Class SBMStructuralModelConformation#

ClassList > SBMStructuralModelConformation

This class describes a structural conformation. More...

#include <SBMStructuralModelConformation.hpp>

Inherits the following classes: SBDDataGraphNode

Public Types inherited from SBDDataGraphNode#

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

Public Functions#

Type	Name
	SBMStructuralModelConformation () Constructs a structural model conformation.
	SBMStructuralModelConformation (const std::string & name, const SBNodeIndexer & nodeIndexer, SBVector< SBPosition3 > * positionData=nullptr, const SBQuantity::energy & energy=SBQuantity::energy::zero, const SBQuantity::time & time=SBQuantity::time::zero, SBVector< SBVelocity3 > * velocityData=nullptr, SBVector< SBForce3 > * forceData=nullptr) Constructs a structural model conformation with name `name` from the nodes in`nodeIndexer` .
bool	addAtom (SBAtom * atom, const SBPosition3 & atomPosition) Adds a `atom` with position`atomPosition` .
void	clearSourceFileName () Clears the name of the file associated to the conformation.
virtual SBMStructuralModelConformation *	clone () override Returns a copy of the node and its descendants.
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 conformation.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) override Performs the* `object` 's`action` on this conformation.
SBPointerIndexer< SBAtom > const *	getAtomIndexer () const Returns the indexer of atoms for which a position is saved.
virtual SBQuantity::energy	getEnergy () const Returns the energy data.
virtual bool	getForce (unsigned int atomIndex, SBForce3 & force) const Retrieves the force of atom `atomIndex` and stores it in`force` .
virtual bool	getForce (SBAtom * atom, SBForce3 & force) const Retrieves the force of atom `atom` and stores it in`force` .
virtual SBVector< SBForce3 > *	getForceData () const Returns the force data.
SBMStructuralModelConformation *	getNextConformation () const Returns the next conformation 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.
unsigned int	getNumberOfAtoms () const Returns the number of atoms for which a position is saved.
bool	getPosition (unsigned int atomIndex, SBPosition3 & atomPosition) const Retrieves the position of atom `atomIndex` and stores it in`atomPosition` .
bool	getPosition (SBAtom * atom, SBPosition3 & atomPosition) const Retrieves the position of atom `atom` and stores it in`atomPosition` .
virtual SBVector< SBPosition3 > *	getPositionData () const Returns the position data.
SBMStructuralModelConformation *	getPreviousConformation () const Returns the previous conformation in the document.
const std::string &	getSourceFileName () const Returns the name of the file associated to the conformation.
virtual SBQuantity::time	getTime () const Returns the time data.
virtual SBNode::Type	getType () override const Returns the data graph node type.
virtual bool	getVelocity (unsigned int atomIndex, SBVelocity3 & velocity) const Retrieves the velocity of atom `atomIndex` and stores it in`velocity` .
virtual bool	getVelocity (SBAtom * atom, SBVelocity3 & velocity) const Retrieves the velocity of atom `atom` and stores it in`velocity` .
virtual 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 conformation has the source file name set.
bool	insertAtom (unsigned int atomIndex, SBAtom * atom, const SBPosition3 & atomPosition) Inserts a `atom` with position`atomPosition` at index`atomIndex` .
virtual bool	isSerializable () override const Returns `true` __
virtual void	print (unsigned int offset=0) override const Prints the conformation.
bool	removeAtom (SBAtom * atom) Removes an atom from the conformation.
void	restore () const Restores the conformation.
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 conformation.
virtual void	setEnergy (const SBQuantity::energy & energy) Sets the energy data.
virtual bool	setForce (unsigned int atomIndex, const SBForce3 & force) Sets the force of atom `atomIndex` to`force` .
virtual bool	setForce (SBAtom * atom, const SBForce3 & force) Sets the force of atom `atom` to`force` .
virtual void	setForceData (SBVector< SBForce3 > * forceData) Sets the force data.
bool	setPosition (unsigned int atomIndex, const SBPosition3 & atomPosition) Sets the position of atom `atomIndex` and stores it in`atomPosition` .
bool	setPosition (SBAtom * atom, const SBPosition3 & atomPosition) Sets the position of atom `atom` and stores it in`atomPosition` .
virtual void	setPositionData (SBVector< SBPosition3 > * positionData) Sets the position data.
void	setSourceFileName (const std::string & fileName) Sets the name of the file associated to the conformation.
virtual void	setTime (const SBQuantity::time & time) Sets the time data.
virtual bool	setVelocity (unsigned int atomIndex, const SBVelocity3 & velocity) Sets the velocity of atom `atomIndex` to`velocity` .
virtual bool	setVelocity (SBAtom * atom, const SBVelocity3 & velocity) Sets the velocity of atom `atom` to`velocity` .
virtual void	setVelocityData (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 conformation.
virtual	~SBMStructuralModelConformation () Destructs the conformation.

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 conformation, i.e.

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

Short name: SBConformation

See also: SBDDocument

Public Functions Documentation#

function SBMStructuralModelConformation [1/2]#

Constructs a structural model conformation.

SBMStructuralModelConformation::SBMStructuralModelConformation ()

Constructs a structural model conformation with the default name "Conformation" and an empty node indexer.

This default constructor delegates to the named constructor.

function SBMStructuralModelConformation [2/2]#

Constructs a structural model conformation with name name from the nodes innodeIndexer .

SBMStructuralModelConformation::SBMStructuralModelConformation (
    const std::string & name,
    const SBNodeIndexer & nodeIndexer,
    SBVector< SBPosition3 > * positionData=nullptr,
    const SBQuantity::energy & energy=SBQuantity::energy::zero,
    const SBQuantity::time & time=SBQuantity::time::zero,
    SBVector< SBVelocity3 > * velocityData=nullptr,
    SBVector< SBForce3 > * forceData=nullptr
)

Constructs a structural model conformation with the given name, node indexer, and optional data.

Parameters:

name The name of the conformation.
nodeIndexer The node indexer describing the nodes included in the conformation.
positionData Optional pointer to a vector of atom positions. May be nullptr.
energy The energy value of the conformation. Defaults to zero.
time The time value of the conformation. Defaults to zero.
velocityData Optional pointer to a vector of atom velocities. May be nullptr.
forceData Optional pointer to a vector of atom forces. May be nullptr.

function addAtom#

Adds a atom with positionatomPosition .

bool SBMStructuralModelConformation::addAtom (
    SBAtom * atom,
    const SBPosition3 & atomPosition
)

Adds an atom with a specified position to the conformation.

The atom is appended to the end of the atom list.

Parameters:

atom Pointer to the atom to add.
atomPosition Position of the atom to be stored.

Returns:

true if the atom was added successfully, otherwise false.

function clearSourceFileName#

Clears the name of the file associated to the conformation.

void SBMStructuralModelConformation::clearSourceFileName ()

Clears the source file name associated with the conformation.

After calling this function, the conformation will no longer have a source file name set.

function clone#

Returns a copy of the node and its descendants.

virtual SBMStructuralModelConformation * SBMStructuralModelConformation::clone () override

Creates a copy of this conformation and its descendants.

The cloned object is a new instance that duplicates the original conformation's data.

Returns:

Pointer to the newly created conformation.

Implements SBDDataGraphNode::clone

function createStructuralModels#

Create structural models corresponding to all steps.

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

Creates structural model nodes corresponding to this conformation and adds them to the provided indexer.

Parameters:

structuralModelIndexer Indexer to which the newly created structural model nodes will be added.

function forEachNodeDepthFirst [1/2]#

Performs the action on this conformation.

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

Executes a callback for this conformation in a depth-first traversal.

The provided function pointer is invoked with this node as its argument.

Parameters:

action Function pointer to be called for each node.

Implements SBDDataGraphNode::forEachNodeDepthFirst

function forEachNodeDepthFirst [2/2]#

Performs the object 'saction on this conformation.

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

Executes a member function callback for this conformation in a depth-first traversal.

The specified member function of the given object is invoked with this node as its argument.

Parameters:

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

Implements SBDDataGraphNode::forEachNodeDepthFirst

function getAtomIndexer#

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

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

Returns a pointer to the atom indexer used by this conformation.

The returned pointer may be null if no atom indexer is present.

Returns:

Pointer to the atom indexer, or nullptr.

function getEnergy#

Returns the energy data.

virtual SBQuantity::energy SBMStructuralModelConformation::getEnergy () const

Retrieves the energy value associated with the conformation.

Returns:

The energy of the conformation.

function getForce [1/2]#

Retrieves the force of atom atomIndex and stores it inforce .

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

Retrieves the force applied to an atom by its index.

Parameters:

atomIndex Index of the atom whose force is requested.
atomForce Output parameter that receives the force of the atom.

Returns:

true if the force data exists and the index is valid; false otherwise.

function getForce [2/2]#

Retrieves the force of atom atom and stores it inforce .

virtual bool SBMStructuralModelConformation::getForce (
    SBAtom * atom,
    SBForce3 & force
) const

Retrieves the force applied to a specific atom.

Parameters:

atom Pointer to the atom whose force is requested.
atomForce Output parameter that receives the force of the atom.

Returns:

true if the force data exists for the atom; false otherwise.

function getForceData#

Returns the force data.

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

Retrieves the force data vector for the conformation.

Returns:

Pointer to the vector of forces, or nullptr if no force data is stored.

function getNextConformation#

Returns the next conformation in the document.

SBMStructuralModelConformation * SBMStructuralModelConformation::getNextConformation () const

Returns the next conformation in the document sequence.

Traverses the linked list of nodes to find the next node that is a conformation.

Returns:

Pointer to the next conformation, 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 SBMStructuralModelConformation::getNodes (
    SBNodeIndexer & nodeIndexer,
    SBNode::Type nodeType,
    bool selectedNodesOnly=false,
    const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(),
    bool includeDependencies=false
) override const

Collects nodes of a specified type into an indexer.

The function adds this conformation and optionally its dependent atoms to the provided node indexer based on the given criteria.

Parameters:

nodeIndexer Container that will receive the collected nodes.
nodeType The type of nodes to collect.
selectedNodesOnly If true, only selected nodes are collected.
visitPredicate Predicate that determines whether this 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 SBMStructuralModelConformation::getNodes (
    SBNodeIndexer & nodeIndexer,
    const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(),
    const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(),
    bool includeDependencies=false
) override const

Collects nodes based on selection and visit predicates into an indexer.

The function adds this conformation and optionally its dependent atoms to the provided node indexer according to the supplied predicates.

Parameters:

nodeIndexer Container that will receive the collected nodes.
selectionPredicate Predicate that selects nodes to be added.
visitPredicate Predicate that determines whether this 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.

unsigned int SBMStructuralModelConformation::getNumberOfAtoms () const

Returns the number of atoms stored in the conformation.

Returns:

The count of atoms.

function getPosition [1/2]#

Retrieves the position of atom atomIndex and stores it inatomPosition .

bool SBMStructuralModelConformation::getPosition (
    unsigned int atomIndex,
    SBPosition3 & atomPosition
) const

Retrieves the position of the atom at the given index.

Parameters:

atomIndex Index of the atom whose position is requested.
atomPosition Output parameter that receives the atom's position.

Returns:

true if the position was retrieved successfully, otherwise false.

function getPosition [2/2]#

Retrieves the position of atom atom and stores it inatomPosition .

bool SBMStructuralModelConformation::getPosition (
    SBAtom * atom,
    SBPosition3 & atomPosition
) const

Retrieves the position of the specified atom.

Parameters:

atom Pointer to the atom whose position is requested.
atomPosition Output parameter that receives the atom's position.

Returns:

true if the position was retrieved successfully, otherwise false.

function getPositionData#

Returns the position data.

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

Returns the position data vector associated with the conformation.

Returns:

Pointer to the vector of atom positions.

function getPreviousConformation#

Returns the previous conformation in the document.

SBMStructuralModelConformation * SBMStructuralModelConformation::getPreviousConformation () const

Returns the previous conformation in the document sequence.

Traverses the linked list of nodes to find the preceding node that is a conformation.

Returns:

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

function getSourceFileName#

Returns the name of the file associated to the conformation.

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

Returns the source file name associated with the conformation.

If a source file name has not been set, the default structural model conformation source file name is returned.

Returns:

Reference to the source file name string.

function getTime#

Returns the time data.

virtual SBQuantity::time SBMStructuralModelConformation::getTime () const

Retrieves the time value associated with the conformation.

Returns:

The time of the conformation.

function getType#

Returns the data graph node type.

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

Returns the type identifier of this data graph node.

The returned value indicates that this node is a conformation.

Returns:

The node type enumeration value.

Implements SBDDataGraphNode::getType

function getVelocity [1/2]#

Retrieves the velocity of atom atomIndex and stores it invelocity .

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

Retrieves the velocity of an atom by its index.

Parameters:

atomIndex Index of the atom whose velocity is requested.
atomVelocity Output parameter that receives the velocity of the atom.

Returns:

true if the velocity data exists and the index is valid; false otherwise.

function getVelocity [2/2]#

Retrieves the velocity of atom atom and stores it invelocity .

virtual bool SBMStructuralModelConformation::getVelocity (
    SBAtom * atom,
    SBVelocity3 & velocity
) const

Retrieves the velocity of a specific atom.

Parameters:

atom Pointer to the atom whose velocity is requested.
atomVelocity Output parameter that receives the velocity of the atom.

Returns:

true if the velocity data exists for the atom; false otherwise.

function getVelocityData#

Returns the velocity data.

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

Retrieves the velocity data vector for the conformation.

Returns:

Pointer to the vector of velocities, or nullptr if no velocity data is stored.

function hasNode [1/2]#

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

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

Checks whether a node of the specified type exists in the conformation.

The check can be limited to selected nodes and may include dependent nodes.

Parameters:

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

Returns:

true if a matching node is found, otherwise false.

Implements SBDDataGraphNode::hasNode

function hasNode [2/2]#

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

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

Checks whether any node satisfying the given selection predicate exists in the conformation.

The check may also include dependent nodes based on the provided flag.

Parameters:

selectionPredicate Predicate that selects nodes to be checked.
visitPredicate Predicate that determines whether this node should be visited.
includeDependencies If true, dependent nodes are also considered.

Returns:

true if a matching node is found, otherwise false.

Implements SBDDataGraphNode::hasNode

function hasSourceFileName#

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

bool SBMStructuralModelConformation::hasSourceFileName () const

Checks whether a source file name is set for the conformation.

Returns:

true if a source file name is set, false otherwise.

function insertAtom#

Inserts a atom with positionatomPosition at indexatomIndex .

bool SBMStructuralModelConformation::insertAtom (
    unsigned int atomIndex,
    SBAtom * atom,
    const SBPosition3 & atomPosition
)

Inserts an atom at a specified index with a given position.

The atom is placed at the provided index, shifting subsequent atoms as needed.

Parameters:

atomIndex Index at which to insert the atom.
atom Pointer to the atom to insert.
atomPosition Position of the atom to be stored.

Returns:

true if the insertion succeeded, otherwise false.

function isSerializable#

Returns true __

virtual bool SBMStructuralModelConformation::isSerializable () override const

Indicates whether the conformation can be serialized.

Returns:

True, indicating that the conformation is serializable.

Implements SBDDataGraphNode::isSerializable

function print#

Prints the conformation.

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

Prints a textual representation of the conformation to standard output.

Parameters:

offset Number of indentation levels to prepend to each printed line.

Implements SBDDataGraphNode::print

function removeAtom#

Removes an atom from the conformation.

bool SBMStructuralModelConformation::removeAtom (
    SBAtom * atom
)

Removes the specified atom from the conformation.

The atom is removed from the internal atom list and its position data is discarded.

Parameters:

atom Pointer to the atom to remove.

Returns:

true if the atom was removed successfully, otherwise false.

function restore#

Restores the conformation.

void SBMStructuralModelConformation::restore () const

Restores the positions of all atoms in the conformation to the stored values.

The function iterates over each atom in the conformation and sets its position to the stored position data.

function serialize#

Serializes the conformation.

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

Serializes the conformation to the given serializer.

Serializes the conformation data, handling version-specific formats and writing atom information, positions, energy, time, velocities, and forces.

Parameters:

serializer The serializer used to write the conformation data.
nodeIndexer The node indexer used to map nodes to their indices for serialization.
sdkVersionNumber The SDK version number for versioned serialization.
classVersionNumber The class version number for versioned serialization.

Implements SBDDataGraphNode::serialize

function setEnergy#

Sets the energy data.

virtual void SBMStructuralModelConformation::setEnergy (
    const SBQuantity::energy & energy
)

Sets the energy value for the conformation.

Parameters:

energy Energy value to assign to the conformation.

function setForce [1/2]#

Sets the force of atom atomIndex toforce .

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

Sets the force applied to an atom specified by its index.

Parameters:

atomIndex Index of the atom to modify.
atomForce New force for the atom.

Returns:

true if the index is valid and the force was set; false otherwise.

function setForce [2/2]#

Sets the force of atom atom toforce .

virtual bool SBMStructuralModelConformation::setForce (
    SBAtom * atom,
    const SBForce3 & force
)

Sets the force applied to a specific atom.

Parameters:

atom Pointer to the atom whose force is to be set.
atomForce New force for the atom.

Returns:

true if the atom is part of the conformation and the force was set; false otherwise.

function setForceData#

Sets the force data.

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

Sets the force data vector for the conformation.

Parameters:

forceData Pointer to a vector of forces to associate with the conformation.

function setPosition [1/2]#

Sets the position of atom atomIndex and stores it inatomPosition .

bool SBMStructuralModelConformation::setPosition (
    unsigned int atomIndex,
    const SBPosition3 & atomPosition
)

Sets the position of an atom specified by its index.

Parameters:

atomIndex Index of the atom to modify.
atomPosition New position for the atom.

Returns:

true if the atom index is valid and the position was set; false otherwise.

function setPosition [2/2]#

Sets the position of atom atom and stores it inatomPosition .

bool SBMStructuralModelConformation::setPosition (
    SBAtom * atom,
    const SBPosition3 & atomPosition
)

Sets the position of a specific atom.

Parameters:

atom Pointer to the atom whose position is to be set.
atomPosition New position for the atom.

Returns:

true if the atom is part of the conformation and the position was set; false otherwise.

function setPositionData#

Sets the position data.

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

Sets the position data vector for the conformation.

Parameters:

positionData Pointer to the new position data vector.

function setSourceFileName#

Sets the name of the file associated to the conformation.

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

Sets the source file name for the conformation.

The provided file name becomes the new source file name associated with this conformation.

Parameters:

fileName The name of the source file to set.

function setTime#

Sets the time data.

virtual void SBMStructuralModelConformation::setTime (
    const SBQuantity::time & time
)

Sets the time value for the conformation.

Parameters:

time Time value to assign to the conformation.

function setVelocity [1/2]#

Sets the velocity of atom atomIndex tovelocity .

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

Sets the velocity of an atom specified by its index.

Parameters:

atomIndex Index of the atom to modify.
atomVelocity New velocity for the atom.

Returns:

true if the index is valid and the velocity was set; false otherwise.

function setVelocity [2/2]#

Sets the velocity of atom atom tovelocity .

virtual bool SBMStructuralModelConformation::setVelocity (
    SBAtom * atom,
    const SBVelocity3 & velocity
)

Sets the velocity of a specific atom.

Parameters:

atom Pointer to the atom whose velocity is to be set.
atomVelocity New velocity for the atom.

Returns:

true if the atom is part of the conformation and the velocity was set; false otherwise.

function setVelocityData#

Sets the velocity data.

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

Sets the velocity data vector for the conformation.

Parameters:

velocityData Pointer to a vector of velocities to associate with the conformation.

function unserialize#

Unserializes the conformation.

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

Unserializes the conformation from the given serializer.

Parameters:

serializer The serializer used to read the conformation data.
nodeIndexer The node indexer used to map indices back to nodes during deserialization.
sdkVersionNumber The SDK version number for versioned deserialization.
classVersionNumber The class version number for versioned deserialization.

Implements SBDDataGraphNode::unserialize

function ~SBMStructuralModelConformation#

Destructs the conformation.

virtual SBMStructuralModelConformation::~SBMStructuralModelConformation ()

Destroys the structural model conformation and emits a node deletion begin event.