Class SBMStructuralModelPath#

ClassList > SBMStructuralModelPath

This class describes a structural path. More...

#include <SBMStructuralModelPath.hpp>

Inherits the following classes: SBDDataGraphNode

Public Types#

Type	Name
enum	AnimationType Animation type.

Public Types inherited from SBDDataGraphNode#

See SBDDataGraphNode

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

Public Functions#

Type	Name
	SBMStructuralModelPath () Constructs a path.
	SBMStructuralModelPath (const std::string & name, const SBNodeIndexer & nodeIndexer=SBNodeIndexer()) Constructs a path with name `name` from the conformations in`nodeIndexer` .
	SBMStructuralModelPath (const std::string & name, const SBNodeIndexer & nodeIndexer, SBVector< SBVector< SBPosition3 > * > * positionData, SBVector< SBQuantity::energy > * energyData=0, SBVector< SBQuantity::time > * timeData=0, SBVector< SBVector< SBVelocity3 > * > * velocityData=0, SBVector< SBVector< SBForce3 > * > * forceData=0) Constructs a path with name `name` from the atoms in`nodeIndexer` .
	SB_DECLARE_DATA (SBMStructuralModelPath)
virtual bool	add (SBConformation * conformation) Adds a frame to the path.
virtual bool	add (SBMStructuralModelPath * path) Adds frames to the path.
virtual bool	add (SBVector< SBPosition3 > * positionData, const SBQuantity::energy & energy=SBQuantity::energy::zero, const SBQuantity::time & time=SBQuantity::time::zero, SBVector< SBVelocity3 > * velocityData=0, SBVector< SBForce3 > * forceData=0) Adds a frame to the path.
virtual bool	add (SBVector< SBVector< SBPosition3 > * > * positionData, SBVector< SBQuantity::energy > * energyData=0, SBVector< SBQuantity::time > * timeData=0, SBVector< SBVector< SBVelocity3 > * > * velocityData=0, SBVector< SBVector< SBForce3 > * > * forceData=0) Adds frames to the path.
bool	addAtom (SBAtom * atom, SBVector< SBPosition3 > * atomPositionVector=0, SBVector< SBVelocity3 > * atomVelocityVector=0, SBVector< SBForce3 > * atomForceVector=0) Adds an `atom` to the path.
virtual SBMStructuralModelPath *	clone () override Returns a copy of the node and its descendants.
virtual SBMStructuralModelPath *	copy (unsigned int firstStep, unsigned int lastStep) Copies frames from the path to create a new path.
virtual void	createConformation (unsigned int step, SBNodeIndexer & conformationIndexer) const Create a conformation corresponding to a specific `step` .
virtual void	createConformations (SBNodeIndexer & conformationIndexer) const Create conformations corresponding to all steps.
virtual void	createStructuralModels (unsigned int step, SBNodeIndexer & structuralModelIndexer) const Create structural models corresponding to a specific `step` .
virtual void	createStructuralModels (SBNodeIndexer & structuralModelIndexer) const Create structural models corresponding to all steps.
virtual void	forEachNodeDepthFirst (void()(SBDDataGraphNode* node) action) override Performs action* `action` on each node of this document.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) override Performs action* `action` of object`object` on each node of this document.
virtual bool	getAnimationFlag () const Returns the animation flag.
virtual AnimationType	getAnimationType () const Returns the animation type.
virtual SBPointerIndexer< SBAtom > const *	getAtomIndexer () const Returns the atoms for which a position is saved.
virtual SBQuantity::energy	getCurrentEnergy () const Returns the current energy.
virtual unsigned int	getCurrentStep () const Returns the current step along the path.
virtual SBQuantity::time	getCurrentTime () const Returns the current time.
virtual bool	getEnergy (unsigned int step, SBQuantity::energy & energy) const Retrieves the energy for a specific `step` .
virtual SBVector< SBQuantity::energy > *	getEnergyData () const Returns the energy data.
virtual bool	getForce (unsigned int step, unsigned int atomIndex, SBForce3 & force) const Retrieves the force of atom `atomIndex` and stores it in`force` for a specific`step` .
virtual bool	getForce (unsigned int step, SBAtom * atom, SBForce3 & force) const Retrieves the force of atom `atom` and stores it in`force` for a specific`step` .
virtual SBVector< SBVector< SBForce3 > * > *	getForceData () const Returns the force data.
virtual bool	getForwardFlag () const Returns the forward flag, which indicates when the animation is moving forward.
SBMStructuralModelPath *	getNextPath () const Returns the next path in the document.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Collects nodes into `nodeIndexer` , based on a`nodeType` , a selection status and a`visitPredicate` , with or without dependencies.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Collects nodes into `nodeIndexer` , based on a`selectionPredicate` and a`visitPredicate` , with or without dependencies.
virtual unsigned int	getNumberOfAtoms () const Returns the number of atoms for which a position is saved.
virtual unsigned int	getNumberOfSteps () const Returns the number of steps in the path.
virtual bool	getPosition (unsigned int step, unsigned int atomIndex, SBPosition3 & position) const Retrieves the position of atom `atomIndex` and stores it in`position` for a specific`step` .
virtual bool	getPosition (unsigned int step, SBAtom * atom, SBPosition3 & position) const Retrieves the position of atom `atom` and stores it in`position` for a specific`step` .
virtual SBVector< SBVector< SBPosition3 > * > *	getPositionData () const Returns the position data.
SBMStructuralModelPath *	getPreviousPath () const Returns the previous path in the document.
virtual unsigned int	getSmoothingWindowSize () const Returns the size of the smoothing window.
virtual SBQuantity::second const &	getStepDuration () const Returns the step duration.
virtual unsigned int	getStride () const Returns the animation stride.
virtual bool	getTime (unsigned int step, SBQuantity::time & time) const Retrieves the time for a specific `step` .
virtual SBVector< SBQuantity::time > *	getTimeData () const Returns the time data.
virtual SBNode::Type	getType () override const Returns the data graph node type.
virtual bool	getVelocity (unsigned int step, unsigned int atomIndex, SBVelocity3 & velocity) const Retrieves the velocity of atom `atomIndex` and stores it in`velocity` for a specific`step` .
virtual bool	getVelocity (unsigned int step, SBAtom * atom, SBVelocity3 & velocity) const Retrieves the velocity of atom `atom` and stores it in`velocity` for a specific`step` .
virtual SBVector< SBVector< SBVelocity3 > * > *	getVelocityData () const Returns the velocity data.
virtual bool	hasNode (SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Checks for nodes based on a `nodeType` , a selection status and a`visitPredicate` , with or without dependencies.
virtual bool	hasNode (const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Checks for nodes based on a `selectionPredicate` and a`visitPredicate` , with or without dependencies.
virtual bool	insert (unsigned int step, SBConformation * conformation) Inserts a frame in the path at position `step` .
virtual bool	insert (unsigned int step, SBMStructuralModelPath * path) Inserts frames in the path at position `step` .
virtual bool	insert (unsigned int step, SBVector< SBPosition3 > * positionData, const SBQuantity::energy & energy=SBQuantity::energy::zero, const SBQuantity::time & time=SBQuantity::time::zero, SBVector< SBVelocity3 > * velocityData=0, SBVector< SBForce3 > * forceData=0) Inserts a frame in the path at position `step` .
virtual bool	insert (unsigned int step, SBVector< SBVector< SBPosition3 > * > * positionData, SBVector< SBQuantity::energy > * energyData=0, SBVector< SBQuantity::time > * timeData=0, SBVector< SBVector< SBVelocity3 > * > * velocityData=0, SBVector< SBVector< SBForce3 > * > * forceData=0) Inserts frames in the path at position `step` .
bool	insertAtom (unsigned int atomIndex, SBAtom * atom, SBVector< SBPosition3 > * atomPositionVector=0, SBVector< SBVelocity3 > * atomVelocityVector=0, SBVector< SBForce3 > * atomForceVector=0) Inserts an `atom` at index`atomIndex` to the path.
virtual bool	isSerializable () override const Returns true.
virtual void	print (unsigned int offset=0) override const Prints the path.
virtual SBConformation *	remove (unsigned int step) Remove a frame from the path to create a conformation.
virtual SBMStructuralModelPath *	remove (unsigned int firstStep, unsigned int lastStep) Removes frames from the path to create a new path.
bool	removeAtom (SBAtom * atom) Removes an atom from the path.
virtual void	serialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override const Serializes the path.
virtual void	setAnimationFlag (bool animationFlag) Sets the animation flag.
virtual void	setAnimationType (AnimationType animationType) Sets the animation type.
virtual void	setCurrentStep (unsigned int currentStep) Sets the current step along the path.
virtual bool	setEnergy (unsigned int step, const SBQuantity::energy & energy) Sets the energy for a specific `step` .
virtual void	setEnergyData (SBVector< SBQuantity::energy > * energyData) Sets the energy data.
virtual bool	setForce (unsigned int step, unsigned int atomIndex, const SBForce3 & force) Sets the force of atom `atomIndex` to`force` for a specific`step` .
virtual bool	setForce (unsigned int step, SBAtom * atom, const SBForce3 & force) Sets the force of atom `atom` to`force` for a specific`step` .
virtual void	setForceData (SBVector< SBVector< SBForce3 > * > * forceData) Sets the force data.
virtual void	setForwardFlag (bool forwardFlag) Sets the forward flag, which indicates when the animation is moving forward.
virtual bool	setPosition (unsigned int step, unsigned int atomIndex, const SBPosition3 & position) Sets the position of atom `atomIndex` to`position` for a specific`step` .
virtual bool	setPosition (unsigned int step, SBAtom * atom, const SBPosition3 & position) Sets the position of atom `atom` to`position` for a specific`step` .
virtual void	setPositionData (SBVector< SBVector< SBPosition3 > * > * positionData) Sets the position data.
virtual void	setSmoothingWindowSize (unsigned int smoothingWindowSize) Sets the size of the smoothing window.
virtual void	setStepDuration (const SBQuantity::second & stepDuration) Sets the step duration.
virtual void	setStride (unsigned int stride) Sets the animation stride.
virtual bool	setTime (unsigned int step, const SBQuantity::time & time) Sets the time for a specific `step` .
virtual void	setTimeData (SBVector< SBQuantity::time > * timeData) Sets the time data.
virtual bool	setVelocity (unsigned int step, unsigned int atomIndex, const SBVelocity3 & velocity) Sets the velocity of atom `atomIndex` to`velocity` for a specific`step` .
virtual bool	setVelocity (unsigned int step, SBAtom * atom, const SBVelocity3 & velocity) Sets the velocity of atom `atom` to`velocity` for a specific`step` .
virtual void	setVelocityData (SBVector< SBVector< SBVelocity3 > * > * velocityData) Sets the velocity data.
virtual void	unserialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override Unserializes the path.
virtual void	updateState () Updates the state along the path according to the animation parameters.
virtual	~SBMStructuralModelPath () Destructs the path.

Public Functions inherited from SBDDataGraphNode#

See SBDDataGraphNode

Type	Name
	SB_DECLARE_DATA (SBDDataGraphNode)
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 an action on each node.*
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) Performs an action on each node.*
virtual unsigned int	getDefaultOpacity () const Returns the default opacity.
virtual 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.
virtual unsigned int	getMaximumOpacity () const Returns the maximum opacity.
virtual unsigned int	getMaximumTransparency () const Returns the maximum transparency.
virtual unsigned int	getMinimumOpacity () const Returns the minimum opacity.
virtual 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.
virtual unsigned int	getOpacitySingleStep () const Returns the opacity single step.
virtual 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.
virtual unsigned int	getTransparencySingleStep () const Returns the transparency single step.
virtual 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.
virtual bool	hasOpacityRange () const Returns whether the node has the opacity range.
virtual 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 ()
unsigned int	getMemoryFootprint () const
void	printReferencesToOwners () const
virtual	~SBCReferenceTarget ()

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 an action for each node in a selection.*
void	forEachNodeInSelection (SBNodeIndexer & nodeIndexer, SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) Performs an action for each node in a selection.*
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

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)
void	removeAllReferenceOwners ()

Detailed Description#

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

Short name: SBPath

See also: SBDDocument

Public Types Documentation#

enum AnimationType#

Animation type.

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

Public Functions Documentation#

function SBMStructuralModelPath [1/3]#

Constructs a path.

SBMStructuralModelPath::SBMStructuralModelPath ()

function SBMStructuralModelPath [2/3]#

Constructs a path with name name from the conformations innodeIndexer .

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

function SBMStructuralModelPath [3/3]#

Constructs a path with name name from the atoms innodeIndexer .

SBMStructuralModelPath::SBMStructuralModelPath (
    const std::string & name,
    const SBNodeIndexer & nodeIndexer,
    SBVector< SBVector< SBPosition3 > * > * positionData,
    SBVector< SBQuantity::energy > * energyData=0,
    SBVector< SBQuantity::time > * timeData=0,
    SBVector< SBVector< SBVelocity3 > * > * velocityData=0,
    SBVector< SBVector< SBForce3 > * > * forceData=0
)

function SB_DECLARE_DATA#

SBMStructuralModelPath::SB_DECLARE_DATA (
    SBMStructuralModelPath
)

function add [1/4]#

Adds a frame to the path.

virtual bool SBMStructuralModelPath::add (
    SBConformation * conformation
)

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

The function returns true when successful.

function add [2/4]#

Adds frames to the path.

virtual bool SBMStructuralModelPath::add (
    SBMStructuralModelPath * path
)

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

The function returns true when successful.

function add [3/4]#

Adds a frame to the path.

virtual bool SBMStructuralModelPath::add (
    SBVector< SBPosition3 > * positionData,
    const SBQuantity::energy & energy=SBQuantity::energy::zero,
    const SBQuantity::time & time=SBQuantity::time::zero,
    SBVector< SBVelocity3 > * velocityData=0,
    SBVector< SBForce3 > * forceData=0
)

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

The function returns true when successful.

function add [4/4]#

Adds frames to the path.

virtual bool SBMStructuralModelPath::add (
    SBVector< SBVector< SBPosition3 > * > * positionData,
    SBVector< SBQuantity::energy > * energyData=0,
    SBVector< SBQuantity::time > * timeData=0,
    SBVector< SBVector< SBVelocity3 > * > * velocityData=0,
    SBVector< SBVector< SBForce3 > * > * forceData=0
)

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

The function returns true when successful.

function addAtom#

Adds an atom to the path.

bool SBMStructuralModelPath::addAtom (
    SBAtom * atom,
    SBVector< SBPosition3 > * atomPositionVector=0,
    SBVector< SBVelocity3 > * atomVelocityVector=0,
    SBVector< SBForce3 > * atomForceVector=0
)

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

The function returns true when insertion is successful, and false otherwise.

function clone#

Returns a copy of the node and its descendants.

virtual SBMStructuralModelPath * SBMStructuralModelPath::clone () override

Implements SBDDataGraphNode::clone

function copy#

Copies frames from the path to create a new path.

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

This function creates a deep copy of all the frames between (and including) steps firstStep and lastStep, and returns a path containing these frames.

function createConformation#

Create a conformation corresponding to a specific step .

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

function createConformations#

Create conformations corresponding to all steps.

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

function createStructuralModels [1/2]#

Create structural models corresponding to a specific step .

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

function createStructuralModels [2/2]#

Create structural models corresponding to all steps.

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

function forEachNodeDepthFirst [1/2]#

Performs action action on each node of this document.

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

Implements SBDDataGraphNode::forEachNodeDepthFirst

function forEachNodeDepthFirst [2/2]#

Performs action action of objectobject on each node of this document.

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

Implements SBDDataGraphNode::forEachNodeDepthFirst

function getAnimationFlag#

Returns the animation flag.

virtual bool SBMStructuralModelPath::getAnimationFlag () const

function getAnimationType#

Returns the animation type.

virtual AnimationType SBMStructuralModelPath::getAnimationType () const

function getAtomIndexer#

Returns the atoms for which a position is saved.

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

function getCurrentEnergy#

Returns the current energy.

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

function getCurrentStep#

Returns the current step along the path.

virtual unsigned int SBMStructuralModelPath::getCurrentStep () const

function getCurrentTime#

Returns the current time.

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

function getEnergy#

Retrieves the energy for a specific step .

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

function getEnergyData#

Returns the energy data.

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

function getForce [1/2]#

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

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

function getForce [2/2]#

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

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

function getForceData#

Returns the force data.

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

function getForwardFlag#

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

virtual bool SBMStructuralModelPath::getForwardFlag () const

function getNextPath#

Returns the next path in the document.

SBMStructuralModelPath * SBMStructuralModelPath::getNextPath () const

function getNodes [1/2]#

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

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

Implements SBDDataGraphNode::getNodes

function getNodes [2/2]#

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

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

Implements SBDDataGraphNode::getNodes

function getNumberOfAtoms#

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

virtual unsigned int SBMStructuralModelPath::getNumberOfAtoms () const

function getNumberOfSteps#

Returns the number of steps in the path.

virtual unsigned int SBMStructuralModelPath::getNumberOfSteps () const

function getPosition [1/2]#

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

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

function getPosition [2/2]#

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

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

function getPositionData#

Returns the position data.

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

function getPreviousPath#

Returns the previous path in the document.

SBMStructuralModelPath * SBMStructuralModelPath::getPreviousPath () const

function getSmoothingWindowSize#

Returns the size of the smoothing window.

virtual unsigned int SBMStructuralModelPath::getSmoothingWindowSize () const

function getStepDuration#

Returns the step duration.

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

function getStride#

Returns the animation stride.

virtual unsigned int SBMStructuralModelPath::getStride () const

function getTime#

Retrieves the time for a specific step .

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

function getTimeData#

Returns the time data.

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

function getType#

Returns the data graph node type.

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

Implements SBDDataGraphNode::getType

function getVelocity [1/2]#

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

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

function getVelocity [2/2]#

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

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

function getVelocityData#

Returns the velocity data.

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

function hasNode [1/2]#

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

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

Implements SBDDataGraphNode::hasNode

function hasNode [2/2]#

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

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

Implements SBDDataGraphNode::hasNode

function insert [1/4]#

Inserts a frame in the path at position step .

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

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

The function returns true when successful.

function insert [2/4]#

Inserts frames in the path at position step .

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

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

The function returns true when successful.

function insert [3/4]#

Inserts a frame in the path at position step .

virtual bool SBMStructuralModelPath::insert (
    unsigned int step,
    SBVector< SBPosition3 > * positionData,
    const SBQuantity::energy & energy=SBQuantity::energy::zero,
    const SBQuantity::time & time=SBQuantity::time::zero,
    SBVector< SBVelocity3 > * velocityData=0,
    SBVector< SBForce3 > * forceData=0
)

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

The function returns true when successful.

function insert [4/4]#

Inserts frames in the path at position step .

virtual bool SBMStructuralModelPath::insert (
    unsigned int step,
    SBVector< SBVector< SBPosition3 > * > * positionData,
    SBVector< SBQuantity::energy > * energyData=0,
    SBVector< SBQuantity::time > * timeData=0,
    SBVector< SBVector< SBVelocity3 > * > * velocityData=0,
    SBVector< SBVector< SBForce3 > * > * forceData=0
)

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

The function returns true when successful.

function insertAtom#

Inserts an atom at indexatomIndex to the path.

bool SBMStructuralModelPath::insertAtom (
    unsigned int atomIndex,
    SBAtom * atom,
    SBVector< SBPosition3 > * atomPositionVector=0,
    SBVector< SBVelocity3 > * atomVelocityVector=0,
    SBVector< SBForce3 > * atomForceVector=0
)

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

The function returns true when insertion is successful, and false otherwise.

function isSerializable#

Returns true.

virtual bool SBMStructuralModelPath::isSerializable () override const

Implements SBDDataGraphNode::isSerializable

function print#

Prints the path.

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

Implements SBDDataGraphNode::print

function remove [1/2]#

Remove a frame from the path to create a conformation.

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

function remove [2/2]#

Removes frames from the path to create a new path.

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

This function creates a deep copy of all the frames between (and including) steps firstStep and lastStep, deletes the corresponding frames in this path, and returns a path containing the copied frames.

function removeAtom#

Removes an atom from the path.

bool SBMStructuralModelPath::removeAtom (
    SBAtom * atom
)

function serialize#

Serializes the path.

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

Implements SBDDataGraphNode::serialize

function setAnimationFlag#

Sets the animation flag.

virtual void SBMStructuralModelPath::setAnimationFlag (
    bool animationFlag
)

function setAnimationType#

Sets the animation type.

virtual void SBMStructuralModelPath::setAnimationType (
    AnimationType animationType
)

function setCurrentStep#

Sets the current step along the path.

virtual void SBMStructuralModelPath::setCurrentStep (
    unsigned int currentStep
)

function setEnergy#

Sets the energy for a specific step .

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

function setEnergyData#

Sets the energy data.

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

function setForce [1/2]#

Sets the force of atom atomIndex toforce for a specificstep .

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

function setForce [2/2]#

Sets the force of atom atom toforce for a specificstep .

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

function setForceData#

Sets the force data.

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

function setForwardFlag#

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

virtual void SBMStructuralModelPath::setForwardFlag (
    bool forwardFlag
)

function setPosition [1/2]#

Sets the position of atom atomIndex toposition for a specificstep .

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

function setPosition [2/2]#

Sets the position of atom atom toposition for a specificstep .

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

function setPositionData#

Sets the position data.

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

function setSmoothingWindowSize#

Sets the size of the smoothing window.

virtual void SBMStructuralModelPath::setSmoothingWindowSize (
    unsigned int smoothingWindowSize
)

function setStepDuration#

Sets the step duration.

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

function setStride#

Sets the animation stride.

virtual void SBMStructuralModelPath::setStride (
    unsigned int stride
)

function setTime#

Sets the time for a specific step .

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

function setTimeData#

Sets the time data.

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

function setVelocity [1/2]#

Sets the velocity of atom atomIndex tovelocity for a specificstep .

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

function setVelocity [2/2]#

Sets the velocity of atom atom tovelocity for a specificstep .

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

function setVelocityData#

Sets the velocity data.

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

function unserialize#

Unserializes the path.

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

Implements SBDDataGraphNode::unserialize

function updateState#

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

virtual void SBMStructuralModelPath::updateState ()

function ~SBMStructuralModelPath#

Destructs the path.

virtual SBMStructuralModelPath::~SBMStructuralModelPath ()