Class SBMStructuralModel#

This class describes a structural model. More...

#include <SBMStructuralModel.hpp>

Inherits the following classes: SBMModel

Public Types inherited from SBDDataGraphNode#

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

Public Functions#

Type	Name
	SBMStructuralModel () Builds a structural model.
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetTitleInformation)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetPrimaryStructureInformation)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetHeterogenInformation)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetSecondaryStructureInformation)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetConnectivityAnnotationInformation)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetMiscellaneousInformation)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetCrystallographicAndTransformationInformation)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasTitleInformation)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasPrimaryStructureInformation)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasHeterogenInformation)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasSecondaryStructureInformation)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasConnectivityAnnotationInformation)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasMiscellaneousInformation)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasCrystallographicAndTransformationInformation)
virtual bool	addChild (SBNode * node, SBNode * nextNode=nullptr) override Adds a child to the node.
virtual bool	canAddChild (const SBNode * node, const SBNode * nextNode=nullptr) override const Returns whether this node can add `node` as a child.
virtual bool	canAddChildType (SBNode::Type nodeType) override const Returns whether this node can add a node with type `nodeType` as a child.
virtual bool	canHaveDescendantType (SBNode::Type nodeType) override const Returns whether this node can have a node with type `nodeType` as a descendant.
bool	centerInUnitCell () Centers the structural model inside its unit cell.
void	centerTransform () Centers the pivot of the transform on the center of mass of the atoms contained in the structural model.
void	clearConnectivityAnnotationInformation () Clears the model's connectivity annotation information.
void	clearCrystallographicAndTransformationInformation () Clears the model's crystallographic and transformation information.
void	clearHeterogenInformation () Clears the model's heterogen information.
void	clearMiscellaneousInformation () Clears the model's miscellaneous information.
void	clearPrimaryStructureInformation () Clears the model's primary structure information.
void	clearSecondaryStructureInformation () Clears the model's secondary structure information.
void	clearTitleInformation () Clears the model's title information.
virtual SBMStructuralModel *	clone () override Returns a copy of the node and its descendants.
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.
bool	computeSecondaryStructure (bool & updated, bool forceUpdate=false) Computes the secondary structure for all residues in the structural model.
void	connectStructuralSignalToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::)(SBStructuralEvent* ) functionPointer, SBStructuralEvent::Type* eventType=SBStructuralEvent::Type::Any, SBCReferenceTarget * nextReferenceTarget=nullptr, void(SBCReferenceTarget::)(SBStructuralEvent* ) nextFunctionPointer=nullptr) Connects the structural signal to a slot.*
void	createCovalentBonds () Builds covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances.
void	createCovalentBonds (SBQuantity::length additionalMargin) Builds covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances with the additional margin `additionalMargin` .
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.
virtual SBMStructuralModel *	createSupercell (unsigned int nA, unsigned int nB, unsigned int nC) const Creates a supercell by replicating the structural model along the lattice vectors.
void	disconnectStructuralSignalFromSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::)(SBStructuralEvent* ) functionPointer, SBStructuralEvent::Type* eventType=SBStructuralEvent::Type::Any) Disconnects the structural signal from a slot.
virtual void	expandBounds (SBIAPosition3 & bounds) const Expands the bounds to make sure the visual model fits inside them.
virtual void	forEachNodeDepthFirst (void()(SBDDataGraphNode* node) action) override Performs the* `action` on each node (this structural model and all its children), depth-first.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) override Performs the* `object` 's`action` on each node (this structural model and all its children), depth-first.
virtual SBPointerList< SBMStructuralModelNode > const *	getChildren () const Returns a list of children.
std::string const &	getConnectivityAnnotationInformation () const Returns the model's connectivity annotation information.
std::string const &	getCrystallographicAndTransformationInformation () const Returns the model's crystallographic and transformation information.
std::string const &	getHeterogenInformation () const Returns the model's heterogen information.
virtual bool	getLockedFlag () override const Returns the locked flag.
SBLength3	getMinimumImageDisplacement (const SBPosition3 & position1, const SBPosition3 & position2) const Returns the minimum-image displacement from `position1` to`position2` using the structural model unit cell.
SBLength3	getMinimumImageDisplacement (const SBMStructuralModelNodeAtom * atom1, const SBMStructuralModelNodeAtom * atom2) const Returns the minimum-image displacement from `atom1` to`atom2` using the structural model unit cell.
SBQuantity::length	getMinimumImageDistance (const SBPosition3 & position1, const SBPosition3 & position2) const Returns the minimum-image distance between `position1` and`position2` using the structural model unit cell.
SBQuantity::length	getMinimumImageDistance (const SBMStructuralModelNodeAtom * atom1, const SBMStructuralModelNodeAtom * atom2) const Returns the minimum-image distance between `atom1` and`atom2` using the structural model unit cell.
std::string const &	getMiscellaneousInformation () const Returns the model's miscellaneous information.
virtual SBDDataGraphNode::Type	getModelType () override const Returns the model type.
virtual SBQuantity::mass	getMolecularWeight () override Returns the molecular weight.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Collects nodes into `nodeIndexer` , based on a`nodeType` , a selection status and a`visitPredicate` , with or without dependencies.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Collects nodes into `nodeIndexer` , based on a`selectionPredicate` and a`visitPredicate` , with or without dependencies.
virtual unsigned int	getNumberOfAtoms () override Returns the number of atoms.
virtual unsigned int	getNumberOfCarbons () override Returns the number of carbons.
virtual unsigned int	getNumberOfChains () override Returns the number of chains.
virtual unsigned int	getNumberOfCoarseGrainedAtoms () override Returns the number of coarse-grained atoms.
virtual unsigned int	getNumberOfHydrogens () override Returns the number of hydrogens.
virtual unsigned int	getNumberOfMolecules () override Returns the number of molecules.
virtual unsigned int	getNumberOfNitrogens () override Returns the number of nitrogens.
virtual unsigned int	getNumberOfOtherAtoms () override Returns the number of other atoms.
virtual unsigned int	getNumberOfOxygens () override Returns the number of oxygens.
virtual unsigned int	getNumberOfResidues () override Returns the number of residues.
virtual unsigned int	getNumberOfSegments () override Returns the number of segments.
virtual unsigned int	getNumberOfStructuralGroups () override Returns the number of structural groups.
virtual unsigned int	getNumberOfStructuralModels () override Returns the number of structural models.
virtual unsigned int	getNumberOfSulfurs () override Returns the number of sulfurs.
SBMatrix33 const &	getOrientation () const Returns the orientation of the structural model.
SBPosition3 const &	getPosition () const Returns the position of the structural model.
std::string const &	getPrimaryStructureInformation () const Returns the model's primary structure information.
std::string const &	getSecondaryStructureInformation () const Returns the model's secondary structure information.
SBMStructuralModelNodeRoot *	getStructuralRoot () const Returns the structural root node of the structural model.
bool	getStructuralSignalFlag () const Returns `true` when the model can send structural signals.
virtual int	getSumOfFormalCharges () override Returns the sum of formal charges.
virtual float	getSumOfPartialCharges () override Returns the sum of partial charges.
std::string const &	getTitleInformation () const Returns the model's title information.
SBSpatialTransform const &	getTransform () const Returns the spatial transform of the structural model.
virtual SBDDataGraphNode::Type	getType () override const Returns the type of the data graph node.
SBUnitCell const &	getUnitCell () const Returns the unit cell of the structural model.
void	getWater (SBNodeIndexer & resultNodeIndexer) const Finds water nodes in the structural model.
bool	hasConnectivityAnnotationInformation () const Returns `true` when the model's connectivity annotation information is set.
bool	hasCrystallographicAndTransformationInformation () const Returns `true` when the model's crystallographic and transformation information is set.
bool	hasFiniteUnitCell () const Returns `true` if and only if the structural model has a finite unit cell.
bool	hasHeterogenInformation () const Returns `true` when the model's heterogen information is set.
bool	hasMiscellaneousInformation () const Returns `true` when the model's miscellaneous information is set.
virtual bool	hasNode (SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Checks for nodes based on a `nodeType` , a selection status and a`visitPredicate` , with or without dependencies.
virtual bool	hasNode (const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Checks for nodes based on a `selectionPredicate` and a`visitPredicate` , with or without dependencies.
bool	hasPrimaryStructureInformation () const Returns `true` when the model's primary structure information is set.
bool	hasSecondaryStructureInformation () const Returns `true` when the model's secondary structure information is set.
bool	hasTitleInformation () const Returns `true` when the model's title information is set.
virtual bool	isLocked () override const Returns whether the model is locked.
bool	isPeriodic () const Returns `true` if and only if the structural model is periodic along at least one axis.
virtual bool	isSerializable () override const Returns `true` __
bool	makeWhole () Reconstructs the bond-connected components of the structural model across periodic boundaries.
bool	populateChainIDs (bool forceRenumbering=false) Populates the chain IDs for all chains in the structural model.
virtual void	print (unsigned int offset=0) override const Prints debugging information.
virtual bool	removeChild (SBNode * node) override Removes a child from the node.
void	rotate (const SBVector3 & axis, const SBQuantity::dimensionless & angle) Rotates the structural model.
virtual void	serialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override const Serializes the node.
void	setConnectivityAnnotationInformation (const std::string & info) Sets the model's connectivity annotation information.
void	setCrystallographicAndTransformationInformation (const std::string & info) Sets the model's crystallographic and transformation information.
void	setHeterogenInformation (const std::string & info) Sets the model's heterogen information.
virtual void	setLockedFlag (bool flag) override Sets the locked flag.
void	setMiscellaneousInformation (const std::string & info) Sets the model's miscellaneous information.
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.
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	setPrimaryStructureInformation (const std::string & info) Sets the model's primary structure information.
void	setSecondaryStructureInformation (const std::string & info) Sets the model's secondary structure information.
void	setStructuralSignalFlag (bool structuralSignalFlag) Sets whether the model can send structural signals.
void	setTitleInformation (const std::string & info) Sets the model's title information.
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.
void	setUnitCell (const SBUnitCell & unitCell) Sets the unit cell of the structural model.
bool	structuralSignalIsConnectedToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::)(SBStructuralEvent* ) functionPointer, SBStructuralEvent::Type* eventType=SBStructuralEvent::Type::Any) const Returns `true` if and only if the structural signal is connected to a given slot.
std::optional< std::string >	toSMILES () const Converts the structural model into a SMILES string.
std::optional< std::string >	toSVG () const Converts the structural model into a 2D SVG representation.
void	transform (const SBSpatialTransform & transform) Applies a spatial transform to the structural model.
void	transformNonHierarchicalModel () Transforms a non-hierarchical, single level, structural model by placing connected components into separate structural groups and combininig similar groups into chains.
void	translate (const SBLength3 & translation) Translates the structural model.
virtual void	unserialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override Unserializes the node.
bool	wrapToUnitCell (bool keepConnectedComponentsWhole=true) Wraps the atoms of the structural model into the primary unit cell.
virtual	~SBMStructuralModel () Destructor.

Public Functions inherited from SBMModel#

See SBMModel

Type	Name
	SB_NODE_GETTER_0 (SB_SBMMODEL_EXPORT, SBDDataGraphNode::Type, GetModelType)
	SB_NODE_PREDICATE_1 (SB_SBMMODEL_EXPORT, IsModelType, SBDDataGraphNode::Type)
void	clearSourceFileName () Clears the name of the file associated to the model.
virtual SBMModel *	clone () override Returns a copy of the node and its descendants.
virtual SBDDataGraphNode::Type	getModelType () const Returns the model type.
SBMModel *	getNextModel () const Returns the next model in the parent.
virtual unsigned int	getOpacity () override const Returns the opacity.
SBMModel *	getPreviousModel () const Returns the previous model in the parent.
bool	getShadowingFlag () const Returns whether the model casts shadows.
const std::string &	getSourceFileName () const Returns the name of the file associated to the model.
virtual unsigned int	getTransparency () override const Returns the transparency.
virtual SBDDataGraphNode::Type	getType () override const Returns the type of the data graph node.
bool	hasSourceFileName () const Returns `true` when the model has the source file name set.
virtual bool	isSerializable () override const Returns `true` __
virtual void	print (unsigned int offset=0) override const Prints debugging information.
virtual void	serialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override const Serializes the node.
virtual void	setOpacity (unsigned int opacity) override Sets the opacity.
void	setShadowingFlag (bool shadowingFlag) Sets whether the model casts shadows.
void	setSourceFileName (const std::string & fileName) Sets the name of the file associated to the model.
virtual void	setTransparency (unsigned int transparency) override Sets the transparency.
virtual void	unserialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override Unserializes the node.
virtual	~SBMModel () Delete the model.

Public Functions inherited from SBDDataGraphNode#

See SBDDataGraphNode

Type	Name
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBCClassProxy *, GetProxy)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, This)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetParent)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetThis)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetNextNode)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetPreviousNode)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDocument *, GetDocument)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetRoot)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, unsigned int, GetNodeIndex)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode::Type, GetType)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetSelectionFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetLockedFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetVisibilityFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetHighlightingFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, unsigned int, GetFlags)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, std::string, GetName)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, std::string, GetClass)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, std::string, GetElement)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBCContainerUUID, GetElementUUID)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, All)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, None)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsAtom)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsBond)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsStructuralNode)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsStructuralModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsVisualModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsMesh)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsLight)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsInteractionModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsDynamicalModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsPropertyModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSimulator)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsBallAndStick)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsLicorice)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsVanDerWaals)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsCartoon)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsRibbon)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsTube)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsGaussianSurface)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSolventAccessibleSurface)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSolventExcludedSurface)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, HasMaterial)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, OwnsMaterial)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsLocked)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSerializable)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsCreated)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsErased)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSelected)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsVisible)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsHighlighted)
	SB_NODE_PREDICATE_1 (SB_SBDDATAGRAPH_EXPORT, IsType, SBDDataGraphNode::Type)
	SB_NODE_PREDICATE_1 (SB_SBDDATAGRAPH_EXPORT, HasOneOf, SBNodeIndexer)
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 the* `action` on this node.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) Performs the* `objects` 's`action` on this node.
unsigned int	getDefaultOpacity () const Returns the default opacity.
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.
unsigned int	getMaximumOpacity () const Returns the maximum opacity.
unsigned int	getMaximumTransparency () const Returns the maximum transparency.
unsigned int	getMinimumOpacity () const Returns the minimum opacity.
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.
unsigned int	getOpacitySingleStep () const Returns the opacity single step.
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.
unsigned int	getTransparencySingleStep () const Returns the transparency single step.
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.
bool	hasOpacityRange () const Returns whether the node has the opacity range.
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 () Builds the reference target.
unsigned int	getMemoryFootprint () const Returns the memory footprint.
void	printReferencesToOwners () const Prints the references to the owners of this reference target.
virtual	~SBCReferenceTarget () Destructor.

Public Static Functions#

Type	Name
bool	bondExists (SBMStructuralModelNodeAtom * atom1, SBMStructuralModelNodeAtom * atom2) Checks whether the bond between atoms `atom1` and`atom2` exists.
bool	centerInUnitCell (const SBNodeIndexer & nodeIndexer) Centers the atoms from `nodeIndexer` using their common unit cell.
bool	centerInUnitCell (const SBNodeIndexer & nodeIndexer, const SBUnitCell & unitCell) Centers the atoms from `nodeIndexer` using`unitCell` .
bool	cloneStructuralNodes (SBNodeIndexer & structuralModelIndexer, const SBNodeIndexer & structuralNodeIndexer) Adds in `structuralModelIndexer` the structural models resulting from cloning the structural nodes in`structuralNodeIndexer` .
SBSpatialDomain	computeDomain (const SBNodeIndexer & nodeIndexer) Computes the domain containing the atoms and bond atoms in the node indexer.
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` .
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.
SBMStructuralModel *	createModel (const std::string & smiles, const std::string & name, bool addHydrogens=true, bool addExplicitHydrogenOnly=false, bool kekulize=true, bool runUFF=true, int uffMaxIters=500, double uffVdwThreshold=10.0, int uffConfId=0) Creates a structural model from a SMILES string.
bool	exportImage (const std::string & smiles, const std::string & outputFile, int widthPx=600, int marginPx=10, double lineWidth=3.0, const std::string & fontFamily="Sans Serif Collection") Exports a molecular structure (SMILES) as an image file (png, jpg, svg).
bool	extractStructuralNodes (SBNodeIndexer & structuralModelIndexer, const SBNodeIndexer & structuralNodeIndexer) Adds in `structuralModelIndexer` the structural models resulting from extracting the structural nodes in`structuralNodeIndexer` .
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.
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.
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.
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.
int	findSubstructureMatchesWithSMARTS (std::vector< SBNodeIndexer > & resultNodeIndexerVector, const SBNodeIndexer & inputNodeIndexer, const std::string & smarts, const SBValueMap & parameterMap=SBValueMap{}) Finds substructure matches in `inputNodeIndexer` based on the given SMARTS string`smarts` and given parameters.
std::set< char >	getAltLocations (const SBNodeIndexer & nodeIndexer) Returns a set of all alternate locations for atoms that belong to nodes present in `nodeIndexer` .
std::set< char >	getAltLocations (const SBIndexer< SBMStructuralModelNodeAtom * > & atomIndexer) Returns a set of all alternate locations of atoms present in the `atomIndexer` .
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.
SBPosition3	getCenterOfFormalCharge (const SBNodeIndexer & nodeIndexer) Returns the center of formal charge of atoms in `nodeIndexer` .
SBPosition3	getCenterOfMass (const SBNodeIndexer & nodeIndexer) Returns the center of mass of atoms in `nodeIndexer` .
SBPosition3	getCenterOfPartialCharge (const SBNodeIndexer & nodeIndexer) Returns the center of partial charge of atoms in `nodeIndexer` .
SBPosition3	getCentroid (const SBNodeIndexer & nodeIndexer) Returns the centroid (the geometric center) of atoms in `nodeIndexer` .
SBMStructuralModel *	getCommonStructuralModel (const SBNodeIndexer & nodeIndexer) Returns the common structural model for `nodeIndexer` , or`nullptr` if there is none.
bool	getCommonUnitCell (const SBNodeIndexer & nodeIndexer, SBUnitCell & unitCell) Retrieves the common unit cell for `nodeIndexer` .
SBQuantity::length	getDipoleMomentAtCenterOfCharge (const SBNodeIndexer & nodeIndexer) Returns the dipole moment of atoms in `nodeIndexer` at their center of charge (based on partial charge)
SBQuantity::length	getDipoleMomentAtCenterOfMass (const SBNodeIndexer & nodeIndexer) Returns the dipole moment of atoms in `nodeIndexer` at their center of mass.
SBPosition3	getDipoleVectorAtCenterOfCharge (const SBNodeIndexer & nodeIndexer) Returns the dipole vector of atoms in `nodeIndexer` at their center of charge (based on partial charge)
SBPosition3	getDipoleVectorAtCenterOfMass (const SBNodeIndexer & nodeIndexer) Returns the dipole vector of atoms in `nodeIndexer` at their center of mass.
SBInertiaTensor33	getInertiaTensor (const SBNodeIndexer & nodeIndexer) Returns the inertia tensor of the system of atoms (based on their positions and masses) in `nodeIndexer` .
SBLength3	getMinimumImageDisplacement (const SBPosition3 & position1, const SBPosition3 & position2, const SBUnitCell & unitCell) Returns the minimum-image displacement from `position1` to`position2` using`unitCell` .
SBLength3	getMinimumImageDisplacement (const SBMStructuralModelNodeAtom * atom1, const SBMStructuralModelNodeAtom * atom2, const SBUnitCell & unitCell) Returns the minimum-image displacement from `atom1` to`atom2` using`unitCell` .
SBQuantity::length	getMinimumImageDistance (const SBPosition3 & position1, const SBPosition3 & position2, const SBUnitCell & unitCell) Returns the minimum-image distance between `position1` and`position2` using`unitCell` .
SBQuantity::length	getMinimumImageDistance (const SBMStructuralModelNodeAtom * atom1, const SBMStructuralModelNodeAtom * atom2, const SBUnitCell & unitCell) Returns the minimum-image distance between `atom1` and`atom2` using`unitCell` .
SBQuantity::mass	getMolecularWeight (const SBNodeIndexer & nodeIndexer) Returns the cumulative molecular weight of nodes in `nodeIndexer` .
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` .
SBQuantity::length	getRadiusOfGyration (const SBNodeIndexer & nodeIndexer) Returns the radius of gyration of the system of atoms (based on their positions and masses) in `nodeIndexer` .
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, positive values correspond to prolate ellipsoid.
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` .
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` .
int	getSumOfFormalCharges (const SBNodeIndexer & nodeIndexer) Returns the sum of formal charges of nodes in `nodeIndexer` .
float	getSumOfPartialCharges (const SBNodeIndexer & nodeIndexer) Returns the sum of partial charges of nodes in `nodeIndexer` .
void	getWater (SBNodeIndexer & resultNodeIndexer, const SBNodeIndexer & nodeIndexer) Finds water nodes in the `nodeIndexer` .
bool	isPlanar (const SBNodeIndexer & nodeIndexer) Returns `true` if all atoms in`nodeIndexer` are in the same plane.
bool	isValidSMARTS (const std::string & smarts) Checks if the given SMARTS string is valid.
bool	isValidSMILES (const std::string & smiles) Checks if the given SMILES string represents a valid molecular structure.
bool	makeWhole (const SBNodeIndexer & nodeIndexer) Reconstructs the bond-connected components from `nodeIndexer` using their common unit cell.
bool	makeWhole (const SBNodeIndexer & nodeIndexer, const SBUnitCell & unitCell) Reconstructs the bond-connected components from `nodeIndexer` using`unitCell` .
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.
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.
std::optional< std::string >	smilesToSVG (const std::string & smiles, int widthPx=600) Converts a SMILES string into an SVG representation.
bool	wrapToUnitCell (const SBNodeIndexer & nodeIndexer, bool keepConnectedComponentsWhole=true) Wraps the atoms from `nodeIndexer` into their common primary unit cell.
bool	wrapToUnitCell (const SBNodeIndexer & nodeIndexer, const SBUnitCell & unitCell, bool keepConnectedComponentsWhole=true) Wraps the atoms from `nodeIndexer` into the primary unit cell`unitCell` .

Public Static Functions inherited from SBDDataGraphNode#

See SBDDataGraphNode

Type	Name
bool	canAddMaterial (SBDDataGraphNode::Type nodeType) Returns whether can add a material to a node of type `nodeType` .
void	clone (const SBNodeIndexer & sourceNodeIndexer, SBNodeIndexer & destinationNodeIndexer) Clones the nodes in `sourceNodeIndexer` (treated as a whole) and places the clones in`destinationNodeIndexer` .
void	forEachNodeInSelection (SBNodeIndexer & nodeIndexer, void()(SBDDataGraphNode* node) action) Performs the* `action` for each node in`nodeIndexer` __
void	forEachNodeInSelection (SBNodeIndexer & nodeIndexer, SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) Performs the* `objects` 's`action` for each node in`nodeIndexer` __
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 A pointer to the private data.

Protected Functions inherited from SBMModel#

See SBMModel

Type	Name
	SBMModel () Builds a model.
	SBMModel (SBMModelData * dataPointer) Builds a model.

Protected Functions inherited from SBDDataGraphNode#

See SBDDataGraphNode

Type	Name
	SBDDataGraphNode () Builds a data graph node.
	SBDDataGraphNode (SBDDataGraphNodeData * dataPointer) Builds a data graph node.
virtual	~SBDDataGraphNode () Destroys the node.

Protected Functions inherited from SBCReferenceTarget#

See SBCReferenceTarget

Type	Name
	SBCReferenceTarget (SBCReferenceTargetData * dataPointer) Protected constructor.
void	removeAllReferenceOwners () Stops all the reference owners from referencing this reference target.

Detailed Description#

Short name: SBStructuralModel

Public Functions Documentation#

function SBMStructuralModel#

Builds a structural model.

SBMStructuralModel::SBMStructuralModel ()

Builds a base model.

function SB_NODE_GETTER_0 [1/7]#

SBMStructuralModel::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetTitleInformation
)

function SB_NODE_GETTER_0 [2/7]#

SBMStructuralModel::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetPrimaryStructureInformation
)

function SB_NODE_GETTER_0 [3/7]#

SBMStructuralModel::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetHeterogenInformation
)

function SB_NODE_GETTER_0 [4/7]#

SBMStructuralModel::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetSecondaryStructureInformation
)

function SB_NODE_GETTER_0 [5/7]#

SBMStructuralModel::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetConnectivityAnnotationInformation
)

function SB_NODE_GETTER_0 [6/7]#

SBMStructuralModel::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetMiscellaneousInformation
)

function SB_NODE_GETTER_0 [7/7]#

SBMStructuralModel::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetCrystallographicAndTransformationInformation
)

function SB_NODE_PREDICATE_0 [1/7]#

SBMStructuralModel::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasTitleInformation
)

function SB_NODE_PREDICATE_0 [2/7]#

SBMStructuralModel::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasPrimaryStructureInformation
)

function SB_NODE_PREDICATE_0 [3/7]#

SBMStructuralModel::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasHeterogenInformation
)

function SB_NODE_PREDICATE_0 [4/7]#

SBMStructuralModel::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasSecondaryStructureInformation
)

function SB_NODE_PREDICATE_0 [5/7]#

SBMStructuralModel::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasConnectivityAnnotationInformation
)

function SB_NODE_PREDICATE_0 [6/7]#

SBMStructuralModel::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasMiscellaneousInformation
)

function SB_NODE_PREDICATE_0 [7/7]#

SBMStructuralModel::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasCrystallographicAndTransformationInformation
)

function addChild#

Adds a child to the node.

virtual bool SBMStructuralModel::addChild (
    SBNode * node,
    SBNode * nextNode=nullptr
) override

Adds a child node to the structural model.

This function is a convenience wrapper for getStructuralRoot() ->addChild(node, nextNode).

Parameters:

node The node to add as a child.
nextNode The node that will follow the new child, or nullptr if none.

Returns:

true if the child was added successfully; false otherwise.

function canAddChild#

Returns whether this node can add node as a child.

virtual bool SBMStructuralModel::canAddChild (
    const SBNode * node,
    const SBNode * nextNode=nullptr
) override const

Checks whether a node can be added as a child of the structural model.

This function is a convenience wrapper for getStructuralRoot() ->canAddChild(node, nextNode).

Parameters:

node The node to test for addition.
nextNode The node that would follow the new child, or nullptr if none.

Returns:

true if the node can be added as a child; false otherwise.

function canAddChildType#

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

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

Checks whether a child of a given type can be added to the structural model.

This function is a convenience wrapper for getStructuralRoot() ->canAddChildType(nodeType).

Parameters:

nodeType The type of node to test for addition.

Returns:

true if a child of the specified type can be added; false otherwise.

Implements SBDDataGraphNode::canAddChildType

function canHaveDescendantType#

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

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

Checks whether the structural model can have a descendant of a given type.

This function is a convenience wrapper for getStructuralRoot() ->canHaveDescendantType(nodeType).

Parameters:

nodeType The type of descendant to test for.

Returns:

true if a descendant of the specified type can exist; false otherwise.

Implements SBDDataGraphNode::canHaveDescendantType

function centerInUnitCell [1/3]#

Centers the structural model inside its unit cell.

bool SBMStructuralModel::centerInUnitCell ()

Returns:

true if the operation completed; otherwise false.

function centerTransform#

Centers the pivot of the transform on the center of mass of the atoms contained in the structural model.

void SBMStructuralModel::centerTransform ()

This changes the transform only, and does not move atoms belonging to the structural model.

function clearConnectivityAnnotationInformation#

Clears the model's connectivity annotation information.

void SBMStructuralModel::clearConnectivityAnnotationInformation ()

function clearCrystallographicAndTransformationInformation#

Clears the model's crystallographic and transformation information.

void SBMStructuralModel::clearCrystallographicAndTransformationInformation ()

function clearHeterogenInformation#

Clears the model's heterogen information.

void SBMStructuralModel::clearHeterogenInformation ()

function clearMiscellaneousInformation#

Clears the model's miscellaneous information.

void SBMStructuralModel::clearMiscellaneousInformation ()

function clearPrimaryStructureInformation#

Clears the model's primary structure information.

void SBMStructuralModel::clearPrimaryStructureInformation ()

function clearSecondaryStructureInformation#

Clears the model's secondary structure information.

void SBMStructuralModel::clearSecondaryStructureInformation ()

function clearTitleInformation#

Clears the model's title information.

void SBMStructuralModel::clearTitleInformation ()

function clone#

Returns a copy of the node and its descendants.

virtual SBMStructuralModel * SBMStructuralModel::clone () override

Creates a copy of the structural model.

The cloned model includes all descendants.

Returns:

A pointer to the newly cloned SBMStructuralModel instance.

Implements SBMModel::clone

function collectAmbientOcclusion#

To collect ambient occlusion data.

virtual void SBMStructuralModel::collectAmbientOcclusion (
    const SBPosition3 & boxOrigin,
    const SBPosition3 & boxSize,
    unsigned int nCellsX,
    unsigned int nCellsY,
    unsigned int nCellsZ,
    float * ambientOcclusionData
)

Collects ambient occlusion data for the model.

Parameters:

boxOrigin Origin of the bounding box for the occlusion calculation.
boxSize Size of the bounding box.
nCellsX Number of cells in the X direction.
nCellsY Number of cells in the Y direction.
nCellsZ Number of cells in the Z direction.
ambientOcclusionData Pointer to the output array where occlusion data will be stored.

function computeSecondaryStructure#

Computes the secondary structure for all residues in the structural model.

bool SBMStructuralModel::computeSecondaryStructure (
    bool & updated,
    bool forceUpdate=false
)

Incrementally computes the secondary structure of the structural model.

This function 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.

Parameters:

secondaryStructureChanged Reference to a boolean that is set to true if the secondary structure changed compared to the previous call.
forceUpdate If true, forces recomputation of the secondary structure even if it appears up to date.

Returns:

true if the computation succeeded, false otherwise.

function connectStructuralSignalToSlot#

Connects the structural signal to a slot.

void SBMStructuralModel::connectStructuralSignalToSlot (
    SBCReferenceTarget * referenceTarget,
    void(SBCReferenceTarget::*)( SBStructuralEvent *) functionPointer,
    SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any,
    SBCReferenceTarget * nextReferenceTarget=nullptr,
    void(SBCReferenceTarget::*)( SBStructuralEvent *) nextFunctionPointer=nullptr
)

Connects a structural signal to a slot on a target object.

Registers a slot (member function) on referenceTarget to be invoked when a structural event of type eventType occurs. An optional secondary slot can be provided via nextReferenceTarget and nextFunctionPointer to form a chain of callbacks.

Parameters:

referenceTarget Pointer to the object that will receive the signal.
functionPointer Pointer to the member function of referenceTarget that handles the event.
eventType Type of the structural event to listen for.
nextReferenceTarget Optional pointer to a second target object for a chained slot; may be null.
nextFunctionPointer Optional pointer to the member function of nextReferenceTarget for the chained slot; may be null.

function createCovalentBonds [1/2]#

Builds covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances.

void SBMStructuralModel::createCovalentBonds ()

Creates covalent bonds for atoms in the structural model.

This function uses the Chemical Component Extension to generate covalent bonds based on atom distances. It does nothing if the model is locked.

function createCovalentBonds [2/2]#

Builds covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances with the additional margin additionalMargin .

void SBMStructuralModel::createCovalentBonds (
    SBQuantity::length additionalMargin
)

Creates covalent bonds for atoms in the structural model with an additional margin.

This function uses the Chemical Component Extension to generate covalent bonds based on atom distances, applying the specified additional margin to the distance criteria. It does nothing if the model is locked.

Parameters:

additionalMargin The additional margin to apply to covalent bond distance thresholds.

function createCovalentBondsByResidueType [1/2]#

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 SBMStructuralModel::createCovalentBondsByResidueType ()

Creates covalent bonds based on residue types for the structural model.

The function invokes the Chemical Component Extension to generate covalent bonds according to the residue types, regardless of inter-atomic distances. It returns the number of bonds created, or 0 if the model is locked or an error occurs.

Returns:

The number of bonds created, or 0 on failure.

function createSupercell#

Creates a supercell by replicating the structural model along the lattice vectors.

virtual SBMStructuralModel * SBMStructuralModel::createSupercell (
    unsigned int nA,
    unsigned int nB,
    unsigned int nC
) const

Parameters:

nA Number of replicas along the first lattice vector.
nB Number of replicas along the second lattice vector.
nC Number of replicas along the third lattice vector.

Returns:

A newly allocated structural model containing the replicated images, or nullptr on failure.

function disconnectStructuralSignalFromSlot#

Disconnects the structural signal from a slot.

void SBMStructuralModel::disconnectStructuralSignalFromSlot (
    SBCReferenceTarget * referenceTarget,
    void(SBCReferenceTarget::*)( SBStructuralEvent *) functionPointer,
    SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any
)

Disconnects a structural signal from a slot.

Removes the connection between the structural signal for eventType and the specified member function functionPointer on referenceTarget, if such a connection exists.

Parameters:

referenceTarget Pointer to the target object from which to disconnect the slot.
functionPointer Pointer to the member function on referenceTarget that was connected.
eventType Type of the structural event associated with the signal.

function expandBounds#

Expands the bounds to make sure the visual model fits inside them.

virtual void SBMStructuralModel::expandBounds (
    SBIAPosition3 & bounds
) const

Expands the bounding box to encompass the model's visual representation.

Parameters:

bounds The bounding box to be expanded.

function forEachNodeDepthFirst [1/2]#

Performs the action on each node (this structural model and all its children), depth-first.

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

Performs the given action on each node in the structural model depth‑first.

The action is invoked for the structural model itself and then recursively for all its children.

Parameters:

action Function pointer to be called for each node.

Implements SBDDataGraphNode::forEachNodeDepthFirst

function forEachNodeDepthFirst [2/2]#

Performs the object 'saction on each node (this structural model and all its children), depth-first.

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

Performs the given member function on each node in the structural model depth‑first.

The member function is invoked on the provided object for the structural model and recursively for its children.

Parameters:

object Pointer to the object whose member function will be called.
action Pointer to the member function to be invoked for each node.

Implements SBDDataGraphNode::forEachNodeDepthFirst

function getChildren#

Returns a list of children.

virtual SBPointerList< SBMStructuralModelNode > const * SBMStructuralModel::getChildren () const

Retrieves the list of child nodes of the structural model.

This function is a convenience wrapper for getStructuralRoot() -> getChildren().

Returns:

A pointer to the list of child nodes, or nullptr if unavailable.

function getConnectivityAnnotationInformation#

Returns the model's connectivity annotation information.

std::string const & SBMStructuralModel::getConnectivityAnnotationInformation () const

function getCrystallographicAndTransformationInformation#

Returns the model's crystallographic and transformation information.

std::string const & SBMStructuralModel::getCrystallographicAndTransformationInformation () const

function getHeterogenInformation#

Returns the model's heterogen information.

std::string const & SBMStructuralModel::getHeterogenInformation () const

function getLockedFlag#

Returns the locked flag.

virtual bool SBMStructuralModel::getLockedFlag () override const

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

Returns:

true if the model is locked; otherwise false.

Implements SBDDataGraphNode::getLockedFlag

function getMinimumImageDisplacement [1/4]#

Returns the minimum-image displacement from position1 toposition2 using the structural model unit cell.

SBLength3 SBMStructuralModel::getMinimumImageDisplacement (
    const SBPosition3 & position1,
    const SBPosition3 & position2
) const

Parameters:

position1 The start position.
position2 The end position.

Returns:

The minimum-image displacement.

function getMinimumImageDisplacement [2/4]#

Returns the minimum-image displacement from atom1 toatom2 using the structural model unit cell.

SBLength3 SBMStructuralModel::getMinimumImageDisplacement (
    const SBMStructuralModelNodeAtom * atom1,
    const SBMStructuralModelNodeAtom * atom2
) const

Parameters:

atom1 The first atom.
atom2 The second atom.

Returns:

The minimum-image displacement.

function getMinimumImageDistance [1/4]#

Returns the minimum-image distance between position1 andposition2 using the structural model unit cell.

SBQuantity::length SBMStructuralModel::getMinimumImageDistance (
    const SBPosition3 & position1,
    const SBPosition3 & position2
) const

Parameters:

position1 The first position.
position2 The second position.

Returns:

The minimum-image distance.

function getMinimumImageDistance [2/4]#

Returns the minimum-image distance between atom1 andatom2 using the structural model unit cell.

SBQuantity::length SBMStructuralModel::getMinimumImageDistance (
    const SBMStructuralModelNodeAtom * atom1,
    const SBMStructuralModelNodeAtom * atom2
) const

Parameters:

atom1 The first atom.
atom2 The second atom.

Returns:

The minimum-image distance.

function getMiscellaneousInformation#

Returns the model's miscellaneous information.

std::string const & SBMStructuralModel::getMiscellaneousInformation () const

function getModelType#

Returns the model type.

virtual SBDDataGraphNode::Type SBMStructuralModel::getModelType () override const

Retrieves the model type identifier for this object.

Returns:

The model type identifier for a structural model.

Implements SBMModel::getModelType

function getMolecularWeight [2/2]#

Returns the molecular weight.

virtual SBQuantity::mass SBMStructuralModel::getMolecularWeight () override

Returns the cumulative molecular weight of the structural model.

If the structural model contains no atoms, returns zero.

Returns:

Molecular weight.

Implements SBDDataGraphNode::getMolecularWeight

function getNodes [1/2]#

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

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

Collects nodes of a specific type from the structural model.

Adds nodes of type nodeType (and optionally only those that are selected) from this structural model and its descendants to nodeIndexer. The collection can be filtered by visitPredicate and may optionally include dependent nodes.

Parameters:

nodeIndexer Indexer that will receive the collected nodes.
nodeType Type of nodes to collect.
selectedNodesOnly If true, only nodes that are selected are collected.
visitPredicate Predicate used to decide whether to traverse a node.
includeDependencies If true, dependent nodes are also included in the collection.

Implements SBDDataGraphNode::getNodes

function getNodes [2/2]#

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

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

Collects nodes into nodeIndexer based on selection and visit predicates.

Traverses the structural model hierarchy and adds nodes that satisfy the given predicates.

Parameters:

nodeIndexer Container that will receive the collected nodes.
selectionPredicate Predicate that determines whether a node should be included in the result.
visitPredicate Predicate that determines whether a node should be visited during traversal.
includeDependencies If true, includes dependent nodes in the collection.

Implements SBDDataGraphNode::getNodes

function getNumberOfAtoms#

Returns the number of atoms.

virtual unsigned int SBMStructuralModel::getNumberOfAtoms () override

Returns the number of atoms in the structural model.

Returns:

Number of atoms.

Implements SBDDataGraphNode::getNumberOfAtoms

function getNumberOfCarbons#

Returns the number of carbons.

virtual unsigned int SBMStructuralModel::getNumberOfCarbons () override

Returns the number of carbon atoms in the structural model.

Returns:

Number of carbon atoms.

Implements SBDDataGraphNode::getNumberOfCarbons

function getNumberOfChains#

Returns the number of chains.

virtual unsigned int SBMStructuralModel::getNumberOfChains () override

Returns the number of chains in the structural model.

Returns:

Number of chains.

Implements SBDDataGraphNode::getNumberOfChains

function getNumberOfCoarseGrainedAtoms#

Returns the number of coarse-grained atoms.

virtual unsigned int SBMStructuralModel::getNumberOfCoarseGrainedAtoms () override

Returns the number of coarse‑grained atoms in the structural model.

Returns:

Number of coarse‑grained atoms.

Implements SBDDataGraphNode::getNumberOfCoarseGrainedAtoms

function getNumberOfHydrogens#

Returns the number of hydrogens.

virtual unsigned int SBMStructuralModel::getNumberOfHydrogens () override

Returns the number of hydrogen atoms in the structural model.

Returns:

Number of hydrogen atoms.

Implements SBDDataGraphNode::getNumberOfHydrogens

function getNumberOfMolecules#

Returns the number of molecules.

virtual unsigned int SBMStructuralModel::getNumberOfMolecules () override

Returns the number of molecules in the structural model.

Returns:

Number of molecules.

Implements SBDDataGraphNode::getNumberOfMolecules

function getNumberOfNitrogens#

Returns the number of nitrogens.

virtual unsigned int SBMStructuralModel::getNumberOfNitrogens () override

Returns the number of nitrogen atoms in the structural model.

Returns:

Number of nitrogen atoms.

Implements SBDDataGraphNode::getNumberOfNitrogens

function getNumberOfOtherAtoms#

Returns the number of other atoms.

virtual unsigned int SBMStructuralModel::getNumberOfOtherAtoms () override

Returns the number of other atoms in the structural model.

Returns:

Number of other atoms.

Implements SBDDataGraphNode::getNumberOfOtherAtoms

function getNumberOfOxygens#

Returns the number of oxygens.

virtual unsigned int SBMStructuralModel::getNumberOfOxygens () override

Returns the number of oxygen atoms in the structural model.

Returns:

Number of oxygen atoms.

Implements SBDDataGraphNode::getNumberOfOxygens

function getNumberOfResidues#

Returns the number of residues.

virtual unsigned int SBMStructuralModel::getNumberOfResidues () override

Returns the number of residues in the structural model.

Returns:

Number of residues.

Implements SBDDataGraphNode::getNumberOfResidues

function getNumberOfSegments#

Returns the number of segments.

virtual unsigned int SBMStructuralModel::getNumberOfSegments () override

Returns the number of segments in the structural model.

Returns:

Number of segments.

Implements SBDDataGraphNode::getNumberOfSegments

function getNumberOfStructuralGroups#

Returns the number of structural groups.

virtual unsigned int SBMStructuralModel::getNumberOfStructuralGroups () override

Returns the number of structural groups in the structural model.

Returns:

Number of structural groups.

Implements SBDDataGraphNode::getNumberOfStructuralGroups

function getNumberOfStructuralModels#

Returns the number of structural models.

virtual unsigned int SBMStructuralModel::getNumberOfStructuralModels () override

For a single model, this always returns 1.

Returns:

Number of structural models (always 1).

Implements SBDDataGraphNode::getNumberOfStructuralModels

function getNumberOfSulfurs#

Returns the number of sulfurs.

virtual unsigned int SBMStructuralModel::getNumberOfSulfurs () override

Returns the number of sulfur atoms in the structural model.

Returns:

Number of sulfur atoms.

Implements SBDDataGraphNode::getNumberOfSulfurs

function getOrientation#

Returns the orientation of the structural model.

SBMatrix33 const & SBMStructuralModel::getOrientation () const

Returns the orientation matrix of the structural model.

The orientation is part of the model's spatial transform.

Returns:

A reference to the orientation matrix.

function getPosition#

Returns the position of the structural model.

SBPosition3 const & SBMStructuralModel::getPosition () const

Returns the position vector of the structural model.

The position is part of the model's spatial transform.

Returns:

A reference to the position vector.

function getPrimaryStructureInformation#

Returns the model's primary structure information.

std::string const & SBMStructuralModel::getPrimaryStructureInformation () const

function getSecondaryStructureInformation#

Returns the model's secondary structure information.

std::string const & SBMStructuralModel::getSecondaryStructureInformation () const

function getStructuralRoot#

Returns the structural root node of the structural model.

SBMStructuralModelNodeRoot * SBMStructuralModel::getStructuralRoot () const

The structural root is a structural node that can be used as a convenient entry point for algorithms operating on structural nodes.

Returns:

A pointer to the structural root node, or nullptr if not available.

function getStructuralSignalFlag#

Returns true when the model can send structural signals.

bool SBMStructuralModel::getStructuralSignalFlag () const

Returns the structural signal flag of the model.

Returns:

true if the model can send structural signals, false otherwise.

function getSumOfFormalCharges [2/2]#

Returns the sum of formal charges.

virtual int SBMStructuralModel::getSumOfFormalCharges () override

Returns the sum of formal charges of all atoms in the structural model.

Returns:

Sum of formal charges.

Implements SBDDataGraphNode::getSumOfFormalCharges

function getSumOfPartialCharges [2/2]#

Returns the sum of partial charges.

virtual float SBMStructuralModel::getSumOfPartialCharges () override

Returns the sum of partial charges of all atoms in the structural model.

Returns:

Sum of partial charges.

Implements SBDDataGraphNode::getSumOfPartialCharges

function getTitleInformation#

Returns the model's title information.

std::string const & SBMStructuralModel::getTitleInformation () const

function getTransform#

Returns the spatial transform of the structural model.

SBSpatialTransform const & SBMStructuralModel::getTransform () const

Retrieves the spatial transform of the structural model.

Returns:

A constant reference to the model's spatial transform.

function getType#

Returns the type of the data graph node.

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

Retrieves the node type of this object.

Returns:

The type identifier for a structural model node.

Implements SBMModel::getType

function getUnitCell#

Returns the unit cell of the structural model.

SBUnitCell const & SBMStructuralModel::getUnitCell () const

Returns:

A constant reference to the unit cell.

function getWater [1/2]#

Finds water nodes in the structural model.

void SBMStructuralModel::getWater (
    SBNodeIndexer & resultNodeIndexer
) const

Finds water nodes in the structural model and adds them to resultNodeIndexer.

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

Parameters:

resultNodeIndexer Indexer that will be populated with the water nodes found.

function hasConnectivityAnnotationInformation#

Returns true when the model's connectivity annotation information is set.

bool SBMStructuralModel::hasConnectivityAnnotationInformation () const

function hasCrystallographicAndTransformationInformation#

Returns true when the model's crystallographic and transformation information is set.

bool SBMStructuralModel::hasCrystallographicAndTransformationInformation () const

function hasFiniteUnitCell#

Returns true if and only if the structural model has a finite unit cell.

bool SBMStructuralModel::hasFiniteUnitCell () const

Returns whether the structural model has a finite unit cell.

Returns:

true if and only if the structural model has a finite unit cell.

function hasHeterogenInformation#

Returns true when the model's heterogen information is set.

bool SBMStructuralModel::hasHeterogenInformation () const

function hasMiscellaneousInformation#

Returns true when the model's miscellaneous information is set.

bool SBMStructuralModel::hasMiscellaneousInformation () const

function hasNode [1/2]#

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

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

Checks whether a node of the specified type exists in the structural model.

The check can be restricted to selected nodes and can be filtered by a visit predicate.

Parameters:

nodeType The type of node to search for.
selectedNodesOnly If true, only considers nodes that are selected.
visitPredicate Predicate used to filter visited nodes.
includeDependencies If true, includes dependent nodes in the search.

Returns:

true if a matching node exists, false otherwise.

Implements SBDDataGraphNode::hasNode

function hasNode [2/2]#

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

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

Checks whether any node satisfying the selection predicate exists in the structural model.

Traverses the model hierarchy applying the selection and visit predicates.

Parameters:

selectionPredicate Predicate that selects nodes to check for existence.
visitPredicate Predicate that determines whether a node should be visited during traversal.
includeDependencies If true, includes dependent nodes in the search.

Returns:

true if a matching node exists, false otherwise.

Implements SBDDataGraphNode::hasNode

function hasPrimaryStructureInformation#

Returns true when the model's primary structure information is set.

bool SBMStructuralModel::hasPrimaryStructureInformation () const

function hasSecondaryStructureInformation#

Returns true when the model's secondary structure information is set.

bool SBMStructuralModel::hasSecondaryStructureInformation () const

function hasTitleInformation#

Returns true when the model's title information is set.

bool SBMStructuralModel::hasTitleInformation () const

function isLocked#

Returns whether the model is locked.

virtual bool SBMStructuralModel::isLocked () override const

Returns whether the structural model is locked (equivalent to getLockedFlag).

See also: getLockedFlag, setLockedFlag

Returns:

true if the model is locked; otherwise false.

Implements SBDDataGraphNode::isLocked

function isPeriodic#

Returns true if and only if the structural model is periodic along at least one axis.

bool SBMStructuralModel::isPeriodic () const

Returns whether the structural model is periodic.

Returns:

true if and only if the structural model is periodic along at least one axis.

function isSerializable#

Returns true __

virtual bool SBMStructuralModel::isSerializable () override const

Indicates whether the model supports serialization.

Returns:

true if the model can be serialized.

Implements SBMModel::isSerializable

function makeWhole [1/3]#

Reconstructs the bond-connected components of the structural model across periodic boundaries.

bool SBMStructuralModel::makeWhole ()

Returns:

true if the operation completed; otherwise false.

function populateChainIDs#

Populates the chain IDs for all chains in the structural model.

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.

Parameters:

forceRenumbering If true, forces renumbering of all chain IDs starting from zero when necessary.

Returns:

true if any chain ID was updated, false otherwise.

function print#

Prints debugging information.

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

Prints debugging information for the structural model.

Outputs the model's name, source file name, and recursively prints its children with indentation.

Parameters:

offset Number of indentation levels to apply before printing.

Implements SBMModel::print

function removeChild#

Removes a child from the node.

virtual bool SBMStructuralModel::removeChild (
    SBNode * node
) override

Removes a child node from the structural model.

This function is a convenience wrapper for getStructuralRoot() ->removeChild(node).

Parameters:

node The child node to remove.

Returns:

true if the child was removed successfully; false otherwise.

function rotate#

Rotates the structural model.

void SBMStructuralModel::rotate (
    const SBVector3 & axis,
    const SBQuantity::dimensionless & angle
)

Rotates the structural model around a given axis.

The rotation is applied as a spatial transform. Atom positions are updated accordingly.

Parameters:

axis The axis of rotation.
angle The rotation angle (dimensionless quantity).

function serialize#

Serializes the node.

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

Serializes the structural model to a serializer.

Parameters:

serializer The serializer used to write data.
nodeIndexer Indexer of nodes to be serialized.
sdkVersionNumber The SDK version number for compatibility.
classVersionNumber The class version number for compatibility.

Implements SBMModel::serialize

function setConnectivityAnnotationInformation#

Sets the model's connectivity annotation information.

void SBMStructuralModel::setConnectivityAnnotationInformation (
    const std::string & info
)

function setCrystallographicAndTransformationInformation#

Sets the model's crystallographic and transformation information.

void SBMStructuralModel::setCrystallographicAndTransformationInformation (
    const std::string & info
)

function setHeterogenInformation#

Sets the model's heterogen information.

void SBMStructuralModel::setHeterogenInformation (
    const std::string & info
)

function setLockedFlag#

Sets the locked flag.

virtual void SBMStructuralModel::setLockedFlag (
    bool flag
) override

Sets the locked flag of the structural model.

Parameters:

flag The new locked flag value. "This function is <a href=\"../undo-and-redo.md">undoable.

See also: isLocked, getLockedFlag

Implements SBDDataGraphNode::setLockedFlag

function setMiscellaneousInformation#

Sets the model's miscellaneous information.

void SBMStructuralModel::setMiscellaneousInformation (
    const std::string & info
)

function setOrientation [1/3]#

Sets the orientation of the structural model.

void SBMStructuralModel::setOrientation (
    const SBMatrix33 & orientation
)

Sets the orientation of the structural model and updates atom positions.

The position remains unchanged. Atom positions are transformed to reflect the new orientation.

Parameters:

orientation The new orientation matrix.

function setOrientation [2/3]#

Sets the orientation of the structural model.

void SBMStructuralModel::setOrientation (
    const SBMatrix33 & orientation,
    bool transformParticles
)

Sets the orientation of the structural model.

Optionally transforms atom positions according to the new orientation.

Parameters:

orientation The new orientation matrix.
transformAtoms If true, atom positions are transformed.

function setOrientation [3/3]#

Sets the newOrientation and theoldOrientation of the structural model.

void SBMStructuralModel::setOrientation (
    SBMatrix33 const & newOrientation,
    SBMatrix33 const & oldOrientation,
    bool transformParticles=true
)

Sets the orientation of the structural model, providing both new and old orientations.

Optionally transforms atom positions based on the change from the old orientation to the new orientation.

Parameters:

newOrientation The new orientation matrix.
oldOrientation The previous orientation matrix.
transformAtoms If true, atom positions are transformed.

function setPosition [1/3]#

Sets the position of the structural model.

void SBMStructuralModel::setPosition (
    const SBPosition3 & position
)

Sets the position of the structural model and updates atom positions.

The orientation remains unchanged. Atom positions are transformed to reflect the new position.

Parameters:

position The new position vector.

function setPosition [2/3]#

Sets the position of the structural model.

void SBMStructuralModel::setPosition (
    const SBPosition3 & position,
    bool transformParticles
)

Sets the position of the structural model.

Optionally transforms atom positions according to the new position.

Parameters:

position The new position vector.
transformAtoms If true, atom positions are transformed.

function setPosition [3/3]#

Sets the newPosition and theoldPosition of the structural model.

void SBMStructuralModel::setPosition (
    SBPosition3 const & newPosition,
    SBPosition3 const & oldPosition,
    bool transformParticles=true
)

Sets the position of the structural model, providing both new and old positions.

Optionally transforms atom positions based on the change from the old position to the new position.

Parameters:

newPosition The new position vector.
oldPosition The previous position vector.
transformAtoms If true, atom positions are transformed.

function setPrimaryStructureInformation#

Sets the model's primary structure information.

void SBMStructuralModel::setPrimaryStructureInformation (
    const std::string & info
)

function setSecondaryStructureInformation#

Sets the model's secondary structure information.

void SBMStructuralModel::setSecondaryStructureInformation (
    const std::string & info
)

function setStructuralSignalFlag#

Sets whether the model can send structural signals.

void SBMStructuralModel::setStructuralSignalFlag (
    bool structuralSignalFlag
)

Sets the structural signal flag of the model.

Parameters:

structuralSignalFlag The new value for the structural signal flag.

function setTitleInformation#

Sets the model's title information.

void SBMStructuralModel::setTitleInformation (
    const std::string & info
)

function setTransform [1/3]#

Sets the spatial transform of the structural model.

void SBMStructuralModel::setTransform (
    const SBSpatialTransform & transform
)

Sets the spatial transform of the structural model.

Parameters:

transform The new spatial transform to apply to the model.

function setTransform [2/3]#

Sets the spatial transform of the structural model.

void SBMStructuralModel::setTransform (
    const SBSpatialTransform & transform,
    bool transformParticles
)

Sets the spatial transform of the structural model.

Updates the model's transform and optionally applies the transform to all atom positions.

Parameters:

transform The new spatial transform to set.
transformAtoms If true, atom positions are transformed according to the new transform.

function setTransform [3/3]#

Sets the newTransform and theoldTransform of the structural model.

void SBMStructuralModel::setTransform (
    SBSpatialTransform const & newTransform,
    SBSpatialTransform const & oldTransform,
    bool transformParticles=true
)

Sets the spatial transform of the structural model, with knowledge of the previous transform.

Updates the model's transform and optionally transforms atom positions, using the provided old and new transforms.

Parameters:

newTransform The new spatial transform to set.
oldTransform The previous spatial transform of the model.
transformAtoms If true, atom positions are transformed according to the new transform.

function setUnitCell#

Sets the unit cell of the structural model.

void SBMStructuralModel::setUnitCell (
    const SBUnitCell & unitCell
)

This updates the periodic boundary information associated with the structural model.

Parameters:

unitCell The new unit cell.

function structuralSignalIsConnectedToSlot#

Returns true if and only if the structural signal is connected to a given slot.

bool SBMStructuralModel::structuralSignalIsConnectedToSlot (
    SBCReferenceTarget * referenceTarget,
    void(SBCReferenceTarget::*)( SBStructuralEvent *) functionPointer,
    SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any
) const

Checks whether a specific slot is connected to a structural signal.

Determines if the structural signal for the given eventType has a connection to the specified member function functionPointer on referenceTarget.

Parameters:

referenceTarget Pointer to the target object whose slot is being checked.
functionPointer Pointer to the member function on referenceTarget.
eventType Type of the structural event associated with the signal.

Returns:

true if the slot is connected to the signal, otherwise false.

function toSMILES#

Converts the structural model into a SMILES string.

std::optional< std::string > SBMStructuralModel::toSMILES () const

This function generates a SMILES representation of the current structural model using the RDKit library.

Returns:

An std::optional<std::string> containing the SMILES string, or std::nullopt if conversion failed.

function toSVG#

Converts the structural model into a 2D SVG representation.

std::optional< std::string > SBMStructuralModel::toSVG () const

Converts the structural model into an SVG representation.

Returns:

An std::optional<std::string> containing the SVG content, or std::nullopt if conversion failed.

This function uses the RDKit library.

function transform#

Applies a spatial transform to the structural model.

void SBMStructuralModel::transform (
    const SBSpatialTransform & transform
)

The current transform is multiplied by the provided transform. Atom positions are updated accordingly.

Parameters:

transform The spatial transform to apply.

function transformNonHierarchicalModel#

Transforms a non-hierarchical, single level, structural model by placing connected components into separate structural groups and combininig similar groups into chains.

void SBMStructuralModel::transformNonHierarchicalModel ()

Transforms a non‑hierarchical structural model into a hierarchical representation.

Checks whether this structural model has multiple connected components and a flat, single level, structure (all atoms are in the same parent, e.g., in a model or in a molecule). If it is the case, then creates a hierarchy based on the connected components: * places connected components into separate structural groups with names based on their atomic compositions; * combines similar groups into chains.

Note that it might change the order of atoms in the model.

function translate#

Translates the structural model.

void SBMStructuralModel::translate (
    const SBLength3 & translation
)

Translates the structural model by a given vector.

The translation is applied as a spatial transform. Atom positions are updated accordingly.

Parameters:

translation The translation vector.

function unserialize#

Unserializes the node.

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

Unserializes the structural model from a serializer.

Parameters:

serializer The serializer used to read data.
nodeIndexer Indexer to resolve node references.
sdkVersionNumber The SDK version number for compatibility.
classVersionNumber The class version number for compatibility.

Implements SBMModel::unserialize

function wrapToUnitCell [1/3]#

Wraps the atoms of the structural model into the primary unit cell.

bool SBMStructuralModel::wrapToUnitCell (
    bool keepConnectedComponentsWhole=true
)

Parameters:

keepConnectedComponentsWhole Whether to keep bond-connected components whole while wrapping.

Returns:

true if the operation completed; otherwise false.

function ~SBMStructuralModel#

Destructor.

virtual SBMStructuralModel::~SBMStructuralModel ()

Deletes the model.

Public Static Functions Documentation#

function bondExists#

Checks whether the bond between atoms atom1 andatom2 exists.

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

Checks whether a bond exists between two atoms.

Parameters:

atom1 The first atom.
atom2 The second atom.

Returns:

true if a bond exists between atom1 and atom2; false otherwise.

function centerInUnitCell [2/3]#

Centers the atoms from nodeIndexer using their common unit cell.

static bool SBMStructuralModel::centerInUnitCell (
    const SBNodeIndexer & nodeIndexer
)

Parameters:

nodeIndexer The nodes whose atoms will be centered.

Returns:

true if the operation completed; otherwise false.

function centerInUnitCell [3/3]#

Centers the atoms from nodeIndexer usingunitCell .

static bool SBMStructuralModel::centerInUnitCell (
    const SBNodeIndexer & nodeIndexer,
    const SBUnitCell & unitCell
)

Parameters:

nodeIndexer The nodes whose atoms will be centered.
unitCell The unit cell to use.

Returns:

true if the operation completed; otherwise false.

function cloneStructuralNodes#

Adds in structuralModelIndexer the structural models resulting from cloning the structural nodes instructuralNodeIndexer .

static bool SBMStructuralModel::cloneStructuralNodes (
    SBNodeIndexer & structuralModelIndexer,
    const SBNodeIndexer & structuralNodeIndexer
)

Clones the specified structural nodes into new structural models.

Creates deep copies of the structural nodes and their ancestors, preserving the hierarchical relationships. The cloned structural models are added to structuralModelIndexer. The input nodes to be cloned are provided in structuralNodeIndexer.

Parameters:

structuralModelIndexer Output indexer that will contain the cloned structural models.
structuralNodeIndexer Input indexer containing the structural nodes to clone.

Returns:

true if cloning succeeded and at least one structural model was created; false otherwise.

function computeDomain#

Computes the domain containing the atoms and bond atoms in the node indexer.

static SBSpatialDomain SBMStructuralModel::computeDomain (
    const SBNodeIndexer & nodeIndexer
)

Computes the spatial domain that encloses all atoms and bond atoms in the given node indexer.

The function gathers atoms and bond atoms from the provided nodes and determines the minimal bounding domain that contains them.

Parameters:

nodeIndexer Indexer containing nodes (atoms, bonds, etc.) from which the domain is computed.

Returns:

The computed SBSpatialDomain; if no atoms are present, an empty domain is returned.

function createBond#

Creates a bond between atom1 andatom2 if there is none; sets the bond order tobondOrder and the bond type tobondType .

static bool SBMStructuralModel::createBond (
    SBMStructuralModelNodeAtom * atom1,
    SBMStructuralModelNodeAtom * atom2,
    double bondOrder=1.0,
    SBBond::BondType bondType=SBBond::BondType::Undefined
)

Creates a bond between two atoms, or updates an existing bond's order and type.

If a bond already exists between the two atoms, its order and type are updated if they differ from the requested values. Otherwise, a new bond is created.

Parameters:

atom1 The first atom.
atom2 The second atom.
bondOrder The desired bond order.
bondType The desired bond type.

Returns:

true if a new bond was created or an existing bond was updated; false otherwise.

function createCovalentBondsByResidueType [2/2]#

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 int SBMStructuralModel::createCovalentBondsByResidueType (
    const SBNodeIndexer & nodeIndexer
)

Creates covalent bonds for the given residues by residue type.

This function creates covalent bonds for the atoms belonging to residues in nodeIndexer according to their residue types, ignoring inter‑atomic distances.

Parameters:

nodeIndexer Node indexer containing the residues for which covalent bonds should be created.

Returns:

The number of bonds created, or zero if the operation fails.

function createModel#

Creates a structural model from a SMILES string.

static SBMStructuralModel * SBMStructuralModel::createModel (
    const std::string & smiles,
    const std::string & name,
    bool addHydrogens=true,
    bool addExplicitHydrogenOnly=false,
    bool kekulize=true,
    bool runUFF=true,
    int uffMaxIters=500,
    double uffVdwThreshold=10.0,
    int uffConfId=0
)

This function creates an SBMStructuralModel instance based on the provided SMILES string. It allows optional steps such as hydrogen addition, kekulization, and energy minimization using UFF.

Parameters:

smiles The SMILES string representing the molecular structure.
name The name to assign to the created model.
addHydrogens Whether to add implicit hydrogen atoms (default: true).
addExplicitHydrogenOnly Whether to add only explicit hydrogens (default: false).
kekulize Whether to perform kekulization (default: true).
runUFF Whether to run the Universal Force Field (UFF) minimization (default: true).
uffMaxIters Maximum number of iterations for UFF minimization (default: 500).
uffVdwThreshold Van der Waals threshold for UFF minimization (default: 10.0).
uffConfId UFF conformation ID (default: 0).

Returns:

A pointer to the created SBMStructuralModel, or nullptr if creation failed.

This function uses RDKit library.

function exportImage#

Exports a molecular structure (SMILES) as an image file (png, jpg, svg).

static bool SBMStructuralModel::exportImage (
    const std::string & smiles,
    const std::string & outputFile,
    int widthPx=600,
    int marginPx=10,
    double lineWidth=3.0,
    const std::string & fontFamily="Sans Serif Collection"
)

Exports a molecular structure as an image file.

This function generates an image of the molecular structure from a given SMILES string and saves it in the specified file format (.png, .jpg, .jpeg, or .svg).

Parameters:

smiles The SMILES string representing the molecule.
outputFile The file path where the image should be saved.
widthPx Image width in pixels (default: 600).
marginPx Margin size in pixels around the structure (default: 10).
lineWidth Thickness of the molecular bonds (default: 3.0).
fontFamily Font family to use for text labels (default: "Sans Serif Collection").

Returns:

true if the export was successful, false otherwise.

This function uses RDKit library.

function extractStructuralNodes#

Adds in structuralModelIndexer the structural models resulting from extracting the structural nodes instructuralNodeIndexer .

static bool SBMStructuralModel::extractStructuralNodes (
    SBNodeIndexer & structuralModelIndexer,
    const SBNodeIndexer & structuralNodeIndexer
)

Extracts structural nodes from a given node indexer into a new structural model indexer.

The function identifies structural nodes and their ascendants, clones them, and populates the provided structuralModelIndexer.

Parameters:

structuralModelIndexer The indexer that will receive the extracted structural model nodes.
structuralNodeIndexer The indexer containing the nodes to extract from.

Returns:

true if structural nodes were extracted; false otherwise.

function findAtom [1/4]#

Returns, if found, an atom from a node indexer nodeIndexer with the typetype and namename ; else returns 0.

static SBMStructuralModelNodeAtom * SBMStructuralModel::findAtom (
    const SBNodeIndexer & nodeIndexer,
    SBElement::Type type,
    const std::string & name
)

Finds an atom with a given element type and name in a node indexer.

The function searches all atom nodes within the provided node indexer for an atom matching the specified element type and name.

Parameters:

nodeIndexer The node indexer to search for atoms.
type The element type of the atom to find.
name The name of the atom to find.

Returns:

A pointer to the matching atom, or nullptr if no such atom exists.

function findAtom [2/4]#

Returns, if found, an atom from an atom node indexer atomIndexer with the typetype and namename ; else returns 0.

static SBMStructuralModelNodeAtom * SBMStructuralModel::findAtom (
    const SBIndexer< SBMStructuralModelNodeAtom * > & atomIndexer,
    SBElement::Type type,
    const std::string & name
)

Finds an atom with a given element type and name in an atom indexer.

The function searches the provided atom indexer for an atom matching the specified element type and name.

Parameters:

atomIndexer The atom indexer to search for atoms.
type The element type of the atom to find.
name The name of the atom to find.

Returns:

A pointer to the matching atom, or nullptr if no such atom exists.

function findAtom [3/4]#

Returns, if found, an atom from a node indexer nodeIndexer with the typetype , namename , and an alternate locationaltLoc (if the atom has an alternate location); else returns 0.

static SBMStructuralModelNodeAtom * SBMStructuralModel::findAtom (
    const SBNodeIndexer & nodeIndexer,
    SBElement::Type type,
    const std::string & name,
    char altLoc
)

Finds an atom with a given element type, name, and alternate location in a node indexer.

The function searches all atom nodes within the provided node indexer for an atom matching the specified element type, name, and alternate location. If the atom does not have an alternate location, it is considered a match.

Parameters:

nodeIndexer The node indexer to search for atoms.
type The element type of the atom to find.
name The name of the atom to find.
altLoc The alternate location character to match; a space or missing alternate location is also accepted.

Returns:

A pointer to the matching atom, or nullptr if no such atom exists.

function findAtom [4/4]#

Returns, if found, an atom from an atom node indexer atomIndexer with the typetype , namename , and an alternate locationaltLoc (if the atom has an alternate location); else returns 0.

static SBMStructuralModelNodeAtom * SBMStructuralModel::findAtom (
    const SBIndexer< SBMStructuralModelNodeAtom * > & atomIndexer,
    SBElement::Type type,
    const std::string & name,
    char altLoc
)

Finds an atom with a given element type, name, and alternate location in an atom indexer.

The function searches the provided atom indexer for an atom matching the specified element type, name, and alternate location. If the atom does not have an alternate location, it is considered a match.

Parameters:

atomIndexer The atom indexer to search for atoms.
type The element type of the atom to find.
name The name of the atom to find.
altLoc The alternate location character to match; a space or missing alternate location is also accepted.

Returns:

A pointer to the matching atom, or nullptr if no such atom exists.

function findSubstructureMatchesWithSMARTS#

Finds substructure matches in inputNodeIndexer based on the given SMARTS stringsmarts and given parameters.

static int SBMStructuralModel::findSubstructureMatchesWithSMARTS (
    std::vector< SBNodeIndexer > & resultNodeIndexerVector,
    const SBNodeIndexer & inputNodeIndexer,
    const std::string & smarts,
    const SBValueMap & parameterMap=SBValueMap {}
)

Finds substructure matches using a SMARTS pattern and returns the number of matches.

Filters atoms and bonds in the input node indexer based on the given SMARTS string and fills the result indexer vector with the filtered fragments.

Parameters:

resultNodeIndexerVector The output vector populated with node indexers, each containing a separate matched structure. This vector is not cleared inside the function.
inputNodeIndexer The input node indexer containing structures to search.
smarts The SMARTS pattern to match.
parameterMap A value map with substructure match parameters (e.g., "maxMatches", "numThreads").

Returns:

The number of matches, or -1 if the SMARTS string is invalid or an error occurs.

This function uses RDKit library.

function getAltLocations [1/2]#

Returns a set of all alternate locations for atoms that belong to nodes present in nodeIndexer .

static std::set< char > SBMStructuralModel::getAltLocations (
    const SBNodeIndexer & nodeIndexer
)

Returns the set of alternate location identifiers for atoms in a node indexer.

The function scans all atom nodes within the provided node indexer and collects the alternate location characters that are present.

Parameters:

nodeIndexer The node indexer containing nodes to inspect for atom alternate locations.

Returns:

A set of characters representing the alternate locations found.

function getAltLocations [2/2]#

Returns a set of all alternate locations of atoms present in the atomIndexer .

static std::set< char > SBMStructuralModel::getAltLocations (
    const SBIndexer< SBMStructuralModelNodeAtom * > & atomIndexer
)

Returns the set of alternate location identifiers for atoms in an atom indexer.

The function scans the given atom indexer and collects the alternate location characters that are present.

Parameters:

atomIndexer The atom indexer containing atoms to inspect for alternate locations.

Returns:

A set of characters representing the alternate locations found.

function getAsphericity#

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.

static double SBMStructuralModel::getAsphericity (
    const SBNodeIndexer & nodeIndexer
)

Returns the asphericity parameter of the system of atoms (based on their positions and masses) in nodeIndexer.

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.

Parameters:

nodeIndexer The node indexer containing the atoms for which the asphericity is computed.

Returns:

The asphericity parameter in the range [0, 1].

function getCenterOfFormalCharge#

Returns the center of formal charge of atoms in nodeIndexer .

static SBPosition3 SBMStructuralModel::getCenterOfFormalCharge (
    const SBNodeIndexer & nodeIndexer
)

Returns the center of formal charge of atoms from nodeIndexer.

The center of formal charge is computed as follows:

R = sum(q_i * r_i, i=1..N) / Q

where N is the number of atoms, q_i is the i-th atom's formal charge, r_i is the i-th atom's position, and Q is the total formal charge 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).

Parameters:

nodeIndexer Node indexer containing atoms (or their parent nodes) to compute the center of formal charge.

Returns:

The center of formal charge position.

function getCenterOfMass#

Returns the center of mass of atoms in nodeIndexer .

static SBPosition3 SBMStructuralModel::getCenterOfMass (
    const SBNodeIndexer & nodeIndexer
)

Returns the center of mass of atoms from nodeIndexer.

The center of mass is computed as follows:

R = 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).

Parameters:

nodeIndexer Node indexer containing atoms (or their parent nodes) to compute the center of mass.

Returns:

The center of mass position.

function getCenterOfPartialCharge#

Returns the center of partial charge of atoms in nodeIndexer .

static SBPosition3 SBMStructuralModel::getCenterOfPartialCharge (
    const SBNodeIndexer & nodeIndexer
)

Returns the center of partial charge of atoms from nodeIndexer.

The center of partial charge is computed as follows:

R = sum(q_i * r_i, i=1..N) / Q

where N is the number of atoms, q_i is the i-th atom's partial charge, r_i is the i-th atom's position, and Q is the total partial charge 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).

Parameters:

nodeIndexer Node indexer containing atoms (or their parent nodes) to compute the center of partial charge.

Returns:

The center of partial charge position.

function getCentroid#

Returns the centroid (the geometric center) of atoms in nodeIndexer .

static SBPosition3 SBMStructuralModel::getCentroid (
    const SBNodeIndexer & nodeIndexer
)

Returns the centroid (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).

Parameters:

nodeIndexer Node indexer containing atoms (or their parent nodes) to compute the centroid.

Returns:

The centroid position.

function getCommonStructuralModel#

Returns the common structural model for nodeIndexer , ornullptr if there is none.

static SBMStructuralModel * SBMStructuralModel::getCommonStructuralModel (
    const SBNodeIndexer & nodeIndexer
)

Returns the common structural model for nodeIndexer.

Parameters:

nodeIndexer The node indexer to inspect.

Returns:

The common structural model for nodeIndexer, or nullptr if there is none.

function getCommonUnitCell#

Retrieves the common unit cell for nodeIndexer .

static bool SBMStructuralModel::getCommonUnitCell (
    const SBNodeIndexer & nodeIndexer,
    SBUnitCell & unitCell
)

Parameters:

nodeIndexer The node indexer to inspect.
unitCell The output unit cell.

Returns:

true if and only if a common unit cell was found.

function getDipoleMomentAtCenterOfCharge#

Returns the dipole moment of atoms in nodeIndexer at their center of charge (based on partial charge)

static SBQuantity::length SBMStructuralModel::getDipoleMomentAtCenterOfCharge (
    const SBNodeIndexer & nodeIndexer
)

Returns the dipole moment of atoms from nodeIndexer at their center of charge.

This function returns the dipole moment of atoms from nodeIndexer at their center of charge.

The dipole moment at center of charge is computed as follows:

m = norm(mu)

where mu is the dipole vector of atoms from nodeIndexer at their center of partial charge.

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

Parameters:

nodeIndexer The node indexer containing the atoms for which the dipole moment is computed.

Returns:

The magnitude of the dipole moment at the center of charge.

function getDipoleMomentAtCenterOfMass#

Returns the dipole moment of atoms in nodeIndexer at their center of mass.

static SBQuantity::length SBMStructuralModel::getDipoleMomentAtCenterOfMass (
    const SBNodeIndexer & nodeIndexer
)

Returns the dipole moment of atoms from nodeIndexer at their center of mass.

This function returns the dipole moment of atoms from nodeIndexer at their center of mass. The dipole moment at center of mass is computed as follows:

m = norm(mu)

where mu is the dipole vector of atoms from nodeIndexer at their center of mass.

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

Parameters:

nodeIndexer The node indexer containing the atoms for which the dipole moment is computed.

Returns:

The magnitude of the dipole moment at the center of mass.

function getDipoleVectorAtCenterOfCharge#

Returns the dipole vector of atoms in nodeIndexer at their center of charge (based on partial charge)

static SBPosition3 SBMStructuralModel::getDipoleVectorAtCenterOfCharge (
    const SBNodeIndexer & nodeIndexer
)

Returns the dipole vector of atoms from nodeIndexer at their center of partial charge.

The dipole vector at center of charge is computed as follows:

mu = sum(q_i * (r_i - r_coc), i=1..N)

where N is the number of atoms, q_i is the i-th atom's partial charge, r_i is the i-th atom's position, and r_coc is the center of partial charge of these atoms.

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

Parameters:

nodeIndexer Node indexer containing atoms (or their parent nodes) to compute the dipole vector.

Returns:

The dipole vector at the center of partial charge.

function getDipoleVectorAtCenterOfMass#

Returns the dipole vector of atoms in nodeIndexer at their center of mass.

static SBPosition3 SBMStructuralModel::getDipoleVectorAtCenterOfMass (
    const SBNodeIndexer & nodeIndexer
)

Returns the dipole vector of atoms from nodeIndexer at their center of mass.

The dipole vector at center of mass is computed as follows:

mu = sum(q_i * (r_i - r_com), i=1..N)

where N is the number of atoms, q_i is the i-th atom's partial charge, r_i is the i-th atom's position, and r_com is the center of mass of these atoms.

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

Parameters:

nodeIndexer Node indexer containing atoms (or their parent nodes) to compute the dipole vector.

Returns:

The dipole vector at the center of mass.

function getInertiaTensor#

Returns the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer .

static SBInertiaTensor33 SBMStructuralModel::getInertiaTensor (
    const SBNodeIndexer & nodeIndexer
)

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.

Parameters:

nodeIndexer The node indexer containing the atoms for which the inertia tensor is computed.

Returns:

The inertia tensor of the atoms relative to their center of mass.

function getMinimumImageDisplacement [3/4]#

Returns the minimum-image displacement from position1 toposition2 usingunitCell .

static SBLength3 SBMStructuralModel::getMinimumImageDisplacement (
    const SBPosition3 & position1,
    const SBPosition3 & position2,
    const SBUnitCell & unitCell
)

Parameters:

position1 The start position.
position2 The end position.
unitCell The unit cell to use.

Returns:

The minimum-image displacement.

function getMinimumImageDisplacement [4/4]#

Returns the minimum-image displacement from atom1 toatom2 usingunitCell .

static SBLength3 SBMStructuralModel::getMinimumImageDisplacement (
    const SBMStructuralModelNodeAtom * atom1,
    const SBMStructuralModelNodeAtom * atom2,
    const SBUnitCell & unitCell
)

Parameters:

atom1 The first atom.
atom2 The second atom.
unitCell The unit cell to use.

Returns:

The minimum-image displacement.

function getMinimumImageDistance [3/4]#

Returns the minimum-image distance between position1 andposition2 usingunitCell .

static SBQuantity::length SBMStructuralModel::getMinimumImageDistance (
    const SBPosition3 & position1,
    const SBPosition3 & position2,
    const SBUnitCell & unitCell
)

Parameters:

position1 The first position.
position2 The second position.
unitCell The unit cell to use.

Returns:

The minimum-image distance.

function getMinimumImageDistance [4/4]#

Returns the minimum-image distance between atom1 andatom2 usingunitCell .

static SBQuantity::length SBMStructuralModel::getMinimumImageDistance (
    const SBMStructuralModelNodeAtom * atom1,
    const SBMStructuralModelNodeAtom * atom2,
    const SBUnitCell & unitCell
)

Parameters:

atom1 The first atom.
atom2 The second atom.
unitCell The unit cell to use.

Returns:

The minimum-image distance.

function getMolecularWeight [1/2]#

Returns the cumulative molecular weight of nodes in nodeIndexer .

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

This function returns the cumulative molecular weight of nodes in nodeIndexer.

Parameters:

nodeIndexer Node indexer containing the nodes whose molecular weight is summed.

Returns:

The total molecular weight of the nodes.

function getPrincipalAxes#

Returns the principal axes of the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer .

static SBMatrix33 SBMStructuralModel::getPrincipalAxes (
    const SBNodeIndexer & 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.

Parameters:

nodeIndexer The node indexer containing the atoms for which the principal axes are computed.

Returns:

The principal axes matrix of the inertia tensor.

function getRadiusOfGyration#

Returns the radius of gyration of the system of atoms (based on their positions and masses) in nodeIndexer .

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

Returns the radius of gyration of the system of atoms (based on their positions and masses) from nodeIndexer.

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.

Parameters:

nodeIndexer The node indexer containing the atoms for which the radius of gyration is computed.

Returns:

The radius of gyration.

function getShapeParameter#

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, positive values correspond to prolate ellipsoid.

static double SBMStructuralModel::getShapeParameter (
    const SBNodeIndexer & nodeIndexer
)

Returns the shape parameter of the system of atoms (based on their positions and masses) in nodeIndexer.

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, positive 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.

Parameters:

nodeIndexer The node indexer containing the atoms for which the shape parameter is computed.

Returns:

The shape parameter S in the range [-0.25, 2].

function getSolventAccessibleSurfaceArea#

Returns the solvent-accessible surface area (SASA) of the system of atoms in nodeIndexer with the probe radiusprobeRadius , and the number of points on a spherenumberOfPointsOnSphere .

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

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.

Parameters:

nodeIndexer The node indexer containing the atoms for which the SASA is calculated.
probeRadius The radius of the probe sphere used to compute the SASA.
numberOfPointsOnSphere The number of points sampled on a sphere for each atom.

Returns:

The solvent-accessible surface area of the atoms.

function getSpatialTransform#

Returns the spatial transform based on the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer .

static SBDTypeSpatialTransform SBMStructuralModel::getSpatialTransform (
    const SBNodeIndexer & 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.

Parameters:

nodeIndexer The node indexer containing the atoms for which the spatial transform is computed.

Returns:

The spatial transform derived from the inertia tensor.

function getSumOfFormalCharges [1/2]#

Returns the sum of formal charges of nodes in nodeIndexer .

static int SBMStructuralModel::getSumOfFormalCharges (
    const SBNodeIndexer & nodeIndexer
)

This function returns the sum of formal charges of nodes in nodeIndexer.

Parameters:

nodeIndexer Node indexer containing the nodes whose formal charges are summed.

Returns:

The sum of formal charges.

function getSumOfPartialCharges [1/2]#

Returns the sum of partial charges of nodes in nodeIndexer .

static float SBMStructuralModel::getSumOfPartialCharges (
    const SBNodeIndexer & nodeIndexer
)

This function returns the sum of partial charges of nodes in nodeIndexer.

Parameters:

nodeIndexer Node indexer containing the nodes whose partial charges are summed.

Returns:

The sum of partial charges.

function getWater [2/2]#

Finds water nodes in the nodeIndexer .

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

Finds water nodes in the given nodeIndexer and adds them to resultNodeIndexer.

The resulting water nodes might include water structural groups and water atoms.

Parameters:

resultNodeIndexer Indexer that will be populated with the water nodes found.
nodeIndexer Indexer specifying the nodes to search for water nodes.

function isPlanar#

Returns true if all atoms innodeIndexer are in the same plane.

static bool SBMStructuralModel::isPlanar (
    const SBNodeIndexer & nodeIndexer
)

Note that for 3 atoms and less it will always return true.

Parameters:

nodeIndexer Node indexer containing the atoms to test.

Returns:

true if all atoms are planar, otherwise false.

function isValidSMARTS#

Checks if the given SMARTS string is valid.

static bool SBMStructuralModel::isValidSMARTS (
    const std::string & smarts
)

Parameters:

smarts The SMARTS string to validate.

Returns:

true if the SMARTS string is valid, false otherwise.

This function uses the RDKit library.

function isValidSMILES#

Checks if the given SMILES string represents a valid molecular structure.

static bool SBMStructuralModel::isValidSMILES (
    const std::string & smiles
)

Parameters:

smiles The SMILES string to validate.

Returns:

true if the SMILES string is valid, false otherwise.

This function uses the RDKit library.

function makeWhole [2/3]#

Reconstructs the bond-connected components from nodeIndexer using their common unit cell.

static bool SBMStructuralModel::makeWhole (
    const SBNodeIndexer & nodeIndexer
)

Parameters:

nodeIndexer The nodes whose atoms will be reconstructed.

Returns:

true if the operation completed; otherwise false.

function makeWhole [3/3]#

Reconstructs the bond-connected components from nodeIndexer usingunitCell .

static bool SBMStructuralModel::makeWhole (
    const SBNodeIndexer & nodeIndexer,
    const SBUnitCell & unitCell
)

Parameters:

nodeIndexer The nodes whose atoms will be reconstructed.
unitCell The unit cell to use.

Returns:

true if the operation completed; otherwise false.

function replaceAtom#

Replaces atom oldAtom with atomnewAtom . All bonds from the old atom are transferred to the new atom.

static void SBMStructuralModel::replaceAtom (
    SBMStructuralModelNodeAtom * oldAtom,
    SBMStructuralModelNodeAtom * newAtom,
    bool preserveOldAtomPosition=false
)

Replaces an atom in the structural model with another atom.

The function removes the old atom, transfers all its bonds to the new atom, and optionally preserves the old atom's position for the new atom.

Parameters:

oldAtom The atom to be replaced.
newAtom The atom that will replace the old atom.
preserveOldAtomPosition If true, the new atom inherits the position of the old atom.

function replaceBond#

Replaces bond oldBond with bondnewBond . All neighboring bonds from the old bond are transferred to the new bond.

static void SBMStructuralModel::replaceBond (
    SBMStructuralModelNodeBond * oldBond,
    SBMStructuralModelNodeBond * newBond,
    bool flipBond=false,
    bool preserveOldBondPosition=false
)

Replaces a bond in the structural model with another bond.

The function erases the old bond and creates a new bond, optionally flipping the bond direction and preserving the positions of the original bond's atoms.

Parameters:

oldBond The bond to be replaced.
newBond The new bond that will replace the old bond.
flipBond If true, the bond direction is flipped (left/right atoms are swapped).
preserveOldBondPosition If true, the new bond's atoms inherit the positions of the old bond's atoms.

function smilesToSVG#

Converts a SMILES string into an SVG representation.

static std::optional< std::string > SBMStructuralModel::smilesToSVG (
    const std::string & smiles,
    int widthPx=600
)

This function takes a molecular structure in SMILES format and returns its SVG representation.

Parameters:

smiles The SMILES string to convert.
widthPx The width of the generated SVG image in pixels.

Returns:

An std::optional<std::string> containing the SVG content, or std::nullopt if conversion failed.

This function uses RDKit library.

function wrapToUnitCell [2/3]#

Wraps the atoms from nodeIndexer into their common primary unit cell.

static bool SBMStructuralModel::wrapToUnitCell (
    const SBNodeIndexer & nodeIndexer,
    bool keepConnectedComponentsWhole=true
)

Parameters:

nodeIndexer The nodes whose atoms will be wrapped.
keepConnectedComponentsWhole Whether to keep bond-connected components whole while wrapping.

Returns:

true if the operation completed; otherwise false.

function wrapToUnitCell [3/3]#

Wraps the atoms from nodeIndexer into the primary unit cellunitCell .

static bool SBMStructuralModel::wrapToUnitCell (
    const SBNodeIndexer & nodeIndexer,
    const SBUnitCell & unitCell,
    bool keepConnectedComponentsWhole=true
)

Parameters:

nodeIndexer The nodes whose atoms will be wrapped.
unitCell The unit cell to use.
keepConnectedComponentsWhole Whether to keep bond-connected components whole while wrapping.

Returns:

true if the operation completed; otherwise false.