coordinates (SBPosition3::zero).

◆ getCentroid()

SBPosition3 SBMStructuralModel::getCentroid ( const SBNodeIndexer & nodeIndexer )

static

This function returns the centroid (the geometric center) of atoms from nodeIndexer

If the nodeIndexer doesn't contain any atoms or their parents then the function returns the center of coordinates (SBPosition3::zero).

◆ getInertiaTensor()

SBInertiaTensor33 SBMStructuralModel::getInertiaTensor ( const SBNodeIndexer & nodeIndexer )

static

This function returns the moment of inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer relative to their center of mass.

If the nodeIndexer doesn't contain any atoms or their parents then the function returns a zero tensor.

◆ getLockedFlag()

bool SBMStructuralModel::getLockedFlag ( ) const

virtual

This function returns the locked flag of the structural model. When the structural model is locked, its geometry (the atoms positions), topology (the bonds) and identities (node names and indices) cannot be edited by the user. However, other properties can still be edited. For example, secondary structure information can still be computed, and materials and color schemes can still be applied. Note that some properties that cannot be edited by users can still be edited by developers.

See also: isLocked; setLockedFlag

Reimplemented from SBDDataGraphNode.

◆ getMolecularWeight() [1/2]

SBQuantity::mass SBMStructuralModel::getMolecularWeight ( const SBNodeIndexer & nodeIndexer )

static

This function returns the cumulative molecular weight of atoms in nodeIndexer

If the nodeIndexer doesn't contain any atoms or their parents then the function returns zero.

◆ getMolecularWeight() [2/2]

SBQuantity::mass SBMStructuralModel::getMolecularWeight ( )

virtual

This function returns the cumulative molecular weight of atoms in the structural model.

If the structural model doesn't contain any atoms then the function returns zero.

Reimplemented from SBDDataGraphNode.

◆ getPrincipalAxes()

SBMatrix33 SBMStructuralModel::getPrincipalAxes ( const SBNodeIndexer & nodeIndexer )

static

Returns the principal axes of the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer. The eigen vectors are sorted by their eigen value in the descending order, i.e. the first one corresponds to the first principal axes. In other words: the first axis corresponds to the longest domain dimension, while the third axis corresponds to the smallest domain dimension.

If the nodeIndexer doesn't contain any atoms or their parents then the function returns a zero matrix.

◆ getRadiusOfGyration()

SBQuantity::length SBMStructuralModel::getRadiusOfGyration ( const SBNodeIndexer & nodeIndexer )

static

This function returns the radius of gyration of the system of atoms (based on their positions and masses) from nodeIndexer. The radius of gyration is computed as follows: Rg = sqrt(sum(m_i * (r_i - r_c)^2, i=1..N) / M) where N is the number of atoms, m_i is the mass of i-th atom, r_i is the i-th atom's position, r_c is the center of mass of all N atoms, M is the total mass of all of the N atoms.

If the nodeIndexer doesn't contain any atoms or their parents then the function returns zero.

◆ getShapeParameter()

double SBMStructuralModel::getShapeParameter ( const SBNodeIndexer & nodeIndexer )

static

This function returns the shape parameter of the system of atoms (based on their positions and masses) in nodeIndexer. The shape parameter, S, changes in the [-0.25, 2] range, where 0 corresponds to a sphere, negative values correspond to oblate ellipsoid, possitive values correspond to prolate ellipsoid.

It is computed as follows: S = prod((lambda_i - lambda_mean), i=1..3) / (lambda_mean^3) where lambda_i is the i-th eigen value of the inertia tensor, lambda_mean is the mean of eigen values and is equal to sum(lambda_i, i=1..3).

If the nodeIndexer doesn't contain any atoms or their parents then the function returns zero.

◆ getSolventAccessibleSurfaceArea()

SBQuantity::squareLength SBMStructuralModel::getSolventAccessibleSurfaceArea	(	const SBNodeIndexer &	nodeIndexer,
		const SBQuantity::length &	probeRadius,
		const unsigned int	numberOfPointsOnSphere
	)

static

This function returns the solvent-accessible surface area (SASA) of the system of atoms in nodeIndexer with the probe radius probeRadius, and the number of points on a sphere numberOfPointsOnSphere.

If the nodeIndexer doesn't contain any atoms or their parents then the function returns zero.

◆ getSpatialTransform()

SBDTypeSpatialTransform SBMStructuralModel::getSpatialTransform ( const SBNodeIndexer & nodeIndexer )

static

Returns the spatial transform based on the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer. The eigen vectors are sorted by their eigen value in the descending order, i.e. the first one corresponds to the first principal axes. In other words: the first axis corresponds to the longest domain dimension, while the third axis corresponds to the smallest domain dimension.

If the nodeIndexer doesn't contain any atoms or their parents then the function returns a zero transform.

◆ 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).

◆ getWater() [1/2]

void SBMStructuralModel::getWater ( SBNodeIndexer & resultNodeIndexer ) const

This function finds water nodes in the structural model and adds them to resultNodeIndexer.

◆ getWater() [2/2]

void SBMStructuralModel::getWater	(	SBNodeIndexer &	resultNodeIndexer,
		const SBNodeIndexer &	nodeIndexer
	)

static

This function finds water nodes in the nodeIndexer and adds them to resultNodeIndexer The resulting water nodes might include water structural groups and water atoms.

◆ isLocked()

bool SBMStructuralModel::isLocked ( ) const

virtual

This function is equivalent to getLockedFlag

See also: getLockedFlag; setLockedFlag

Reimplemented from SBDDataGraphNode.

◆ isPlanar()

bool SBMStructuralModel::isPlanar ( const SBNodeIndexer & nodeIndexer )

static

This function returns true if all atoms in nodeIndexer are in the same plane Note that for 3 atoms and less it will always return true

◆ populateChainIDs()

bool SBMStructuralModel::populateChainIDs ( bool forceRenumbering = false )

This function populates the chain IDs for all chains in the structural model.

The numbering of chain IDs for the chains with missing IDs will start from the maximum chain ID present in the structural model, for example, if there are chains with IDs 0, 1, 4 then the numbering of other chains with missing IDs will commence from 5.

If some chains have the same IDs then the repetitions will be renumbered, for example, chain IDs 0, 2, 2 will become 0, 2, 3.

If forceRenumbering is set to true then it renumbers chains IDs starting from 0 iff at least on of the chains has a missing ID or has the same ID as another chain in the structural model.

◆ removeChild()

bool SBMStructuralModel::removeChild ( SBNode * node )

virtual

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

◆ setLockedFlag()

void SBMStructuralModel::setLockedFlag ( bool flag )

virtual

This function sets the locked flag of the structural model.

This function is undoable

See also: isLocked; getLockedFlag

Reimplemented from SBDDataGraphNode.

Public Member Functions

Constructors and destructors

Serialization

Rendering

Geometry

Topology

Locking

Identity

Atoms

Bonds

Chains

Secondary structure

Messaging

Selection functions

Utility functions

Visitor functions

Properties

Statistics

Debugging

Additional Inherited Members

Member Function Documentation

◆ addChild()

◆ bondExists()

◆ canAddChild()

◆ canAddChildType()

◆ canHaveDescendantType()

◆ centerTransform()

◆ computeSecondaryStructure()

◆ getAsphericity()

◆ getCenterOfMass()

◆ getCentroid()

◆ getInertiaTensor()

◆ getLockedFlag()

◆ getMolecularWeight() [1/2]

◆ getMolecularWeight() [2/2]

◆ getPrincipalAxes()

◆ getRadiusOfGyration()

◆ getShapeParameter()

◆ getSolventAccessibleSurfaceArea()

◆ getSpatialTransform()

◆ getStructuralRoot()

◆ getWater() [1/2]

◆ getWater() [2/2]

◆ isLocked()

◆ isPlanar()

◆ populateChainIDs()

◆ removeChild()

◆ setLockedFlag()