Class SBMStructuralModelPath#

ClassList > SBMStructuralModelPath

This class describes a structural path (trajectory) More...

#include <SBMStructuralModelPath.hpp>

Inherits the following classes: SBDDataGraphNode

Public Types#

Type	Name
enum	AnimationType Path animation types.

Public Types inherited from SBDDataGraphNode#

See SBDDataGraphNode

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

Public Functions#

Type	Name
	SBMStructuralModelPath () Constructs a path.
	SBMStructuralModelPath (const std::string & name, const SBNodeIndexer & nodeIndexer=SBNodeIndexer()) Constructs a path with name `name` from the conformations in`nodeIndexer` .
	SBMStructuralModelPath (const std::string & name, const SBNodeIndexer & nodeIndexer, SBVector< SBVector< SBPosition3 > * > * positionData, SBVector< SBQuantity::energy > * energyData=nullptr, SBVector< SBQuantity::time > * timeData=nullptr, SBVector< SBVector< SBVelocity3 > * > * velocityData=nullptr, SBVector< SBVector< SBForce3 > * > * forceData=nullptr, SBVector< SBUnitCell > * unitCellData=nullptr, SBVector< SBQuantity::mass > * massData=nullptr) Constructs a path with name `name` from the atoms in`nodeIndexer` .
virtual bool	add (SBConformation * conformation) Adds a frame to the path.
virtual bool	add (SBMStructuralModelPath * path) Adds frames to the path.
virtual bool	add (SBVector< SBPosition3 > * positionData, const SBQuantity::energy & energy=SBQuantity::energy::zero, const SBQuantity::time & time=SBQuantity::time::zero, SBVector< SBVelocity3 > * velocityData=nullptr, SBVector< SBForce3 > * forceData=nullptr) Adds a frame to the path.
virtual bool	add (SBVector< SBVector< SBPosition3 > * > * positionData, SBVector< SBQuantity::energy > * energyData=nullptr, SBVector< SBQuantity::time > * timeData=nullptr, SBVector< SBVector< SBVelocity3 > * > * velocityData=nullptr, SBVector< SBVector< SBForce3 > * > * forceData=nullptr) Adds frames to the path.
bool	addAtom (SBAtom * atom, SBVector< SBPosition3 > * atomPositionVector=nullptr, SBVector< SBVelocity3 > * atomVelocityVector=nullptr, SBVector< SBForce3 > * atomForceVector=nullptr) Adds an `atom` to the path.
void	clearSourceFileName () Clears the name of the file associated to the path.
virtual SBMStructuralModelPath *	clone () override Returns a copy of the node and its descendants.
virtual SBMStructuralModelPath *	copy (unsigned int firstStep, unsigned int lastStep) Copies frames from the path to create a new path.
virtual void	createConformation (unsigned int step, SBNodeIndexer & conformationIndexer) const Create a conformation corresponding to a specific `step` .
virtual void	createConformations (SBNodeIndexer & conformationIndexer) const Create conformations corresponding to all steps.
virtual void	createStructuralModels (unsigned int step, SBNodeIndexer & structuralModelIndexer) const Create structural models corresponding to a specific `step` .
virtual void	createStructuralModels (SBNodeIndexer & structuralModelIndexer) const Create structural models corresponding to all steps.
virtual void	forEachNodeDepthFirst (void()(SBDDataGraphNode* node) action) override Performs the* `action` on this path node.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) override Performs the* `object` 's`action` on this path node.
virtual bool	getAnimationFlag () const Returns the animation flag.
virtual AnimationType	getAnimationType () const Returns the animation type.
virtual SBPointerIndexer< SBAtom > const *	getAtomIndexer () const Returns the atoms for which a position is saved.
virtual SBQuantity::energy	getCurrentEnergy () const Returns the current energy.
virtual unsigned int	getCurrentStep () const Returns the current step along the path.
virtual SBQuantity::time	getCurrentTime () const Returns the current time.
virtual bool	getEnergy (unsigned int step, SBQuantity::energy & energy) const Retrieves the energy for a specific `step` .
virtual SBVector< SBQuantity::energy > *	getEnergyData () const Returns the energy data.
virtual bool	getForce (unsigned int step, unsigned int atomIndex, SBForce3 & force) const Retrieves the force of atom `atomIndex` and stores it in`force` for a specific`step` .
virtual bool	getForce (unsigned int step, SBAtom * atom, SBForce3 & force) const Retrieves the force of atom `atom` and stores it in`force` for a specific`step` .
virtual SBVector< SBVector< SBForce3 > * > *	getForceData () const Returns the force data.
virtual bool	getForwardFlag () const Returns the forward flag, which indicates when the animation is moving forward.
virtual bool	getMass (unsigned int atomIndex, SBQuantity::mass & mass) const Retrieves the mass of atom `atomIndex` .
virtual bool	getMass (SBAtom * atom, SBQuantity::mass & mass) const Retrieves the mass of atom `atom` .
virtual SBVector< SBQuantity::mass > *	getMassData () const Returns the mass data.
SBMStructuralModelPath *	getNextPath () const Returns the next path in the document.
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 () const Returns the number of atoms for which a position is saved.
virtual unsigned int	getNumberOfSteps () const Returns the number of steps in the path.
virtual bool	getPosition (unsigned int step, unsigned int atomIndex, SBPosition3 & position) const Retrieves the position of atom `atomIndex` and stores it in`position` for a specific`step` .
virtual bool	getPosition (unsigned int step, SBAtom * atom, SBPosition3 & position) const Retrieves the position of atom `atom` and stores it in`position` for a specific`step` .
virtual SBVector< SBVector< SBPosition3 > * > *	getPositionData () const Returns the position data.
SBMStructuralModelPath *	getPreviousPath () const Returns the previous path in the document.
virtual unsigned int	getSmoothingWindowSize () const Returns the size of the smoothing window.
const std::string &	getSourceFileName () const Returns the name of the file associated to the path.
virtual SBQuantity::second const &	getStepDuration () const Returns the step duration.
virtual unsigned int	getStride () const Returns the animation stride.
virtual bool	getTime (unsigned int step, SBQuantity::time & time) const Retrieves the time for a specific `step` .
virtual SBVector< SBQuantity::time > *	getTimeData () const Returns the time data.
virtual SBNode::Type	getType () override const Returns the data graph node type.
virtual bool	getUnitCell (unsigned int step, SBUnitCell & unitCell) const Retrieves the unit cell for a specific `step` .
virtual SBVector< SBUnitCell > *	getUnitCellData () const Returns the unit-cell data.
virtual bool	getUnwrappedPosition (unsigned int step, unsigned int atomIndex, SBPosition3 & position) const Retrieves the unwrapped position of atom `atomIndex` for a specific`step` .
virtual bool	getUnwrappedPosition (unsigned int step, SBAtom * atom, SBPosition3 & position) const Retrieves the unwrapped position of atom `atom` for a specific`step` .
virtual bool	getVelocity (unsigned int step, unsigned int atomIndex, SBVelocity3 & velocity) const Retrieves the velocity of atom `atomIndex` and stores it in`velocity` for a specific`step` .
virtual bool	getVelocity (unsigned int step, SBAtom * atom, SBVelocity3 & velocity) const Retrieves the velocity of atom `atom` and stores it in`velocity` for a specific`step` .
virtual SBVector< SBVector< SBVelocity3 > * > *	getVelocityData () const Returns the velocity data.
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	hasSourceFileName () const Returns `true` when the path has the source file name set.
virtual bool	insert (unsigned int step, SBConformation * conformation) Inserts a frame in the path at position `step` .
virtual bool	insert (unsigned int step, SBMStructuralModelPath * path) Inserts frames in the path at position `step` .
virtual bool	insert (unsigned int step, SBVector< SBPosition3 > * positionData, const SBQuantity::energy & energy=SBQuantity::energy::zero, const SBQuantity::time & time=SBQuantity::time::zero, SBVector< SBVelocity3 > * velocityData=nullptr, SBVector< SBForce3 > * forceData=nullptr) Inserts a frame in the path at position `step` .
virtual bool	insert (unsigned int step, SBVector< SBVector< SBPosition3 > * > * positionData, SBVector< SBQuantity::energy > * energyData=nullptr, SBVector< SBQuantity::time > * timeData=nullptr, SBVector< SBVector< SBVelocity3 > * > * velocityData=nullptr, SBVector< SBVector< SBForce3 > * > * forceData=nullptr) Inserts frames in the path at position `step` .
bool	insertAtom (unsigned int atomIndex, SBAtom * atom, SBVector< SBPosition3 > * atomPositionVector=nullptr, SBVector< SBVelocity3 > * atomVelocityVector=nullptr, SBVector< SBForce3 > * atomForceVector=nullptr) Inserts an `atom` at index`atomIndex` to the path.
virtual bool	isSerializable () override const Returns `true` __
virtual bool	makeWholeAllSteps () Reconstructs bond-connected components across periodic boundaries for all steps.
virtual bool	makeWholeStep (unsigned int step) Reconstructs bond-connected components across periodic boundaries for a specific `step` .
virtual void	print (unsigned int offset=0) override const Prints the path.
virtual SBConformation *	remove (unsigned int step) Remove a frame from the path to create a conformation.
virtual SBMStructuralModelPath *	remove (unsigned int firstStep, unsigned int lastStep) Removes frames from the path to create a new path.
bool	removeAtom (SBAtom * atom) Removes an atom from the path.
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 path.
virtual void	setAnimationFlag (bool animationFlag) Sets the animation flag.
virtual void	setAnimationType (AnimationType animationType) Sets the animation type.
virtual void	setCurrentStep (unsigned int currentStep) Sets the current step along the path.
virtual bool	setEnergy (unsigned int step, const SBQuantity::energy & energy) Sets the energy for a specific `step` .
virtual void	setEnergyData (SBVector< SBQuantity::energy > * energyData) Sets the energy data.
virtual bool	setForce (unsigned int step, unsigned int atomIndex, const SBForce3 & force) Sets the force of atom `atomIndex` to`force` for a specific`step` .
virtual bool	setForce (unsigned int step, SBAtom * atom, const SBForce3 & force) Sets the force of atom `atom` to`force` for a specific`step` .
virtual void	setForceData (SBVector< SBVector< SBForce3 > * > * forceData) Sets the force data.
virtual void	setForwardFlag (bool forwardFlag) Sets the forward flag, which indicates when the animation is moving forward.
virtual bool	setMass (unsigned int atomIndex, const SBQuantity::mass & mass) Sets the mass of atom `atomIndex` .
virtual bool	setMass (SBAtom * atom, const SBQuantity::mass & mass) Sets the mass of atom `atom` .
virtual void	setMassData (SBVector< SBQuantity::mass > * massData) Sets the mass data.
virtual bool	setPosition (unsigned int step, unsigned int atomIndex, const SBPosition3 & position) Sets the position of atom `atomIndex` to`position` for a specific`step` .
virtual bool	setPosition (unsigned int step, SBAtom * atom, const SBPosition3 & position) Sets the position of atom `atom` to`position` for a specific`step` .
virtual void	setPositionData (SBVector< SBVector< SBPosition3 > * > * positionData) Sets the position data.
virtual void	setSmoothingWindowSize (unsigned int smoothingWindowSize) Sets the size of the smoothing window.
void	setSourceFileName (const std::string & fileName) Sets the name of the file associated to the path.
virtual void	setStepDuration (const SBQuantity::second & stepDuration) Sets the step duration.
virtual void	setStride (unsigned int stride) Sets the animation stride.
virtual bool	setTime (unsigned int step, const SBQuantity::time & time) Sets the time for a specific `step` .
virtual void	setTimeData (SBVector< SBQuantity::time > * timeData) Sets the time data.
virtual bool	setUnitCell (unsigned int step, const SBUnitCell & unitCell) Sets the unit cell for a specific `step` .
virtual void	setUnitCellData (SBVector< SBUnitCell > * unitCellData) Sets the unit-cell data.
virtual bool	setVelocity (unsigned int step, unsigned int atomIndex, const SBVelocity3 & velocity) Sets the velocity of atom `atomIndex` to`velocity` for a specific`step` .
virtual bool	setVelocity (unsigned int step, SBAtom * atom, const SBVelocity3 & velocity) Sets the velocity of atom `atom` to`velocity` for a specific`step` .
virtual void	setVelocityData (SBVector< SBVector< SBVelocity3 > * > * velocityData) Sets the velocity data.
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 path.
virtual bool	unwrap () Unwraps the trajectory over time using successive minimum-image displacements.
virtual void	updateState () Updates the state along the path according to the animation parameters.
virtual bool	wrapAllSteps (bool keepConnectedComponentsWhole=true) Wraps the positions of all steps into their primary unit cells.
virtual bool	wrapStep (unsigned int step, bool keepConnectedComponentsWhole=true) Wraps the positions of a specific `step` into the primary unit cell.
virtual	~SBMStructuralModelPath () Destructs the path.

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 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 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#

This class describes a structural path, i.e.

a set of positions of atoms. In SAMSON, the user may name and save a structural path. Stored paths appear in the document view, and the user may thus restore structural paths by right-clicking on them.

Short name: SBPath

See also: SBDDocument

Public Types Documentation#

enum AnimationType#

Path animation types.

enum SBMStructuralModelPath::AnimationType {
    Once = 1,
    Loop = 2,
    Bounce = 3
};

Public Functions Documentation#

function SBMStructuralModelPath [1/3]#

Constructs a path.

SBMStructuralModelPath::SBMStructuralModelPath ()

Constructs an empty structural path.

Creates a new SBMStructuralModelPath instance with no name and no associated atoms.

function SBMStructuralModelPath [2/3]#

Constructs a path with name name from the conformations innodeIndexer .

SBMStructuralModelPath::SBMStructuralModelPath (
    const std::string & name,
    const SBNodeIndexer & nodeIndexer=SBNodeIndexer ()
)

Constructs a structural path with a given name and set of atoms.

Creates a SBMStructuralModelPath using the specified name and atom indexer.

Parameters:

name The name of the path.
nodeIndexer The indexer that provides the atoms (conformations) to be included in the path.

function SBMStructuralModelPath [3/3]#

Constructs a path with name name from the atoms innodeIndexer .

SBMStructuralModelPath::SBMStructuralModelPath (
    const std::string & name,
    const SBNodeIndexer & nodeIndexer,
    SBVector< SBVector< SBPosition3 > * > * positionData,
    SBVector< SBQuantity::energy > * energyData=nullptr,
    SBVector< SBQuantity::time > * timeData=nullptr,
    SBVector< SBVector< SBVelocity3 > * > * velocityData=nullptr,
    SBVector< SBVector< SBForce3 > * > * forceData=nullptr,
    SBVector< SBUnitCell > * unitCellData=nullptr,
    SBVector< SBQuantity::mass > * massData=nullptr
)

Constructs a structural path with detailed data.

Creates a SBMStructuralModelPath with the specified name, atom indexer, and optional position, energy, time, velocity, and force data.

Parameters:

name The name of the path.
nodeIndexer The indexer that provides the atoms to be included in the path.
positionData Pointer to a vector of position vectors for each step; each inner vector holds the positions of all atoms for that step.
energyData Pointer to a vector of energy values for each step (optional).
timeData Pointer to a vector of time values for each step (optional).
velocityData Pointer to a vector of velocity vectors for each step (optional).
forceData Pointer to a vector of force vectors for each step (optional).
unitCellData Pointer to a vector of unit cells for each step (optional).
massData Pointer to a vector of masses for each atom (optional).

function add [1/4]#

Adds a frame to the path.

virtual bool SBMStructuralModelPath::add (
    SBConformation * conformation
)

Adds a step to the path by copying information from a conformation.

The conformation needs to have all information that the path has. For example, if the path has velocity data, then the conformation needs to have velocity data as well. Furthermore, all atoms indexed by the path need be indexed by the conformation as well (but the conformation may have more information than necessary). Since all information is copied, the conformation may be deleted afterwards.

Parameters:

conformation The conformation to copy data from.

Returns:

true on success, false otherwise.

function add [2/4]#

Adds frames to the path.

virtual bool SBMStructuralModelPath::add (
    SBMStructuralModelPath * path
)

Adds frames to the path by copying information from another path.

The provided path needs to have all information that this path has. For example, if this path has velocity data, then the provided path needs to have velocity data as well. Furthermore, all atoms indexed by this path need be indexed by the provided path as well (but the provided path may have more information than necessary). Since all information is copied, the provided path may be deleted afterwards.

Parameters:

path The source path to copy frames from.

Returns:

true on success, false otherwise.

function add [3/4]#

Adds a frame to the path.

virtual bool SBMStructuralModelPath::add (
    SBVector< SBPosition3 > * positionData,
    const SBQuantity::energy & energy=SBQuantity::energy::zero,
    const SBQuantity::time & time=SBQuantity::time::zero,
    SBVector< SBVelocity3 > * velocityData=nullptr,
    SBVector< SBForce3 > * forceData=nullptr
)

Adds a step to the path using the provided data vectors.

All necessary information has to be provided. For example, if the path has velocity data, then velocity data must be provided. Furthermore, the size of the provided vectors must be equal to the number of atoms indexed in the path. The passed information is copied, and may thus be deleted after the function returns.

Parameters:

positionData Vector of positions for each atom.
energy Energy value for the step.
time Time value for the step.
velocityData Optional vector of velocities for each atom.
forceData Optional vector of forces for each atom.

Returns:

true on success, false otherwise.

function add [4/4]#

Adds frames to the path.

virtual bool SBMStructuralModelPath::add (
    SBVector< SBVector< SBPosition3 > * > * positionData,
    SBVector< SBQuantity::energy > * energyData=nullptr,
    SBVector< SBQuantity::time > * timeData=nullptr,
    SBVector< SBVector< SBVelocity3 > * > * velocityData=nullptr,
    SBVector< SBVector< SBForce3 > * > * forceData=nullptr
)

Adds steps to the path using the provided multi-step data vectors.

All necessary information has to be provided. For example, if the path has velocity data, then velocity data must be provided. Furthermore, the size of the provided vectors must be equal to the number of atoms indexed in the path. The passed information is copied, and may thus be deleted after the function returns.

Parameters:

positionData Vector of vectors of positions for each atom at each step.
energyData Optional vector of energy values for each step.
timeData Optional vector of time values for each step.
velocityData Optional vector of vectors of velocities for each atom at each step.
forceData Optional vector of vectors of forces for each atom at each step.

Returns:

true on success, false otherwise.

function addAtom#

Adds an atom to the path.

bool SBMStructuralModelPath::addAtom (
    SBAtom * atom,
    SBVector< SBPosition3 > * atomPositionVector=nullptr,
    SBVector< SBVelocity3 > * atomVelocityVector=nullptr,
    SBVector< SBForce3 > * atomForceVector=nullptr
)

Adds an atom to the path.

It expects position, velocity and force data to fill the path data. For example, if the path contains one hundred steps (frames) in the position data, then the size of the position vector atomPositionVector should be one hundred, since each frame will need to have one new position inserted, corresponding to the inserted atom. The atom is added at the end of the path indexer.

Parameters:

atom Pointer to the atom to add.
atomPositionVector Optional vector of positions for the atom across steps.
atomVelocityVector Optional vector of velocities for the atom across steps.
atomForceVector Optional vector of forces for the atom across steps.

Returns:

true when insertion is successful; otherwise false.

function clearSourceFileName#

Clears the name of the file associated to the path.

void SBMStructuralModelPath::clearSourceFileName ()

Clears the source file name associated with the path.

function clone#

Returns a copy of the node and its descendants.

virtual SBMStructuralModelPath * SBMStructuralModelPath::clone () override

Creates a copy of this path node and its descendants.

Returns:

Pointer to the cloned SBMStructuralModelPath.

Implements SBDDataGraphNode::clone

function copy#

Copies frames from the path to create a new path.

virtual SBMStructuralModelPath * SBMStructuralModelPath::copy (
    unsigned int firstStep,
    unsigned int lastStep
)

Creates a deep copy of a range of steps from the path.

Copies all the frames between (and including) steps firstStep and lastStep into a new SBMStructuralModelPath instance. The original path remains unchanged. Returns nullptr if the parameters are invalid or required data is missing.

Parameters:

firstStep Index of the first step to copy (inclusive).
lastStep Index of the last step to copy (inclusive).

Returns:

Pointer to a new SBMStructuralModelPath containing the copied frames, or nullptr on failure.

function createConformation#

Create a conformation corresponding to a specific step .

virtual void SBMStructuralModelPath::createConformation (
    unsigned int step,
    SBNodeIndexer & conformationIndexer
) const

Creates a conformation for a specific step and adds it to the provided node indexer.

Parameters:

step The step index for which to create the conformation.
conformationIndexer The node indexer to which the new conformation will be added.

function createConformations#

Create conformations corresponding to all steps.

virtual void SBMStructuralModelPath::createConformations (
    SBNodeIndexer & conformationIndexer
) const

Creates conformations for all steps and adds them to the provided node indexer.

Parameters:

conformationIndexer The node indexer to which the new conformations will be added.

function createStructuralModels [1/2]#

Create structural models corresponding to a specific step .

virtual void SBMStructuralModelPath::createStructuralModels (
    unsigned int step,
    SBNodeIndexer & structuralModelIndexer
) const

Creates structural models for a specific step and adds them to the provided node indexer.

Parameters:

step The step index for which to create the structural models.
structuralModelIndexer The node indexer to which the new structural models will be added.

function createStructuralModels [2/2]#

Create structural models corresponding to all steps.

virtual void SBMStructuralModelPath::createStructuralModels (
    SBNodeIndexer & structuralModelIndexer
) const

Creates structural models for all steps and adds them to the provided node indexer.

Parameters:

structuralModelIndexer The node indexer to which the new structural models will be added.

function forEachNodeDepthFirst [1/2]#

Performs the action on this path node.

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

Executes an action for this path node in a depth‑first traversal.

Parameters:

action Function pointer that takes a pointer to a SBDDataGraphNode and performs an operation.

Implements SBDDataGraphNode::forEachNodeDepthFirst

function forEachNodeDepthFirst [2/2]#

Performs the object 'saction on this path node.

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

Executes a member function for this path node in a depth‑first traversal.

Parameters:

object Pointer to the object whose member function will be invoked.
action Pointer to the member function of object that takes a SBDDataGraphNode* argument.

Implements SBDDataGraphNode::forEachNodeDepthFirst

function getAnimationFlag#

Returns the animation flag.

virtual bool SBMStructuralModelPath::getAnimationFlag () const

Returns the animation flag indicating whether animation is active.

Returns:

true if animation is active, false otherwise.

function getAnimationType#

Returns the animation type.

virtual AnimationType SBMStructuralModelPath::getAnimationType () const

Returns:

The current animation type.

function getAtomIndexer#

Returns the atoms for which a position is saved.

virtual SBPointerIndexer< SBAtom > const * SBMStructuralModelPath::getAtomIndexer () const

Returns a constant pointer to the atom indexer associated with the path.

Returns:

Pointer to a constant SBPointerIndexer<SBAtom>.

function getCurrentEnergy#

Returns the current energy.

virtual SBQuantity::energy SBMStructuralModelPath::getCurrentEnergy () const

Returns the current energy of the path.

Returns:

The current energy value, possibly smoothed over a window.

function getCurrentStep#

Returns the current step along the path.

virtual unsigned int SBMStructuralModelPath::getCurrentStep () const

Returns the current step of the path animation.

Returns:

The current step index.

function getCurrentTime#

Returns the current time.

virtual SBQuantity::time SBMStructuralModelPath::getCurrentTime () const

Returns the current time of the path.

This function returns the time associated with the current step of the path. If smoothing is enabled, the returned value is the average over the smoothing window.

Returns:

The current time value (zero if no time data is available or the current step is invalid).

function getEnergy#

Retrieves the energy for a specific step .

virtual bool SBMStructuralModelPath::getEnergy (
    unsigned int step,
    SBQuantity::energy & energy
) const

Retrieves the energy value for a specific step of the path.

Retrieves the energy value for the specified step, applying smoothing if the smoothing window is set.

Parameters:

step Index of the step from which to retrieve the energy.
energy Output parameter that receives the energy value.

Returns:

true if the energy was successfully retrieved; false if the energy data is unavailable or the step index is out of range.

function getEnergyData#

Returns the energy data.

virtual SBVector< SBQuantity::energy > * SBMStructuralModelPath::getEnergyData () const

Retrieves the container of energy data for the path.

Returns:

Pointer to the vector of energy values for each step, or nullptr if not set.

function getForce [1/2]#

Retrieves the force of atom atomIndex and stores it inforce for a specificstep .

virtual bool SBMStructuralModelPath::getForce (
    unsigned int step,
    unsigned int atomIndex,
    SBForce3 & force
) const

Retrieves the force of a specific atom at a given step.

Parameters:

step Index of the step from which to retrieve the force.
atomIndex Index of the atom within the atom indexer.
atomForce Output parameter that receives the force of the specified atom.

Returns:

true if the force was successfully retrieved; false if the force data is unavailable, the step index is out of range, or the atom index is invalid.

function getForce [2/2]#

Retrieves the force of atom atom and stores it inforce for a specificstep .

virtual bool SBMStructuralModelPath::getForce (
    unsigned int step,
    SBAtom * atom,
    SBForce3 & force
) const

Retrieves the force of a specific atom at a given step.

Parameters:

step Index of the step from which to retrieve the force.
atom Pointer to the atom for which to retrieve the force.
atomForce Output parameter that receives the force of the specified atom.

Returns:

true if the force was successfully retrieved; false if the force data is unavailable, the step index is out of range, or the atom is not found in the indexer.

function getForceData#

Returns the force data.

virtual SBVector< SBVector< SBForce3 > * > * SBMStructuralModelPath::getForceData () const

Retrieves a pointer to the vector containing per‑step force vectors for each atom.

Returns:

Pointer to the force data vector, or nullptr if no force data is set.

function getForwardFlag#

Returns the forward flag, which indicates when the animation is moving forward.

virtual bool SBMStructuralModelPath::getForwardFlag () const

Returns the forward flag indicating the direction of animation.

Returns:

true if animation is moving forward, false if moving backward.

function getMass [1/2]#

Retrieves the mass of atom atomIndex .

virtual bool SBMStructuralModelPath::getMass (
    unsigned int atomIndex,
    SBQuantity::mass & mass
) const

Retrieves the mass of a specific atom by index.

Parameters:

atomIndex Index of the atom.
mass Output parameter that receives the mass.

Returns:

true if the mass was successfully retrieved; otherwise false.

function getMass [2/2]#

Retrieves the mass of atom atom .

virtual bool SBMStructuralModelPath::getMass (
    SBAtom * atom,
    SBQuantity::mass & mass
) const

Retrieves the mass of a specific atom.

Parameters:

atom Pointer to the atom.
mass Output parameter that receives the mass.

Returns:

true if the mass was successfully retrieved; otherwise false.

function getMassData#

Returns the mass data.

virtual SBVector< SBQuantity::mass > * SBMStructuralModelPath::getMassData () const

Retrieves the mass data.

Returns:

Pointer to the vector of masses for each atom, or nullptr if not set.

function getNextPath#

Returns the next path in the document.

SBMStructuralModelPath * SBMStructuralModelPath::getNextPath () const

Retrieves the next path node in the document, if any.

Returns:

Pointer to the next SBMStructuralModelPath, or nullptr if none exists.

function getNodes [1/2]#

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

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

Collects nodes of a given type into an indexer.

The function adds nodes of type nodeType to nodeIndexer. If selectedNodesOnly is true, only selected nodes are considered. The optional visitPredicate determines whether a node should be visited, and includeDependencies controls whether dependent nodes (e.g., atoms) are also collected.

Parameters:

nodeIndexer The indexer that will receive the collected nodes.
nodeType The type of nodes to collect.
selectedNodesOnly If true, only selected nodes are added; otherwise all nodes of the specified type are added.
visitPredicate Predicate that determines whether a node should be visited.
includeDependencies If true, dependent nodes (e.g., atoms) are also collected.

Implements SBDDataGraphNode::getNodes

function getNodes [2/2]#

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

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

Collects nodes that satisfy a selection predicate into an indexer.

The function adds nodes for which selectionPredicate evaluates to true to nodeIndexer. The optional visitPredicate determines whether a node should be visited, and includeDependencies controls whether dependent nodes are also collected.

Parameters:

nodeIndexer The indexer that will receive the collected nodes.
selectionPredicate Predicate used to select nodes.
visitPredicate Predicate that determines whether a node should be visited.
includeDependencies If true, dependent nodes are also collected.

Implements SBDDataGraphNode::getNodes

function getNumberOfAtoms#

Returns the number of atoms for which a position is saved.

virtual unsigned int SBMStructuralModelPath::getNumberOfAtoms () const

Returns the number of atoms.

Returns:

Number of atoms.

function getNumberOfSteps#

Returns the number of steps in the path.

virtual unsigned int SBMStructuralModelPath::getNumberOfSteps () const

The number of steps corresponds to the number of position frames stored in the path.

Returns:

The number of steps.

function getPosition [1/2]#

Retrieves the position of atom atomIndex and stores it inposition for a specificstep .

virtual bool SBMStructuralModelPath::getPosition (
    unsigned int step,
    unsigned int atomIndex,
    SBPosition3 & position
) const

Retrieves the position of an atom at a given step.

If smoothing is enabled, the position is averaged over a window of steps.

Parameters:

step Index of the step.
atomIndex Index of the atom.
atomPosition Reference to a SBPosition3 that receives the atom position.

Returns:

true if the position was successfully retrieved, false otherwise.

function getPosition [2/2]#

Retrieves the position of atom atom and stores it inposition for a specificstep .

virtual bool SBMStructuralModelPath::getPosition (
    unsigned int step,
    SBAtom * atom,
    SBPosition3 & position
) const

Retrieves the position of a specific atom at a given step.

If smoothing is enabled, the position is averaged over a window of steps.

Parameters:

step Index of the step.
atom Pointer to the atom.
atomPosition Reference to a SBPosition3 that receives the atom position.

Returns:

true if the position was successfully retrieved, false otherwise.

function getPositionData#

Returns the position data.

virtual SBVector< SBVector< SBPosition3 > * > * SBMStructuralModelPath::getPositionData () const

Retrieves the container of position data for the path.

Returns:

Pointer to the vector of position vectors for each step, or nullptr if not set.

function getPreviousPath#

Returns the previous path in the document.

SBMStructuralModelPath * SBMStructuralModelPath::getPreviousPath () const

Retrieves the previous path node in the document, if any.

Returns:

Pointer to the previous SBMStructuralModelPath, or nullptr if none exists.

function getSmoothingWindowSize#

Returns the size of the smoothing window.

virtual unsigned int SBMStructuralModelPath::getSmoothingWindowSize () const

Returns the size of the smoothing window used for position smoothing.

Returns:

The smoothing window size.

function getSourceFileName#

Returns the name of the file associated to the path.

const std::string & SBMStructuralModelPath::getSourceFileName () const

Retrieves the source file name associated with the path.

Returns:

The source file name if set; otherwise a default empty string.

function getStepDuration#

Returns the step duration.

virtual SBQuantity::second const & SBMStructuralModelPath::getStepDuration () const

Returns:

The step duration as a time quantity.

function getStride#

Returns the animation stride.

virtual unsigned int SBMStructuralModelPath::getStride () const

Returns:

The stride value.

function getTime#

Retrieves the time for a specific step .

virtual bool SBMStructuralModelPath::getTime (
    unsigned int step,
    SBQuantity::time & time
) const

Retrieves the time value for a specific step of the path.

Retrieves the time value for the specified step, applying smoothing if the smoothing window is set.

Parameters:

step Index of the step from which to retrieve the time.
time Output parameter that receives the time value.

Returns:

true if the time was successfully retrieved; false if the time data is unavailable or the step index is out of range.

function getTimeData#

Returns the time data.

virtual SBVector< SBQuantity::time > * SBMStructuralModelPath::getTimeData () const

Retrieves a pointer to the vector containing time values for each step.

Returns:

Pointer to the time data vector, or nullptr if no time data is set.

function getType#

Returns the data graph node type.

virtual SBNode::Type SBMStructuralModelPath::getType () override const

Returns the node type of this object.

Returns:

The node type SBNode::Path.

Implements SBDDataGraphNode::getType

function getUnitCell#

Retrieves the unit cell for a specific step .

virtual bool SBMStructuralModelPath::getUnitCell (
    unsigned int step,
    SBUnitCell & unitCell
) const

Retrieves the unit cell for a specific step.

Parameters:

step Index of the step.
unitCell Output parameter that receives the unit cell.

Returns:

true if the unit cell was successfully retrieved; otherwise false.

function getUnitCellData#

Returns the unit-cell data.

virtual SBVector< SBUnitCell > * SBMStructuralModelPath::getUnitCellData () const

Retrieves the unit-cell data.

Returns:

Pointer to the vector of unit cells for each step, or nullptr if not set.

function getUnwrappedPosition [1/2]#

Retrieves the unwrapped position of atom atomIndex for a specificstep .

virtual bool SBMStructuralModelPath::getUnwrappedPosition (
    unsigned int step,
    unsigned int atomIndex,
    SBPosition3 & position
) const

Parameters:

step The step index.
atomIndex The atom index.
position The output position.

Returns:

true if the position was successfully retrieved; otherwise false.

function getUnwrappedPosition [2/2]#

Retrieves the unwrapped position of atom atom for a specificstep .

virtual bool SBMStructuralModelPath::getUnwrappedPosition (
    unsigned int step,
    SBAtom * atom,
    SBPosition3 & position
) const

Parameters:

step The step index.
atom The atom pointer.
position The output position.

Returns:

true if the position was successfully retrieved; otherwise false.

function getVelocity [1/2]#

Retrieves the velocity of atom atomIndex and stores it invelocity for a specificstep .

virtual bool SBMStructuralModelPath::getVelocity (
    unsigned int step,
    unsigned int atomIndex,
    SBVelocity3 & velocity
) const

Retrieves the velocity of a specific atom at a given step.

Retrieves the velocity of the specified atom at the given step, applying smoothing if configured.

Parameters:

step Index of the step from which to retrieve the velocity.
atomIndex Index of the atom within the atom indexer.
atomVelocity Output parameter that receives the velocity of the specified atom.

Returns:

true if the velocity was successfully retrieved; false if the velocity data is unavailable, the step index is out of range, or the atom index is invalid.

function getVelocity [2/2]#

Retrieves the velocity of atom atom and stores it invelocity for a specificstep .

virtual bool SBMStructuralModelPath::getVelocity (
    unsigned int step,
    SBAtom * atom,
    SBVelocity3 & velocity
) const

Retrieves the velocity of a specific atom at a given step.

Retrieves the velocity of the given atom at the specified step, applying smoothing if configured.

Parameters:

step Index of the step from which to retrieve the velocity.
atom Pointer to the atom for which to retrieve the velocity.
atomVelocity Output parameter that receives the velocity of the specified atom.

Returns:

true if the velocity was successfully retrieved; false if the velocity data is unavailable, the step index is out of range, or the atom is not found in the indexer.

function getVelocityData#

Returns the velocity data.

virtual SBVector< SBVector< SBVelocity3 > * > * SBMStructuralModelPath::getVelocityData () const

Retrieves a pointer to the vector containing per‑step velocity vectors for each atom.

Returns:

Pointer to the velocity data vector, or nullptr if no velocity data is set.

function hasNode [1/2]#

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

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

Checks whether the path contains a node of a given type.

The function returns true if a node of type nodeType is found. If selectedNodesOnly is true, only selected nodes are considered. The optional visitPredicate determines whether a node should be visited, and includeDependencies controls whether dependent nodes are also examined.

Parameters:

nodeType The type of node to search for.
selectedNodesOnly If true, only selected nodes are considered.
visitPredicate Predicate that determines whether a node should be visited.
includeDependencies If true, dependent nodes are also examined.

Returns:

true if a matching node exists; otherwise false.

Implements SBDDataGraphNode::hasNode

function hasNode [2/2]#

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

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

Checks whether the path contains any node satisfying a selection predicate.

The function returns true if a node for which selectionPredicate evaluates to true is found. The optional visitPredicate determines whether a node should be visited, and includeDependencies controls whether dependent nodes are also examined.

Parameters:

selectionPredicate Predicate used to select nodes.
visitPredicate Predicate that determines whether a node should be visited.
includeDependencies If true, dependent nodes are also examined.

Returns:

true if a matching node exists; otherwise false.

Implements SBDDataGraphNode::hasNode

function hasSourceFileName#

Returns true when the path has the source file name set.

bool SBMStructuralModelPath::hasSourceFileName () const

Checks whether the path has a source file name set.

Returns:

true if a source file name is associated with the path; otherwise false.

function insert [1/4]#

Inserts a frame in the path at position step .

virtual bool SBMStructuralModelPath::insert (
    unsigned int step,
    SBConformation * conformation
)

Inserts a step to the path at the specified position by copying information from a conformation.

The conformation must contain all information that the path stores (positions, velocities, forces, etc.). Additionally, all atoms indexed by the path must also be indexed by the conformation (the conformation may contain additional atoms). The required data is copied into the path, after which the conformation can be safely deleted.

Parameters:

step Position at which to insert the new step.
conformation The conformation from which to copy the data.

Returns:

true if the insertion succeeded, false otherwise.

function insert [2/4]#

Inserts frames in the path at position step .

virtual bool SBMStructuralModelPath::insert (
    unsigned int step,
    SBMStructuralModelPath * path
)

Inserts a deep copy of the provided path at the given step.

This function inserts a deep copy of the provided path at a given step. All necessary information has to be provided. For example, if this path has velocity data, then the provided path must contain velocity data as well. Note that the provided path may have more information than necessary, and may index more atoms than necessary. In that case, only the necessary information is copied. Since all passed information is copied, the provided path may be deleted after the function returns.

Parameters:

step The index at which to insert the copied data from path.
path Pointer to the source path to be copied.

Returns:

true if the insertion succeeded, false otherwise.

function insert [3/4]#

Inserts a frame in the path at position step .

virtual bool SBMStructuralModelPath::insert (
    unsigned int step,
    SBVector< SBPosition3 > * positionData,
    const SBQuantity::energy & energy=SBQuantity::energy::zero,
    const SBQuantity::time & time=SBQuantity::time::zero,
    SBVector< SBVelocity3 > * velocityData=nullptr,
    SBVector< SBForce3 > * forceData=nullptr
)

Inserts a step into the path at the specified position.

This function inserts a step to the path at position step. All necessary information has to be provided. For example, if the path has velocity data, then velocity data must be provided. Furthermore, the size of the provided vectors must be equal to the number of atoms indexed in the path. The passed information is copied, and may thus be deleted after the function returns.

Parameters:

step The index at which to insert the new step.
positionData Pointer to the vector of positions for each atom for the new step. Must be non-null if the path stores positions.
energy The energy value for the new step.
time The time value for the new step.
velocityData Pointer to the vector of velocities for each atom for the new step. Must be non-null if the path stores velocities.
forceData Pointer to the vector of forces for each atom for the new step. Must be non-null if the path stores forces.

Returns:

true if the insertion succeeded, false otherwise.

function insert [4/4]#

Inserts frames in the path at position step .

virtual bool SBMStructuralModelPath::insert (
    unsigned int step,
    SBVector< SBVector< SBPosition3 > * > * positionData,
    SBVector< SBQuantity::energy > * energyData=nullptr,
    SBVector< SBQuantity::time > * timeData=nullptr,
    SBVector< SBVector< SBVelocity3 > * > * velocityData=nullptr,
    SBVector< SBVector< SBForce3 > * > * forceData=nullptr
)

Inserts multiple steps into the path at the specified position.

This function inserts steps to the path at position step. All necessary information has to be provided. For example, if the path has velocity data, then velocity data must be provided. Furthermore, the size of the provided vectors must be equal to the number of atoms indexed in the path. The passed information is copied, and may thus be deleted after the function returns.

Parameters:

step The index at which to start inserting the new steps.
positionData Pointer to a vector of position vectors for each new step. Must be non-null if the path stores positions.
energyData Pointer to a vector of energy values for each new step. Must be non-null if the path stores energies.
timeData Pointer to a vector of time values for each new step. Must be non-null if the path stores times.
velocityData Pointer to a vector of velocity vectors for each new step. Must be non-null if the path stores velocities.
forceData Pointer to a vector of force vectors for each new step. Must be non-null if the path stores forces.

Returns:

true if the insertion succeeded, false otherwise.

function insertAtom#

Inserts an atom at indexatomIndex to the path.

bool SBMStructuralModelPath::insertAtom (
    unsigned int atomIndex,
    SBAtom * atom,
    SBVector< SBPosition3 > * atomPositionVector=nullptr,
    SBVector< SBVelocity3 > * atomVelocityVector=nullptr,
    SBVector< SBForce3 > * atomForceVector=nullptr
)

Inserts an atom into the path at a specified index.

It expects position, velocity and force data to fill the path data. For example, if the path contains one hundred steps (frames) in the position data, then the size of the position vector atomPositionVector should be one hundred, since each frame will need to have one new position inserted, corresponding to the inserted atom. The atom is inserted at position atomIndex in the path indexer.

Parameters:

atomIndex Index at which the atom will be inserted.
atom Pointer to the atom to insert.
atomPositionVector Optional vector of positions for the atom across steps.
atomVelocityVector Optional vector of velocities for the atom across steps.
atomForceVector Optional vector of forces for the atom across steps.

Returns:

true when insertion is successful; otherwise false.

function isSerializable#

Returns true __

virtual bool SBMStructuralModelPath::isSerializable () override const

Indicates whether the path can be serialized.

This method always returns true for SBMStructuralModelPath.

Returns:

True, indicating that the path supports serialization.

Implements SBDDataGraphNode::isSerializable

function makeWholeAllSteps#

Reconstructs bond-connected components across periodic boundaries for all steps.

virtual bool SBMStructuralModelPath::makeWholeAllSteps ()

Returns:

true if the operation completed; otherwise false.

function makeWholeStep#

Reconstructs bond-connected components across periodic boundaries for a specific step .

virtual bool SBMStructuralModelPath::makeWholeStep (
    unsigned int step
)

Parameters:

step The step index.

Returns:

true if the operation completed; otherwise false.

function print#

Prints the path.

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

Prints a human‑readable representation of the path to standard output.

The function prints the number of atoms, source file name, and optionally the position, energy, time, velocity, and force data for each step. Each line is prefixed with a number of tab characters specified by offset.

Parameters:

offset Number of tab characters used for indentation of each printed line.

Implements SBDDataGraphNode::print

function remove [1/2]#

Remove a frame from the path to create a conformation.

virtual SBConformation * SBMStructuralModelPath::remove (
    unsigned int step
)

Removes a single step from the path and returns it as a new conformation.

Extracts the position, energy, time, velocity, and force data for the specified step, creates a new SBConformation object containing this data, removes the step from the path, and returns the created conformation. If the step index is out of range or required data is missing, returns nullptr.

Parameters:

step Index of the step to remove (zero‑based).

Returns:

Pointer to the newly created SBConformation, or nullptr if removal fails.

function remove [2/2]#

Removes frames from the path to create a new path.

virtual SBMStructuralModelPath * SBMStructuralModelPath::remove (
    unsigned int firstStep,
    unsigned int lastStep
)

Removes a range of steps from the path and returns them as a new path.

Creates a deep copy of all the frames between (and including) steps firstStep and lastStep, deletes the corresponding frames in this path, and returns a new SBMStructuralModelPath containing the copied frames. Returns nullptr if the parameters are invalid or required data is missing.

Parameters:

firstStep Index of the first step to remove (inclusive).
lastStep Index of the last step to remove (inclusive).

Returns:

Pointer to a new SBMStructuralModelPath containing the removed steps, *nullptr on failure.

function removeAtom#

Removes an atom from the path.

bool SBMStructuralModelPath::removeAtom (
    SBAtom * atom
)

Removes the specified atom from the path and deletes its associated position, velocity, and force data for each step.

Parameters:

atom Pointer to the atom to be removed.

Returns:

true if the atom was successfully removed, false otherwise.

function serialize#

Serializes the path.

virtual void SBMStructuralModelPath::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 path to a serializer.

Writes the path's data, including name, source file name, atom list, and any associated position, energy, time, velocity, and force data, as well as animation parameters, to the provided serializer.

Parameters:

serializer The serializer used to write the path data.
nodeIndexer The node indexer used to resolve atom references.
sdkVersionNumber The version of the SDK for compatibility checks; defaults to the current SDK version.
classVersionNumber The version of the class for compatibility; defaults to version 1.0.0.

Implements SBDDataGraphNode::serialize

function setAnimationFlag#

Sets the animation flag.

virtual void SBMStructuralModelPath::setAnimationFlag (
    bool animationFlag
)

Sets the animation flag indicating whether animation is active.

Parameters:

animationFlag True to enable animation, false to disable.

function setAnimationType#

Sets the animation type.

virtual void SBMStructuralModelPath::setAnimationType (
    AnimationType animationType
)

Parameters:

animationType The animation type to set.

function setCurrentStep#

Sets the current step along the path.

virtual void SBMStructuralModelPath::setCurrentStep (
    unsigned int currentStep
)

Sets the current step of the path animation.

Parameters:

currentStep The step index to set as current.

function setEnergy#

Sets the energy for a specific step .

virtual bool SBMStructuralModelPath::setEnergy (
    unsigned int step,
    const SBQuantity::energy & energy
)

Sets the energy value for a specific step of the path.

Parameters:

step Index of the step for which to set the energy.
energy Energy value to assign to the specified step.

Returns:

true if the energy was successfully set; false if the energy data is unavailable or the step index is out of range.

function setEnergyData#

Sets the energy data.

virtual void SBMStructuralModelPath::setEnergyData (
    SBVector< SBQuantity::energy > * energyData
)

Sets the container of energy data for the path.

Parameters:

energyData Pointer to the new energy data container.

function setForce [1/2]#

Sets the force of atom atomIndex toforce for a specificstep .

virtual bool SBMStructuralModelPath::setForce (
    unsigned int step,
    unsigned int atomIndex,
    const SBForce3 & force
)

Sets the force of a specific atom at a given step.

Parameters:

step Index of the step for which to set the force.
atomIndex Index of the atom within the atom indexer.
atomForce Force value to assign to the specified atom at the given step.

Returns:

true if the force was successfully set; false if the force data is unavailable, the step index is out of range, or the atom index is invalid.

function setForce [2/2]#

Sets the force of atom atom toforce for a specificstep .

virtual bool SBMStructuralModelPath::setForce (
    unsigned int step,
    SBAtom * atom,
    const SBForce3 & force
)

Sets the force of a specific atom at a given step.

Parameters:

step Index of the step for which to set the force.
atom Pointer to the atom for which to set the force.
atomForce Force value to assign to the specified atom at the given step.

Returns:

true if the force was successfully set; false if the force data is unavailable, the step index is out of range, or the atom is not found in the indexer.

function setForceData#

Sets the force data.

virtual void SBMStructuralModelPath::setForceData (
    SBVector< SBVector< SBForce3 > * > * forceData
)

Sets the force data vector for the path.

Parameters:

forceData Pointer to a vector of per‑step force vectors to associate with the path.

function setForwardFlag#

Sets the forward flag, which indicates when the animation is moving forward.

virtual void SBMStructuralModelPath::setForwardFlag (
    bool forwardFlag
)

Sets the forward flag indicating the direction of animation.

Parameters:

forwardFlag True to set animation moving forward, false for backward.

function setMass [1/2]#

Sets the mass of atom atomIndex .

virtual bool SBMStructuralModelPath::setMass (
    unsigned int atomIndex,
    const SBQuantity::mass & mass
)

Sets the mass of a specific atom by index.

Parameters:

atomIndex Index of the atom.
mass Mass to assign.

Returns:

true if the mass was successfully updated; otherwise false.

function setMass [2/2]#

Sets the mass of atom atom .

virtual bool SBMStructuralModelPath::setMass (
    SBAtom * atom,
    const SBQuantity::mass & mass
)

Sets the mass of a specific atom.

Parameters:

atom Pointer to the atom.
mass Mass to assign.

Returns:

true if the mass was successfully updated; otherwise false.

function setMassData#

Sets the mass data.

virtual void SBMStructuralModelPath::setMassData (
    SBVector< SBQuantity::mass > * massData
)

Parameters:

massData Pointer to the mass data.

function setPosition [1/2]#

Sets the position of atom atomIndex toposition for a specificstep .

virtual bool SBMStructuralModelPath::setPosition (
    unsigned int step,
    unsigned int atomIndex,
    const SBPosition3 & position
)

Sets the position of an atom at a specific step.

Parameters:

step Index of the step.
atomIndex Index of the atom.
atomPosition The new position to set for the atom.

Returns:

true if the position was successfully set, false otherwise.

function setPosition [2/2]#

Sets the position of atom atom toposition for a specificstep .

virtual bool SBMStructuralModelPath::setPosition (
    unsigned int step,
    SBAtom * atom,
    const SBPosition3 & position
)

Sets the position of a specific atom at a specific step.

Parameters:

step Index of the step.
atom Pointer to the atom.
atomPosition The new position to set for the atom.

Returns:

true if the position was successfully set, false otherwise.

function setPositionData#

Sets the position data.

virtual void SBMStructuralModelPath::setPositionData (
    SBVector< SBVector< SBPosition3 > * > * positionData
)

Sets the container of position data for the path.

Parameters:

positionData Pointer to the new position data container.

function setSmoothingWindowSize#

Sets the size of the smoothing window.

virtual void SBMStructuralModelPath::setSmoothingWindowSize (
    unsigned int smoothingWindowSize
)

Sets the size of the smoothing window used for position smoothing.

Parameters:

smoothingWindowSize The new smoothing window size.

function setSourceFileName#

Sets the name of the file associated to the path.

void SBMStructuralModelPath::setSourceFileName (
    const std::string & fileName
)

Sets the source file name for the path.

Parameters:

fileName The new source file name to associate with the path.

function setStepDuration#

Sets the step duration.

virtual void SBMStructuralModelPath::setStepDuration (
    const SBQuantity::second & stepDuration
)

Parameters:

stepDuration The step duration to set.

function setStride#

Sets the animation stride.

virtual void SBMStructuralModelPath::setStride (
    unsigned int stride
)

Parameters:

stride The stride value to set.

function setTime#

Sets the time for a specific step .

virtual bool SBMStructuralModelPath::setTime (
    unsigned int step,
    const SBQuantity::time & time
)

Sets the time value for a specific step of the path.

Parameters:

step Index of the step for which to set the time.
time Time value to assign to the specified step.

Returns:

true if the time was successfully set; false if the time data is unavailable or the step index is out of range.

function setTimeData#

Sets the time data.

virtual void SBMStructuralModelPath::setTimeData (
    SBVector< SBQuantity::time > * timeData
)

Sets the time data vector for the path.

Parameters:

timeData Pointer to a vector of time values to associate with the path.

function setUnitCell#

Sets the unit cell for a specific step .

virtual bool SBMStructuralModelPath::setUnitCell (
    unsigned int step,
    const SBUnitCell & unitCell
)

Sets the unit cell for a specific step.

Parameters:

step Index of the step.
unitCell The unit cell to assign.

Returns:

true if the unit cell was successfully updated; otherwise false.

function setUnitCellData#

Sets the unit-cell data.

virtual void SBMStructuralModelPath::setUnitCellData (
    SBVector< SBUnitCell > * unitCellData
)

Parameters:

unitCellData Pointer to the unit-cell data.

function setVelocity [1/2]#

Sets the velocity of atom atomIndex tovelocity for a specificstep .

virtual bool SBMStructuralModelPath::setVelocity (
    unsigned int step,
    unsigned int atomIndex,
    const SBVelocity3 & velocity
)

Sets the velocity of a specific atom at a given step.

Parameters:

step Index of the step for which to set the velocity.
atomIndex Index of the atom within the atom indexer.
atomVelocity Velocity value to assign to the specified atom at the given step.

Returns:

true if the velocity was successfully set; false if the velocity data is unavailable, the step index is out of range, or the atom index is invalid.

function setVelocity [2/2]#

Sets the velocity of atom atom tovelocity for a specificstep .

virtual bool SBMStructuralModelPath::setVelocity (
    unsigned int step,
    SBAtom * atom,
    const SBVelocity3 & velocity
)

Sets the velocity of a specific atom at a given step.

Parameters:

step Index of the step for which to set the velocity.
atom Pointer to the atom for which to set the velocity.
atomVelocity Velocity value to assign to the specified atom at the given step.

Returns:

true if the velocity was successfully set; false if the velocity data is unavailable, the step index is out of range, or the atom is not found in the indexer.

function setVelocityData#

Sets the velocity data.

virtual void SBMStructuralModelPath::setVelocityData (
    SBVector< SBVector< SBVelocity3 > * > * velocityData
)

Sets the velocity data vector for the path.

Parameters:

velocityData Pointer to a vector of per‑step velocity vectors to associate with the path.

function unserialize#

Unserializes the path.

virtual void SBMStructuralModelPath::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 path from a serializer.

Restores the path's data, including its name, source file name, atom list, and associated position, energy, time, velocity, and force arrays. The function supports both legacy and current serialization formats based on the SDK and class version numbers.

Parameters:

serializer Pointer to the serializer from which data is read.
nodeIndexer Indexer that maps node indices to node pointers, used to resolve atom references.
sdkVersionNumber Version of the SDK that wrote the data, influencing how the data is interpreted.
classVersionNumber Version of the class serialization format.

Implements SBDDataGraphNode::unserialize

function unwrap#

Unwraps the trajectory over time using successive minimum-image displacements.

virtual bool SBMStructuralModelPath::unwrap ()

Returns:

true if the operation completed; otherwise false.

function updateState#

Updates the state along the path according to the animation parameters.

virtual void SBMStructuralModelPath::updateState ()

Updates the current state of the path based on the animation parameters.

This function advances the current step according to the stride and animation type, and updates atom positions accordingly.

function wrapAllSteps#

Wraps the positions of all steps into their primary unit cells.

virtual bool SBMStructuralModelPath::wrapAllSteps (
    bool keepConnectedComponentsWhole=true
)

Parameters:

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

Returns:

true if the operation completed; otherwise false.

function wrapStep#

Wraps the positions of a specific step into the primary unit cell.

virtual bool SBMStructuralModelPath::wrapStep (
    unsigned int step,
    bool keepConnectedComponentsWhole=true
)

Parameters:

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

Returns:

true if the operation completed; otherwise false.

function ~SBMStructuralModelPath#

Destructs the path.

virtual SBMStructuralModelPath::~SBMStructuralModelPath ()

Destroys the structural path.

Performs necessary cleanup before the SBMStructuralModelPath object is destroyed.