Class SBMDynamicalModelParticleSystem

ClassList > SBMDynamicalModelParticleSystem

This class describes a dynamical particle system. More...

• #include <SBMDynamicalModelParticleSystem.hpp>

Inherits the following classes: SBMDynamicalModel

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
	SBMDynamicalModelParticleSystem () Builds an empty particle system.
	SBMDynamicalModelParticleSystem (const SBNodeIndexer & nodeIndexer) Builds a particle system associated to a set of nodes.
unsigned int	addAtom (SBAtom * atom) Adds an atom to the particle system.
void	addAtoms (const SBNodeIndexer & nodeIndexer) Adds atoms of a node indexer.
void	correctDistanceWithPBC (SBLength3 & distance) Adjusts a distance vector to account for periodic boundary conditions.
virtual bool	enforcePeriodicBoundaryConditions () override Enforces the periodic boundary conditions.
virtual void	flushMomentumBuffer () Flushes the momentum buffer.
virtual void	flushPositionBuffer () override Flushes the position buffer.
bool	getActivityFlag (SBAtom * atom) const Returns the activity flag of an atom.
bool	getActivityFlag (unsigned int atomIndex) const Returns the activity flag of an atom.
SBPointerIndexer< SBAtom > const *	getAtomIndexer () const Returns the atoms associated to the particle system.
virtual unsigned int	getChangedMomentumIndex (unsigned int i) const Returns the index of an changed momentum.
virtual unsigned int	getChangedPositionIndex (unsigned int i) override const Returns the index of an changed position.
virtual SBDDataGraphNode::Type	getDynamicalModelType () override const Returns the dynamical model type (returns SBDDataGraphNode::DynamicalModelParticleSystem )
SBQuantity::inverseMass	getInverseMass (SBAtom * atom) const Returns the inverse mass of an atom.
SBQuantity::inverseMass	getInverseMass (unsigned int atomIndex) const Returns the inverse mass of an atom.
SBQuantity::mass	getMass (SBAtom * atom) const Returns the mass of an atom.
SBQuantity::mass	getMass (unsigned int atomIndex) const Returns the mass of an atom.
virtual SBMomentum3 const &	getMomentum (unsigned int i) const Returns the momentum of an atom.
virtual unsigned int	getNumberOfChangedMomentums () const Returns the number of changed momentums.
virtual unsigned int	getNumberOfChangedPositions () override const Returns the number of changed positions.
virtual SBPosition3 const &	getPosition (unsigned int i) const Returns the position of an atom.
virtual bool	getPositionChanged (unsigned int i) override const Returns whether position i has been changed since the last flush.
virtual SBDDataGraphNode::Type	getType () override const Returns the type of the data graph node (returns SBDDataGraphNode::DynamicalModelParticleSystem )
virtual void	print (unsigned int offset=0) override const Prints debugging information.
void	removeAtom (SBAtom * atom) Removes an atom from the particle system.
void	removeAtom (unsigned int atomIndex) Removes an atom from the particle system.
void	removeAtoms (const SBNodeIndexer & nodeIndexer) Removes atoms of a node indexer.
int	roundForPBC (const SBQuantity::length & d) Computes the integer rounding of a length value for periodic boundary correction.
void	setActivityFlag (SBAtom * atom, bool flag) Sets the activity flag of an atom.
void	setActivityFlag (unsigned int atomIndex, bool flag) Sets the activity flag of an atom.
void	setMass (SBAtom * atom, SBQuantity::mass mass) Sets the mass of an atom.
void	setMass (unsigned int atomIndex, SBQuantity::mass mass) Sets the mass of an atom.
virtual void	setMomentum (unsigned int i, const SBMomentum3 & newMomentum) Updates the momentum of an atom.
virtual void	setPosition (unsigned int i, const SBPosition3 & newPosition) Updates the position of an atom.
virtual void	updateStructuralNodes () override Updates the structural nodes based on the state of the particle system.
virtual	~SBMDynamicalModelParticleSystem () Deletes the particle system.

Public Functions inherited from SBMDynamicalModel

See SBMDynamicalModel

Type	Name
virtual SBMDynamicalModel *	clone () override Returns a copy of the node and its descendants.
void	connectDynamicalSignalToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBDynamicalEvent *) functionPointer, SBCReferenceTarget * nextReferenceTarget=0, void(SBCReferenceTarget::*)(SBDynamicalEvent *) nextFunctionPointer=0) Connects the dynamical signal to a slot.
void	disconnectDynamicalSignalFromSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBDynamicalEvent *) functionPointer) Disconnects the dynamical signal from a slot.
bool	dynamicalSignalIsConnectedToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBDynamicalEvent *) functionPointer) const Returns true if and only if the dynamical signal is connected to a given slot.
virtual bool	enforcePeriodicBoundaryConditions () Enforces the periodic boundary conditions.
virtual void	flushPositionBuffer () Flushes the position buffer.
virtual void	forEachNodeDepthFirst (void(*)(SBDDataGraphNode *node) action) override Performs the action on each node in the root of the dynamical model, depth-first.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) override Performs the object 'saction on each node in the root of the dynamical model, depth-first.
virtual unsigned int	getChangedPositionIndex (unsigned int i) const Returns the index of a changed position.
virtual SBDDataGraphNode::Type	getDynamicalModelType () const Returns the dynamical model type.
SBMDynamicalModelNodeRoot *	getDynamicalRoot () const Returns the root of the dynamical model.
virtual SBDDataGraphNode::Type	getModelType () override const Returns the model type.
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 anodeType , a selection status and avisitPredicate , 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 aselectionPredicate and avisitPredicate , with or without dependencies.
virtual unsigned int	getNumberOfChangedPositions () const Returns the number of changed positions.
SBIAPosition3 const &	getPeriodicBoundaryConditions () const Returns the periodic boundary conditions.
bool	getPeriodicBoundaryConditionsFlag () const Returns the periodic boundary conditions flag.
virtual bool	getPositionChanged (unsigned int i) const Returns whether position i has been changed since the last flush.
virtual SBDDataGraphNode::Type	getType () override const Returns the node type ( SBNode::DynamicalModel )
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 avisitPredicate , 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 avisitPredicate , with or without dependencies.
virtual bool	isSerializable () override const Returns true when the class is serializable.
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.
void	setPeriodicBoundaryConditions (SBIAPosition3 const & box) Sets the periodic boundary conditions.
void	setPeriodicBoundaryConditionsFlag (bool flag) Sets the periodic boundary conditions flag.
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 void	updateStructuralNodes () Updates structural nodes based on the state of the dynamical model.

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 avisitPredicate , 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 avisitPredicate , with or without dependencies.
void	create () Creates the node.
bool	descendsFrom (const SBDDataGraphNode * node) const Returns true if and only if this node isnode , or descends from it.
bool	descendsFrom (const SBNodeIndexer & nodeIndexer) const Returns true if and only if this node is one of the nodes of thenodeIndexer , 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 thenodePointerIndexer , 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 'saction 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 anodeType , a selection status and avisitPredicate , 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 aselectionPredicate and avisitPredicate , 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 avisitPredicate , 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 avisitPredicate , with or without dependencies.
bool	hasOneOf (const SBNodeIndexer & nodeIndexer) const Returns true if and only if this node is one of the nodes of thenodeIndexer , 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 isnode , or descends from it, or belongs to a group stored innode .
bool	isIn (const SBNodeIndexer & nodeIndexer) const Returns true if and only if this node is one of the nodes of thenodeIndexer , or descends from one of them, or belongs to a group stored in one of the nodes of thenodeIndexer .
bool	isIn (SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer) const Returns true if and only if this node is one of the nodes of thenodePointerIndexer , or descends from one of them, or belongs to a group stored in of the nodes of thenodePointerIndexer .
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 thenodeIndexer .
bool	isOneOf (SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer) const Returns true if and only if this node is one of the nodes of thenodePointerIndexer .
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 totype .
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 indestinationNodeIndexer .
void	forEachNodeInSelection (SBNodeIndexer & nodeIndexer, void(*)(SBDDataGraphNode *node) action) Performs the action for each node innodeIndexer __
void	forEachNodeInSelection (SBNodeIndexer & nodeIndexer, SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) Performs the objects 'saction for each node innodeIndexer __
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 SBMDynamicalModel

See SBMDynamicalModel

Type	Name
	SBMDynamicalModel () Builds a dynamical model.
	SBMDynamicalModel (SBMDynamicalModelData * dataPointer) Builds a dynamical model.
virtual	~SBMDynamicalModel () Deletes the dynamical model.

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

The class SBMDynamicalModelParticleSystem describes a particle system in SAMSON, i.e.

a dynamical system composed of particles. A particle system has two buffers - a position buffer and a momentum buffer - which may be used to write adaptive simulation algorithms.

Short name: SBParticleSystem

See also: SBCContainerBuffer

Public Functions Documentation

function SBMDynamicalModelParticleSystem [1/2]

Builds an empty particle system.

SBMDynamicalModelParticleSystem::SBMDynamicalModelParticleSystem () 

Constructs an empty particle system.

The default constructor builds an empty particle system.

See also: addAtom

---

function SBMDynamicalModelParticleSystem [2/2]

Builds a particle system associated to a set of nodes.

SBMDynamicalModelParticleSystem::SBMDynamicalModelParticleSystem (
    const SBNodeIndexer & nodeIndexer
) 

Constructs a particle system associated to a set of nodes.

Builds a particle system using the given node indexer.

Parameters:

• nodeIndexer The node indexer specifying the nodes to associate with the particle system.

---

function addAtom

Adds an atom to the particle system.

unsigned int SBMDynamicalModelParticleSystem::addAtom (
    SBAtom * atom
) 

Adds the given atom to the particle system and returns its index.

Parameters:

• atom The atom to add.

Returns:

The index of the added atom, or 0 if the atom is null or the system is not initialized.

---

function addAtoms

Adds atoms of a node indexer.

void SBMDynamicalModelParticleSystem::addAtoms (
    const SBNodeIndexer & nodeIndexer
) 

Adds multiple atoms to the particle system.

Adds atoms from the given node indexer to the particle system.

Parameters:

• nodeIndexer The node indexer containing atoms to add.

---

function correctDistanceWithPBC

Adjusts a distance vector to account for periodic boundary conditions.

void SBMDynamicalModelParticleSystem::correctDistanceWithPBC (
    SBLength3 & distance
) 

Parameters:

• distance Distance vector to be corrected in-place.

---

function enforcePeriodicBoundaryConditions

Enforces the periodic boundary conditions.

virtual bool SBMDynamicalModelParticleSystem::enforcePeriodicBoundaryConditions () override

Enforces periodic boundary conditions on all particle positions.

The function adjusts positions that lie outside the periodic box and updates the structural buffers.

Returns:

true if any particle position was modified, false otherwise.

Implements SBMDynamicalModel::enforcePeriodicBoundaryConditions

---

function flushMomentumBuffer

Flushes the momentum buffer.

virtual void SBMDynamicalModelParticleSystem::flushMomentumBuffer () 

Flushes the momentum buffer, emitting signals before and after the operation.

---

function flushPositionBuffer

Flushes the position buffer.

virtual void SBMDynamicalModelParticleSystem::flushPositionBuffer () override

Flushes the position buffer, emitting events before and after the flush.

This updates any listeners about the pending position changes.

Implements SBMDynamicalModel::flushPositionBuffer

---

function getActivityFlag [1/2]

Returns the activity flag of an atom.

bool SBMDynamicalModelParticleSystem::getActivityFlag (
    SBAtom * atom
) const

Returns the activity flag of the specified atom.

Retrieves the activity flag for the given atom, if it exists.

Parameters:

• atom The atom whose activity flag is queried.

Returns:

The activity flag of the atom, or false if the atom is not found or the system is not initialized.

---

function getActivityFlag [2/2]

Returns the activity flag of an atom.

bool SBMDynamicalModelParticleSystem::getActivityFlag (
    unsigned int atomIndex
) const

Returns the activity flag of the atom at the given index.

Retrieves the activity flag for the atom at the specified index.

Parameters:

• index The index of the atom.

Returns:

The activity flag of the atom, or false if the index is out of range or the system is not initialized.

---

function getAtomIndexer

Returns the atoms associated to the particle system.

SBPointerIndexer< SBAtom > const * SBMDynamicalModelParticleSystem::getAtomIndexer () const

Returns a constant pointer to the atom indexer.

Returns:

Pointer to the atom indexer, or nullptr if unavailable.

---

function getChangedMomentumIndex

Returns the index of an changed momentum.

virtual unsigned int SBMDynamicalModelParticleSystem::getChangedMomentumIndex (
    unsigned int i
) const

Returns the index of the i-th changed momentum.

This may be used by adaptive simulation algorithms, ir order to know which momenta have been changed at a given time step.

Assume for example that particle 17, 32, and 529 have had their momentum changed since the last flush of the momentum buffer. Then the following code:

unsigned int nChangedMomenta=particleSystem->getNumberOfChangedMomentums();

for (unsigned int i=0;i<nChangedMomenta;i++) {

    // changedMomentumIndex is the index of the i-th changed momentum
    unsigned int changedMomentumIndex=particleSystem->getChangedMomentumIndex(i); 
    std::cout << changedMomentumIndex << std::endl;

}

outputs

17
32
529

Parameters:

• i The index of the changed momentum.

Returns:

Index of the i-th changed momentum.

See also: getMomentum, getChangedMomentumIndex, flushMomentumBuffer

---

function getChangedPositionIndex

Returns the index of an changed position.

virtual unsigned int SBMDynamicalModelParticleSystem::getChangedPositionIndex (
    unsigned int i
) override const

Returns the index of the i-th changed particle position.

Parameters:

• i Index in the list of changed positions (0-based).

Returns:

Index of the particle whose position changed.

Implements SBMDynamicalModel::getChangedPositionIndex

---

function getDynamicalModelType

Returns the dynamical model type (returns SBDDataGraphNode::DynamicalModelParticleSystem )

virtual SBDDataGraphNode::Type SBMDynamicalModelParticleSystem::getDynamicalModelType () override const

Returns the dynamical model type of the node.

Returns SBDDataGraphNode::DynamicalModelParticleSystem.

Returns:

The dynamical model type.

Implements SBMDynamicalModel::getDynamicalModelType

---

function getInverseMass [1/2]

Returns the inverse mass of an atom.

SBQuantity::inverseMass SBMDynamicalModelParticleSystem::getInverseMass (
    SBAtom * atom
) const

Returns the inverse mass of the specified atom.

Retrieves the inverse mass for the given atom, if it exists.

Parameters:

• atom The atom whose inverse mass is queried.

Returns:

The inverse mass of the atom, or zero if the atom is not found or the system is not initialized.

---

function getInverseMass [2/2]

Returns the inverse mass of an atom.

SBQuantity::inverseMass SBMDynamicalModelParticleSystem::getInverseMass (
    unsigned int atomIndex
) const

Returns the inverse mass of the atom at the given index.

Retrieves the inverse mass for the atom at the specified index.

Parameters:

• index The index of the atom.

Returns:

The inverse mass of the atom, or zero if the index is out of range or the system is not initialized.

---

function getMass [1/2]

Returns the mass of an atom.

SBQuantity::mass SBMDynamicalModelParticleSystem::getMass (
    SBAtom * atom
) const

Returns the mass of the specified atom.

Retrieves the mass for the given atom, if it exists.

Parameters:

• atom The atom whose mass is queried.

Returns:

The mass of the atom, or zero mass if the atom is not found or the system is not initialized.

---

function getMass [2/2]

Returns the mass of an atom.

SBQuantity::mass SBMDynamicalModelParticleSystem::getMass (
    unsigned int atomIndex
) const

Returns the mass of the atom at the given index.

Retrieves the mass for the atom at the specified index.

Parameters:

• index The index of the atom.

Returns:

The mass of the atom, or zero mass if the index is out of range or the system is not initialized.

---

function getMomentum

Returns the momentum of an atom.

virtual SBMomentum3 const & SBMDynamicalModelParticleSystem::getMomentum (
    unsigned int i
) const

Returns the momentum of a particle.

Parameters:

• i The index of the particle.

Returns:

Const reference to the momentum of the particle.

---

function getNumberOfChangedMomentums

Returns the number of changed momentums.

virtual unsigned int SBMDynamicalModelParticleSystem::getNumberOfChangedMomentums () const

Returns the number of changed momenta since the last flush of the momentum buffer.

Returns:

Number of changed momenta.

See also: getMomentum, getChangedMomentumIndex, flushMomentumBuffer

---

function getNumberOfChangedPositions

Returns the number of changed positions.

virtual unsigned int SBMDynamicalModelParticleSystem::getNumberOfChangedPositions () override const

Returns the number of particle positions that have changed since the last buffer flush.

Returns:

Number of changed positions.

Implements SBMDynamicalModel::getNumberOfChangedPositions

---

function getPosition

Returns the position of an atom.

virtual SBPosition3 const & SBMDynamicalModelParticleSystem::getPosition (
    unsigned int i
) const

Returns the position of the specified particle.

Parameters:

• i Index of the particle.

Returns:

Const reference to the particle's position.

---

function getPositionChanged

Returns whether position i has been changed since the last flush.

virtual bool SBMDynamicalModelParticleSystem::getPositionChanged (
    unsigned int i
) override const

Checks whether the position of the specified particle has changed since the last buffer flush.

Parameters:

• i Index of the particle.

Returns:

true if the particle's position has changed, false otherwise.

Implements SBMDynamicalModel::getPositionChanged

---

function getType

Returns the type of the data graph node (returns SBDDataGraphNode::DynamicalModelParticleSystem )

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

Returns the type of the data graph node.

Returns SBDDataGraphNode::DynamicalModelParticleSystem.

Returns:

The data graph node type.

Implements SBMDynamicalModel::getType

---

function print

Prints debugging information.

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

Prints debugging information for the particle system.

Parameters:

• offset Number of indentation levels (tabs) to apply before each printed line.

Implements SBMDynamicalModel::print

---

function removeAtom [1/2]

Removes an atom from the particle system.

void SBMDynamicalModelParticleSystem::removeAtom (
    SBAtom * atom
) 

Removes the given atom from the particle system if it exists.

Parameters:

• atom The atom to remove.

---

function removeAtom [2/2]

Removes an atom from the particle system.

void SBMDynamicalModelParticleSystem::removeAtom (
    unsigned int atomIndex
) 

Removes an atom from the particle system by index.

Removes the atom at the given index from the particle system if the index is valid.

Parameters:

• index The index of the atom to remove.

---

function removeAtoms

Removes atoms of a node indexer.

void SBMDynamicalModelParticleSystem::removeAtoms (
    const SBNodeIndexer & nodeIndexer
) 

Removes multiple atoms from the particle system.

Removes atoms specified by the given node indexer from the particle system.

Parameters:

• nodeIndexer The node indexer containing atoms to remove.

---

function roundForPBC

Computes the integer rounding of a length value for periodic boundary correction.

int SBMDynamicalModelParticleSystem::roundForPBC (
    const SBQuantity::length & d
) 

Parameters:

• d Length value to be rounded.

Returns:

Rounded integer value.

---

function setActivityFlag [1/2]

Sets the activity flag of an atom.

void SBMDynamicalModelParticleSystem::setActivityFlag (
    SBAtom * atom,
    bool flag
) 

Sets the activity flag of the specified atom.

Updates the activity flag for the given atom, if the atom exists. Generates an activity flag changed event.

Parameters:

• atom The atom whose activity flag is to be set.
• flag The new activity flag value.

---

function setActivityFlag [2/2]

Sets the activity flag of an atom.

void SBMDynamicalModelParticleSystem::setActivityFlag (
    unsigned int atomIndex,
    bool flag
) 

Sets the activity flag of the atom at the given index.

Updates the activity flag for the atom at the specified index, if the index is valid. Generates an activity flag changed event.

Parameters:

• index The index of the atom.
• flag The new activity flag value.

---

function setMass [1/2]

Sets the mass of an atom.

void SBMDynamicalModelParticleSystem::setMass (
    SBAtom * atom,
    SBQuantity::mass mass
) 

Sets the mass of the specified atom.

Updates the mass (and corresponding inverse mass) for the given atom, if the atom exists. Generates a mass changed event.

Parameters:

• atom The atom whose mass is to be set.
• mass The new mass value.

---

function setMass [2/2]

Sets the mass of an atom.

void SBMDynamicalModelParticleSystem::setMass (
    unsigned int atomIndex,
    SBQuantity::mass mass
) 

Sets the mass of the atom at the given index.

Parameters:

• index The index of the atom.
• mass The new mass value.

---

function setMomentum

Updates the momentum of an atom.

virtual void SBMDynamicalModelParticleSystem::setMomentum (
    unsigned int i,
    const SBMomentum3 & newMomentum
) 

Updates the momentum of the atom at the given index.

Parameters:

• i Index of the atom whose momentum is to be updated.
• newMomentum New momentum value to assign to the atom.

---

function setPosition

Updates the position of an atom.

virtual void SBMDynamicalModelParticleSystem::setPosition (
    unsigned int i,
    const SBPosition3 & newPosition
) 

Sets the position of the specified particle.

The function applies periodic boundary conditions if they are enabled and updates the structural position buffer.

Parameters:

• i Index of the particle.
• newPosition Desired new position of the particle.

---

function updateStructuralNodes

Updates the structural nodes based on the state of the particle system.

virtual void SBMDynamicalModelParticleSystem::updateStructuralNodes () override

Updates the structural nodes based on the current particle positions.

This function propagates position changes from the particle system to the associated structural nodes.

Implements SBMDynamicalModel::updateStructuralNodes

---

function ~SBMDynamicalModelParticleSystem

Deletes the particle system.

virtual SBMDynamicalModelParticleSystem::~SBMDynamicalModelParticleSystem () 

Destroys the particle system.

Deletes the model.

---