class describing a molecule More...

#include <vtkMolecule.h>

Inheritance diagram for vtkMolecule:

Collaboration diagram for vtkMolecule:

Public Types
typedef vtkUndirectedGraph	Superclass

Public Types inherited from vtkUndirectedGraph
typedef vtkGraph	Superclass

Public Types inherited from vtkGraph
typedef vtkDataObject	Superclass

Public Types inherited from vtkDataObject
enum	FieldAssociations { FIELD_ASSOCIATION_POINTS , FIELD_ASSOCIATION_CELLS , FIELD_ASSOCIATION_NONE , FIELD_ASSOCIATION_POINTS_THEN_CELLS , FIELD_ASSOCIATION_VERTICES , FIELD_ASSOCIATION_EDGES , FIELD_ASSOCIATION_ROWS , NUMBER_OF_ASSOCIATIONS }
	Possible values for the FIELD_ASSOCIATION information entry. More...

enum	AttributeTypes { POINT , CELL , FIELD , POINT_THEN_CELL , VERTEX , EDGE , ROW , NUMBER_OF_ATTRIBUTE_TYPES }
	Possible attribute types. More...

enum	FieldOperations { FIELD_OPERATION_PRESERVED , FIELD_OPERATION_REINTERPOLATED , FIELD_OPERATION_MODIFIED , FIELD_OPERATION_REMOVED }
	Possible values for the FIELD_OPERATION information entry. More...

typedef vtkObject	Superclass

Public Member Functions
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkMolecule *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

void	Initialize () override
	Initialize to an empty graph.

int	GetDataObjectType () override
	Return what type of dataset this is.

vtkAtom	AppendAtom ()
	Add new atom with atomic number 0 (dummy atom) at origin.

vtkAtom	GetAtom (vtkIdType atomId)
	Return a vtkAtom that refers to the atom with the specified id.

vtkIdType	GetNumberOfAtoms ()
	Return the number of atoms in the molecule.

vtkBond	GetBond (vtkIdType bondId)
	Return a vtkAtom that refers to the bond with the specified id.

vtkIdType	GetNumberOfBonds ()
	Return the number of bonds in the molecule.

unsigned short	GetAtomAtomicNumber (vtkIdType atomId)
	Return the atomic number of the atom with the specified id.

void	SetAtomAtomicNumber (vtkIdType atomId, unsigned short atomicNum)
	Set the atomic number of the atom with the specified id.

double	GetBondLength (vtkIdType bondId)
	Get the bond length of the bond with the specified id.

bool	CheckedShallowCopy (vtkGraph *g) override
	Performs the same operation as ShallowCopy(), but instead of reporting an error for an incompatible graph, returns false.

bool	CheckedDeepCopy (vtkGraph *g) override
	Performs the same operation as DeepCopy(), but instead of reporting an error for an incompatible graph, returns false.

void	ShallowCopy (vtkDataObject *obj) override
	Shallow copies the data object into this molecule.

void	DeepCopy (vtkDataObject *obj) override
	Deep copies the data object into this molecule.

virtual void	ShallowCopyStructure (vtkMolecule *m)
	Shallow copies the atoms and bonds from m into this.

virtual void	DeepCopyStructure (vtkMolecule *m)
	Deep copies the atoms and bonds from m into this.

virtual void	ShallowCopyAttributes (vtkMolecule *m)
	Shallow copies attributes (i.e.

virtual void	DeepCopyAttributes (vtkMolecule *m)
	Deep copies attributes (i.e.

bool	HasLattice ()
	Return true if a unit cell lattice is defined.

void	ClearLattice ()
	Remove any unit cell lattice information from the molecule.

vtkMatrix3x3 *	GetLattice ()
	Get the unit cell lattice vectors.

vtkUnsignedCharArray *	GetAtomGhostArray ()
	Get the array that defines the ghost type of each atom.

void	AllocateAtomGhostArray ()
	Allocate ghost array for atoms.

vtkUnsignedCharArray *	GetBondGhostArray ()
	Get the array that defines the ghost type of each bond.

void	AllocateBondGhostArray ()
	Allocate ghost array for bonds.

int	Initialize (vtkPoints atomPositions, vtkDataArray atomicNumberArray, vtkDataSetAttributes *atomData)
	Initialize a molecule with an atom per input point.

int	Initialize (vtkPoints atomPositions, vtkDataSetAttributes atomData)
	Overloads Initialize method.

int	Initialize (vtkMolecule *molecule)
	Use input molecule points, atomic number and atomic data to initialize the new molecule.

vtkDataSetAttributes *	GetAtomData ()
	Return the VertexData of the underlying graph.

vtkDataSetAttributes *	GetBondData ()
	Return the EdgeData of the underlying graph.

vtkIdType	GetBondId (vtkIdType a, vtkIdType b)
	Return the edge id from the underlying graph.

unsigned long	GetActualMemorySize () override
	Return the actual size of the data in kibibytes (1024 bytes).


vtkAtom	AppendAtom (unsigned short atomicNumber, double x, double y, double z)
	Add new atom with the specified atomic number and position.

vtkAtom	AppendAtom (unsigned short atomicNumber, const vtkVector3f &pos)
	Add new atom with the specified atomic number and position.

vtkAtom	AppendAtom (unsigned short atomicNumber, double pos[3])
	Add new atom with the specified atomic number and position.


vtkBond	AppendBond (vtkIdType atom1, vtkIdType atom2, unsigned short order=1)
	Add a bond between the specified atoms, optionally setting the bond order (default: 1).

vtkBond	AppendBond (const vtkAtom &atom1, const vtkAtom &atom2, unsigned short order=1)
	Add a bond between the specified atoms, optionally setting the bond order (default: 1).


void	SetAtomPosition (vtkIdType atomId, const vtkVector3f &pos)
	Set the position of the atom with the specified id.

void	SetAtomPosition (vtkIdType atomId, double x, double y, double z)
	Set the position of the atom with the specified id.

void	SetAtomPosition (vtkIdType atomId, double pos[3])
	Set the position of the atom with the specified id.


vtkVector3f	GetAtomPosition (vtkIdType atomId)
	Get the position of the atom with the specified id.

void	GetAtomPosition (vtkIdType atomId, float pos[3])
	Get the position of the atom with the specified id.

void	GetAtomPosition (vtkIdType atomId, double pos[3])
	Get the position of the atom with the specified id.


void	SetBondOrder (vtkIdType bondId, unsigned short order)
	Get/Set the bond order of the bond with the specified id.

unsigned short	GetBondOrder (vtkIdType bondId)
	Get/Set the bond order of the bond with the specified id.


vtkPoints *	GetAtomicPositionArray ()
	Access the raw arrays used in this vtkMolecule instance.

vtkUnsignedShortArray *	GetAtomicNumberArray ()
	Access the raw arrays used in this vtkMolecule instance.

vtkUnsignedShortArray *	GetBondOrdersArray ()
	Access the raw arrays used in this vtkMolecule instance.


virtual vtkAbstractElectronicData *	GetElectronicData ()
	Set/Get the AbstractElectronicData-subclassed object for this molecule.

virtual void	SetElectronicData (vtkAbstractElectronicData *)
	Set/Get the AbstractElectronicData-subclassed object for this molecule.


void	SetLattice (vtkMatrix3x3 *matrix)
	The unit cell vectors.

void	SetLattice (const vtkVector3d &a, const vtkVector3d &b, const vtkVector3d &c)
	The unit cell vectors.


void	GetLattice (vtkVector3d &a, vtkVector3d &b, vtkVector3d &c)
	Get the unit cell lattice vectors, and optionally, the origin.

void	GetLattice (vtkVector3d &a, vtkVector3d &b, vtkVector3d &c, vtkVector3d &origin)
	Get the unit cell lattice vectors, and optionally, the origin.


virtual vtkVector3d	GetLatticeOrigin ()
	Get the unit cell origin (for rendering purposes).

virtual void	SetLatticeOrigin (vtkVector3d)
	Get the unit cell origin (for rendering purposes).


virtual void	SetAtomicNumberArrayName (const char *)
	Get/Set the atomic number array name.

virtual char *	GetAtomicNumberArrayName ()
	Get/Set the atomic number array name.


virtual void	SetBondOrdersArrayName (const char *)
	Get/Set the bond orders array name.

virtual char *	GetBondOrdersArrayName ()
	Get/Set the bond orders array name.

Public Member Functions inherited from vtkUndirectedGraph
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkUndirectedGraph *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

int	GetDataObjectType () override
	Return what type of dataset this is.

vtkIdType	GetInDegree (vtkIdType v) override
	Returns the full degree of the vertex.

vtkInEdgeType	GetInEdge (vtkIdType v, vtkIdType i) override
	Random-access method for retrieving the in edges of a vertex.

void	GetInEdge (vtkIdType v, vtkIdType i, vtkGraphEdge *e) override
	Random-access method for retrieving incoming edges to vertex v.

void	GetInEdges (vtkIdType v, vtkInEdgeIterator *it) override
	Initialize the iterator to get the incoming edges to a vertex.

bool	IsStructureValid (vtkGraph *g) override
	Check the structure, and accept it if it is a valid undirected graph.

Public Member Functions inherited from vtkGraph
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkGraph *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

int	GetDataObjectType () override
	Return what type of dataset this is.

void	Initialize () override
	Initialize to an empty graph.

void	ComputeBounds ()
	Compute the bounds of the graph.

vtkMTimeType	GetMTime () override
	The modified time of the graph.

virtual void	GetOutEdges (vtkIdType v, vtkOutEdgeIterator *it)
	Initializes the out edge iterator to iterate over all outgoing edges of vertex v.

virtual vtkIdType	GetDegree (vtkIdType v)
	The total of all incoming and outgoing vertices for vertex v.

virtual vtkIdType	GetOutDegree (vtkIdType v)
	The number of outgoing edges from vertex v.

virtual vtkOutEdgeType	GetOutEdge (vtkIdType v, vtkIdType index)
	Random-access method for retrieving outgoing edges from vertex v.

virtual void	GetOutEdge (vtkIdType v, vtkIdType index, vtkGraphEdge *e)
	Random-access method for retrieving outgoing edges from vertex v.

virtual void	GetInEdges (vtkIdType v, vtkInEdgeIterator *it)
	Initializes the in edge iterator to iterate over all incoming edges to vertex v.

virtual vtkIdType	GetInDegree (vtkIdType v)
	The number of incoming edges to vertex v.

virtual vtkInEdgeType	GetInEdge (vtkIdType v, vtkIdType index)
	Random-access method for retrieving incoming edges to vertex v.

virtual void	GetInEdge (vtkIdType v, vtkIdType index, vtkGraphEdge *e)
	Random-access method for retrieving incoming edges to vertex v.

virtual void	GetAdjacentVertices (vtkIdType v, vtkAdjacentVertexIterator *it)
	Initializes the adjacent vertex iterator to iterate over all outgoing vertices from vertex v.

virtual void	GetEdges (vtkEdgeListIterator *it)
	Initializes the edge list iterator to iterate over all edges in the graph.

virtual vtkIdType	GetNumberOfEdges ()
	The number of edges in the graph.

virtual void	GetVertices (vtkVertexListIterator *it)
	Initializes the vertex list iterator to iterate over all vertices in the graph.

virtual vtkIdType	GetNumberOfVertices ()
	The number of vertices in the graph.

void	SetDistributedGraphHelper (vtkDistributedGraphHelper *helper)
	Sets the distributed graph helper of this graph, turning it into a distributed graph.

vtkDistributedGraphHelper *	GetDistributedGraphHelper ()
	Retrieves the distributed graph helper for this graph.

vtkIdType	FindVertex (const vtkVariant &pedigreeID)
	Retrieve the vertex with the given pedigree ID.

void	ShallowCopy (vtkDataObject *obj) override
	Shallow copies the data object into this graph.

void	DeepCopy (vtkDataObject *obj) override
	Deep copies the data object into this graph.

virtual void	CopyStructure (vtkGraph *g)
	Does a shallow copy of the topological information, but not the associated attributes.

virtual bool	CheckedShallowCopy (vtkGraph *g)
	Performs the same operation as ShallowCopy(), but instead of reporting an error for an incompatible graph, returns false.

virtual bool	CheckedDeepCopy (vtkGraph *g)
	Performs the same operation as DeepCopy(), but instead of reporting an error for an incompatible graph, returns false.

virtual void	Squeeze ()
	Reclaim unused memory.

unsigned long	GetActualMemorySize () override
	Return the actual size of the data in kibibytes (1024 bytes).

void	ReorderOutVertices (vtkIdType v, vtkIdTypeArray *vertices)
	Reorder the outgoing vertices of a vertex.

bool	IsSameStructure (vtkGraph *other)
	Returns true if both graphs point to the same adjacency structure.

vtkIdType	GetNumberOfEdgePoints (vtkIdType e)
	Get the number of edge points associated with an edge.

double *	GetEdgePoint (vtkIdType e, vtkIdType i)
	Get the x,y,z location of a point along edge e.

void	ClearEdgePoints (vtkIdType e)
	Clear all points associated with an edge.

void	SetEdgePoint (vtkIdType e, vtkIdType i, const double x[3])
	Set an x,y,z location of a point along an edge.

void	SetEdgePoint (vtkIdType e, vtkIdType i, double x, double y, double z)

void	AddEdgePoint (vtkIdType e, const double x[3])
	Adds a point to the end of the list of edge points for a certain edge.

void	AddEdgePoint (vtkIdType e, double x, double y, double z)

vtkGraphInternals *	GetGraphInternals (bool modifying)
	Returns the internal representation of the graph.

void	GetInducedEdges (vtkIdTypeArray verts, vtkIdTypeArray edges)
	Fills a list of edge indices with the edges contained in the induced subgraph formed by the vertices in the vertex list.

vtkFieldData *	GetAttributesAsFieldData (int type) override
	Returns the attributes of the data object as a vtkFieldData.

vtkIdType	GetNumberOfElements (int type) override
	Get the number of elements for a specific attribute type (VERTEX, EDGE, etc.).

void	Dump ()
	Dump the contents of the graph to standard output.

vtkIdType	GetEdgeId (vtkIdType a, vtkIdType b)
	Returns the Id of the edge between vertex a and vertex b.

bool	ToDirectedGraph (vtkDirectedGraph *g)
	Convert the graph to a directed graph.

bool	ToUndirectedGraph (vtkUndirectedGraph *g)
	Convert the graph to an undirected graph.

virtual vtkDataSetAttributes *	GetVertexData ()
	Get the vertex or edge data.

virtual vtkDataSetAttributes *	GetEdgeData ()
	Get the vertex or edge data.

double *	GetPoint (vtkIdType ptId)
	These methods return the point (0,0,0) until the points structure is created, when it returns the actual point position.

void	GetPoint (vtkIdType ptId, double x[3])
	These methods return the point (0,0,0) until the points structure is created, when it returns the actual point position.

vtkPoints *	GetPoints ()
	Returns the points array for this graph.

virtual void	SetPoints (vtkPoints *points)
	Returns the points array for this graph.

double *	GetBounds ()
	Return a pointer to the geometry bounding box in the form (xmin,xmax, ymin,ymax, zmin,zmax).

void	GetBounds (double bounds[6])
	Return a pointer to the geometry bounding box in the form (xmin,xmax, ymin,ymax, zmin,zmax).

vtkIdType	GetSourceVertex (vtkIdType e)
	Retrieve the source and target vertices for an edge id.

vtkIdType	GetTargetVertex (vtkIdType e)
	Retrieve the source and target vertices for an edge id.

void	SetEdgePoints (vtkIdType e, vtkIdType npts, const double pts[])
	Get/Set the internal edge control points associated with each edge.

void	GetEdgePoints (vtkIdType e, vtkIdType &npts, double *&pts)
	Get/Set the internal edge control points associated with each edge.

void	ShallowCopyEdgePoints (vtkGraph *g)
	Copy the internal edge point data from another graph into this graph.

void	DeepCopyEdgePoints (vtkGraph *g)
	Copy the internal edge point data from another graph into this graph.

Public Member Functions inherited from vtkDataObject
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkDataObject *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

vtkMTimeType	GetMTime () override
	Data objects are composite objects and need to check each part for MTime.

virtual void	Initialize ()
	Restore data object to initial state,.

void	ReleaseData ()
	Release data back to system to conserve memory resource.

virtual int	GetDataObjectType ()
	Return class name of data type.

vtkMTimeType	GetUpdateTime ()
	Used by Threaded ports to determine if they should initiate an asynchronous update (still in development).

virtual unsigned long	GetActualMemorySize ()
	Return the actual size of the data in kibibytes (1024 bytes).

virtual void	CopyInformationFromPipeline (vtkInformation *vtkNotUsed(info))
	Copy from the pipeline information to the data object's own information.

virtual void	CopyInformationToPipeline (vtkInformation *vtkNotUsed(info))
	Copy information from this data object to the pipeline information.

void	DataHasBeenGenerated ()
	This method is called by the source when it executes to generate data.

virtual void	PrepareForNewData ()
	make the output data ready for new data to be inserted.

virtual void	ShallowCopy (vtkDataObject *src)
	The goal of the method is to copy the data up to the array pointers only.

virtual void	DeepCopy (vtkDataObject *src)
	The goal of the method is to copy the complete data from src into this object.

virtual int	GetExtentType ()
	The ExtentType will be left as VTK_PIECES_EXTENT for data objects such as vtkPolyData and vtkUnstructuredGrid.

virtual void	Crop (const int *updateExtent)
	This method crops the data object (if necessary) so that the extent matches the update extent.

virtual vtkDataSetAttributes *	GetAttributes (int type)
	Returns the attributes of the data object of the specified attribute type.

virtual vtkUnsignedCharArray *	GetGhostArray (int type)
	Returns the ghost arrays of the data object of the specified attribute type.

virtual bool	SupportsGhostArray (int type)
	Returns if this type of data object support ghost array for specified type.

virtual vtkFieldData *	GetAttributesAsFieldData (int type)
	Returns the attributes of the data object as a vtkFieldData.

virtual int	GetAttributeTypeForArray (vtkAbstractArray *arr)
	Retrieves the attribute type that an array came from.

virtual vtkIdType	GetNumberOfElements (int type)
	Get the number of elements for a specific attribute type (POINT, CELL, etc.).

virtual vtkInformation *	GetInformation ()
	Set/Get the information object associated with this data object.

virtual void	SetInformation (vtkInformation *)
	Set/Get the information object associated with this data object.

virtual vtkTypeBool	GetDataReleased ()
	Get the flag indicating the data has been released.

virtual void	SetFieldData (vtkFieldData *)
	Assign or retrieve a general field data to this data object.

virtual vtkFieldData *	GetFieldData ()
	Assign or retrieve a general field data to this data object.

void	GlobalReleaseDataFlagOn ()
	Turn on/off flag to control whether every object releases its data after being used by a filter.

void	GlobalReleaseDataFlagOff ()
	Turn on/off flag to control whether every object releases its data after being used by a filter.

Public Member Functions inherited from vtkObject
	vtkBaseTypeMacro (vtkObject, vtkObjectBase)

virtual void	DebugOn ()
	Turn debugging output on.

virtual void	DebugOff ()
	Turn debugging output off.

bool	GetDebug ()
	Get the value of the debug flag.

void	SetDebug (bool debugFlag)
	Set the value of the debug flag.

virtual void	Modified ()
	Update the modification time for this object.

virtual vtkMTimeType	GetMTime ()
	Return this object's modified time.

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

void	RemoveObserver (unsigned long tag)

void	RemoveObservers (unsigned long event)

void	RemoveObservers (const char *event)

void	RemoveAllObservers ()

vtkTypeBool	HasObserver (unsigned long event)

vtkTypeBool	HasObserver (const char *event)

vtkTypeBool	InvokeEvent (unsigned long event)

vtkTypeBool	InvokeEvent (const char *event)

std::string	GetObjectDescription () const override
	The object description printed in messages and PrintSelf output.

unsigned long	AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

unsigned long	AddObserver (const char event, vtkCommand , float priority=0.0f)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

vtkCommand *	GetCommand (unsigned long tag)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

void	RemoveObserver (vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

void	RemoveObservers (unsigned long event, vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

void	RemoveObservers (const char event, vtkCommand )
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

vtkTypeBool	HasObserver (unsigned long event, vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

vtkTypeBool	HasObserver (const char event, vtkCommand )
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::*callback)(), float priority=0.0f)
	Overloads to AddObserver that allow developers to add class member functions as callbacks for events.

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)
	Overloads to AddObserver that allow developers to add class member functions as callbacks for events.

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, bool(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)
	Allow user to set the AbortFlagOn() with the return value of the callback method.

vtkTypeBool	InvokeEvent (unsigned long event, void *callData)
	This method invokes an event and return whether the event was aborted or not.

vtkTypeBool	InvokeEvent (const char event, void callData)
	This method invokes an event and return whether the event was aborted or not.

virtual void	SetObjectName (const std::string &objectName)
	Set/get the name of this object for reporting purposes.

virtual std::string	GetObjectName () const
	Set/get the name of this object for reporting purposes.

Public Member Functions inherited from vtkObjectBase
const char *	GetClassName () const
	Return the class name as a string.

virtual std::string	GetObjectDescription () const
	The object description printed in messages and PrintSelf output.

virtual vtkTypeBool	IsA (const char *name)
	Return 1 if this class is the same type of (or a subclass of) the named class.

virtual vtkIdType	GetNumberOfGenerationsFromBase (const char *name)
	Given the name of a base class of this class type, return the distance of inheritance between this class type and the named class (how many generations of inheritance are there between this class and the named class).

virtual void	Delete ()
	Delete a VTK object.

virtual void	FastDelete ()
	Delete a reference to this object.

void	InitializeObjectBase ()

void	Print (ostream &os)
	Print an object to an ostream.

void	Register (vtkObjectBase *o)
	Increase the reference count (mark as used by another object).

virtual void	UnRegister (vtkObjectBase *o)
	Decrease the reference count (release by another object).

int	GetReferenceCount ()
	Return the current reference count of this object.

void	SetReferenceCount (int)
	Sets the reference count.

bool	GetIsInMemkind () const
	A local state flag that remembers whether this object lives in the normal or extended memory space.

virtual void	PrintHeader (ostream &os, vtkIndent indent)
	Methods invoked by print to print information about the object including superclasses.

virtual void	PrintTrailer (ostream &os, vtkIndent indent)
	Methods invoked by print to print information about the object including superclasses.

virtual bool	UsesGarbageCollector () const
	Indicate whether the class uses `vtkGarbageCollector` or not.

Static Public Member Functions
static vtkMolecule *	New ()

static vtkTypeBool	IsTypeOf (const char *type)

static vtkMolecule *	SafeDownCast (vtkObjectBase *o)


static bool	GetPlaneFromBond (const vtkBond &bond, const vtkVector3f &normal, vtkPlane *plane)
	Obtain the plane that passes through the indicated bond with the given normal.

static bool	GetPlaneFromBond (const vtkAtom &atom1, const vtkAtom &atom2, const vtkVector3f &normal, vtkPlane *plane)
	Obtain the plane that passes through the indicated bond with the given normal.


static vtkMolecule *	GetData (vtkInformation *info)
	Retrieve a molecule from an information vector.

static vtkMolecule *	GetData (vtkInformationVector *v, int i=0)
	Retrieve a molecule from an information vector.

Static Public Member Functions inherited from vtkUndirectedGraph
static vtkUndirectedGraph *	New ()

static vtkTypeBool	IsTypeOf (const char *type)

static vtkUndirectedGraph *	SafeDownCast (vtkObjectBase *o)

static vtkUndirectedGraph *	GetData (vtkInformation *info)
	Retrieve a graph from an information vector.

static vtkUndirectedGraph *	GetData (vtkInformationVector *v, int i=0)
	Retrieve a graph from an information vector.

Static Public Member Functions inherited from vtkGraph
static vtkTypeBool	IsTypeOf (const char *type)

static vtkGraph *	SafeDownCast (vtkObjectBase *o)

static vtkGraph *	GetData (vtkInformation *info)
	Retrieve a graph from an information vector.

static vtkGraph *	GetData (vtkInformationVector *v, int i=0)
	Retrieve a graph from an information vector.

Static Public Member Functions inherited from vtkDataObject
static vtkDataObject *	New ()

static vtkTypeBool	IsTypeOf (const char *type)

static vtkDataObject *	SafeDownCast (vtkObjectBase *o)

static vtkInformation *	GetActiveFieldInformation (vtkInformation *info, int fieldAssociation, int attributeType)
	Return the information object within the input information object's field data corresponding to the specified association (FIELD_ASSOCIATION_POINTS or FIELD_ASSOCIATION_CELLS) and attribute (SCALARS, VECTORS, NORMALS, TCOORDS, or TENSORS)

static vtkInformation *	GetNamedFieldInformation (vtkInformation info, int fieldAssociation, const char name)
	Return the information object within the input information object's field data corresponding to the specified association (FIELD_ASSOCIATION_POINTS or FIELD_ASSOCIATION_CELLS) and name.

static void	RemoveNamedFieldInformation (vtkInformation info, int fieldAssociation, const char name)
	Remove the info associated with an array.

static vtkInformation *	SetActiveAttribute (vtkInformation info, int fieldAssociation, const char attributeName, int attributeType)
	Set the named array to be the active field for the specified type (SCALARS, VECTORS, NORMALS, TCOORDS, or TENSORS) and association (FIELD_ASSOCIATION_POINTS or FIELD_ASSOCIATION_CELLS).

static void	SetActiveAttributeInfo (vtkInformation info, int fieldAssociation, int attributeType, const char name, int arrayType, int numComponents, int numTuples)
	Set the name, array type, number of components, and number of tuples within the passed information object for the active attribute of type attributeType (in specified association, FIELD_ASSOCIATION_POINTS or FIELD_ASSOCIATION_CELLS).

static void	SetPointDataActiveScalarInfo (vtkInformation *info, int arrayType, int numComponents)
	Convenience version of previous method for use (primarily) by the Imaging filters.

static const char *	GetAssociationTypeAsString (int associationType)
	Given an integer association type, this static method returns a string type for the attribute (i.e.

static int	GetAssociationTypeFromString (const char *associationName)
	Given a string association name, this static method returns an integer association type for the attribute (i.e.

static vtkInformationStringKey *	DATA_TYPE_NAME ()

static vtkInformationDataObjectKey *	DATA_OBJECT ()

static vtkInformationIntegerKey *	DATA_EXTENT_TYPE ()

static vtkInformationIntegerPointerKey *	DATA_EXTENT ()

static vtkInformationIntegerVectorKey *	ALL_PIECES_EXTENT ()

static vtkInformationIntegerKey *	DATA_PIECE_NUMBER ()

static vtkInformationIntegerKey *	DATA_NUMBER_OF_PIECES ()

static vtkInformationIntegerKey *	DATA_NUMBER_OF_GHOST_LEVELS ()

static vtkInformationDoubleKey *	DATA_TIME_STEP ()

static vtkInformationInformationVectorKey *	POINT_DATA_VECTOR ()

static vtkInformationInformationVectorKey *	CELL_DATA_VECTOR ()

static vtkInformationInformationVectorKey *	VERTEX_DATA_VECTOR ()

static vtkInformationInformationVectorKey *	EDGE_DATA_VECTOR ()

static vtkInformationIntegerKey *	FIELD_ARRAY_TYPE ()

static vtkInformationIntegerKey *	FIELD_ASSOCIATION ()

static vtkInformationIntegerKey *	FIELD_ATTRIBUTE_TYPE ()

static vtkInformationIntegerKey *	FIELD_ACTIVE_ATTRIBUTE ()

static vtkInformationIntegerKey *	FIELD_NUMBER_OF_COMPONENTS ()

static vtkInformationIntegerKey *	FIELD_NUMBER_OF_TUPLES ()

static vtkInformationIntegerKey *	FIELD_OPERATION ()

static vtkInformationDoubleVectorKey *	FIELD_RANGE ()

static vtkInformationIntegerVectorKey *	PIECE_EXTENT ()

static vtkInformationStringKey *	FIELD_NAME ()

static vtkInformationDoubleVectorKey *	ORIGIN ()

static vtkInformationDoubleVectorKey *	SPACING ()

static vtkInformationDoubleVectorKey *	DIRECTION ()

static vtkInformationDoubleVectorKey *	BOUNDING_BOX ()

static vtkInformationDataObjectKey *	SIL ()

static vtkDataObject *	GetData (vtkInformation *info)
	Retrieve an instance of this class from an information object.

static vtkDataObject *	GetData (vtkInformationVector *v, int i=0)
	Retrieve an instance of this class from an information object.

static void	SetGlobalReleaseDataFlag (vtkTypeBool val)
	Turn on/off flag to control whether every object releases its data after being used by a filter.

static vtkTypeBool	GetGlobalReleaseDataFlag ()
	Turn on/off flag to control whether every object releases its data after being used by a filter.

Static Public Member Functions inherited from vtkObject
static vtkObject *	New ()
	Create an object with Debug turned off, modified time initialized to zero, and reference counting on.

static void	BreakOnError ()
	This method is called when vtkErrorMacro executes.

static void	SetGlobalWarningDisplay (vtkTypeBool val)
	This is a global flag that controls whether any debug, warning or error messages are displayed.

static void	GlobalWarningDisplayOn ()
	This is a global flag that controls whether any debug, warning or error messages are displayed.

static void	GlobalWarningDisplayOff ()
	This is a global flag that controls whether any debug, warning or error messages are displayed.

static vtkTypeBool	GetGlobalWarningDisplay ()
	This is a global flag that controls whether any debug, warning or error messages are displayed.

Static Public Member Functions inherited from vtkObjectBase
static vtkTypeBool	IsTypeOf (const char *name)
	Return 1 if this class type is the same type of (or a subclass of) the named class.

static vtkIdType	GetNumberOfGenerationsFromBaseType (const char *name)
	Given a the name of a base class of this class type, return the distance of inheritance between this class type and the named class (how many generations of inheritance are there between this class and the named class).

static vtkObjectBase *	New ()
	Create an object with Debug turned off, modified time initialized to zero, and reference counting on.

static void	SetMemkindDirectory (const char *directoryname)
	The name of a directory, ideally mounted -o dax, to memory map an extended memory space within.

static bool	GetUsingMemkind ()
	A global state flag that controls whether vtkObjects are constructed in the usual way (the default) or within the extended memory space.

Protected Member Functions
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkMolecule ()

	~vtkMolecule () override

virtual void	CopyStructureInternal (vtkMolecule *m, bool deep)
	Copy bonds and atoms.

virtual void	CopyAttributesInternal (vtkMolecule *m, bool deep)
	Copy everything but bonds and atoms.

Protected Member Functions inherited from vtkUndirectedGraph
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkUndirectedGraph ()

	~vtkUndirectedGraph () override

void	GetInEdges (vtkIdType v, const vtkInEdgeType *&edges, vtkIdType &nedges) override
	For iterators, returns the same edge list as GetOutEdges().

Protected Member Functions inherited from vtkGraph
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkGraph ()

	~vtkGraph () override

void	AddVertexInternal (vtkVariantArray propertyArr=nullptr, vtkIdType vertex=nullptr)
	Protected method for adding vertices, optionally with properties, used by mutable subclasses.

void	AddVertexInternal (const vtkVariant &pedigree, vtkIdType *vertex)
	Adds a vertex with the given pedigree ID to the graph.

void	RemoveVertexInternal (vtkIdType v, bool directed)
	Removes a vertex from the graph, along with any adjacent edges.

void	RemoveEdgeInternal (vtkIdType e, bool directed)
	Removes an edge from the graph.

void	RemoveVerticesInternal (vtkIdTypeArray *arr, bool directed)
	Removes a collection of vertices from the graph, along with any adjacent edges.

void	RemoveEdgesInternal (vtkIdTypeArray *arr, bool directed)
	Removes a collection of edges from the graph.

virtual bool	IsStructureValid (vtkGraph *g)=0
	Subclasses override this method to accept the structure based on their requirements.

virtual void	CopyInternal (vtkGraph *g, bool deep)
	Copy internal data structure.

void	SetInternals (vtkGraphInternals *internals)
	Private method for setting internals.

void	SetEdgePoints (vtkGraphEdgePoints *edgePoints)
	Private method for setting edge points.

void	ForceOwnership ()
	If this instance does not own its internals, it makes a copy of the internals.

void	BuildEdgeList ()
	Builds a mapping from edge id to source/target vertex id.

void	AddEdgeInternal (vtkIdType u, vtkIdType v, bool directed, vtkVariantArray propertyArr, vtkEdgeType edge)
	Protected method for adding edges of a certain directedness used by mutable subclasses.

void	AddEdgeInternal (const vtkVariant &uPedigree, vtkIdType v, bool directed, vtkVariantArray propertyArr, vtkEdgeType edge)
	Protected method for adding edges of a certain directedness used by mutable subclasses.

void	AddEdgeInternal (vtkIdType u, const vtkVariant &vPedigree, bool directed, vtkVariantArray propertyArr, vtkEdgeType edge)
	Protected method for adding edges of a certain directedness used by mutable subclasses.

void	AddEdgeInternal (const vtkVariant &uPedigree, const vtkVariant &vPedigree, bool directed, vtkVariantArray propertyArr, vtkEdgeType edge)
	Protected method for adding edges of a certain directedness used by mutable subclasses.

virtual void	GetOutEdges (vtkIdType v, const vtkOutEdgeType *&edges, vtkIdType &nedges)
	Fast access functions for iterators.

virtual vtkIdTypeArray *	GetEdgeList ()
	The optional mapping from edge id to source/target ids.

virtual void	SetEdgeList (vtkIdTypeArray *list)
	The optional mapping from edge id to source/target ids.

Protected Member Functions inherited from vtkDataObject
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkDataObject ()

	~vtkDataObject () override

Protected Member Functions inherited from vtkObject
	vtkObject ()

	~vtkObject () override

void	RegisterInternal (vtkObjectBase *, vtkTypeBool check) override

void	UnRegisterInternal (vtkObjectBase *, vtkTypeBool check) override

void	InternalGrabFocus (vtkCommand mouseEvents, vtkCommand keypressEvents=nullptr)
	These methods allow a command to exclusively grab all events.

void	InternalReleaseFocus ()
	These methods allow a command to exclusively grab all events.

Protected Member Functions inherited from vtkObjectBase
	vtkObjectBase ()

virtual	~vtkObjectBase ()

virtual void	RegisterInternal (vtkObjectBase *, vtkTypeBool check)

virtual void	UnRegisterInternal (vtkObjectBase *, vtkTypeBool check)

virtual void	ReportReferences (vtkGarbageCollector *)

virtual void	ObjectFinalize ()

	vtkObjectBase (const vtkObjectBase &)

void	operator= (const vtkObjectBase &)

Protected Attributes
vtkAbstractElectronicData *	ElectronicData

vtkSmartPointer< vtkMatrix3x3 >	Lattice

vtkVector3d	LatticeOrigin

vtkUnsignedCharArray *	AtomGhostArray

vtkUnsignedCharArray *	BondGhostArray

char *	AtomicNumberArrayName

char *	BondOrdersArrayName

Protected Attributes inherited from vtkGraph
vtkGraphInternals *	Internals
	The adjacency list internals of this graph.

vtkDistributedGraphHelper *	DistributedHelper
	The distributed graph helper.

vtkGraphEdgePoints *	EdgePoints
	The structure for holding the edge points.

double	Bounds [6]
	(xmin,xmax, ymin,ymax, zmin,zmax) geometric bounds.

vtkTimeStamp	ComputeTime
	Time at which bounds were computed.

vtkDataSetAttributes *	VertexData
	The vertex and edge data.

vtkDataSetAttributes *	EdgeData
	The vertex and edge data.

vtkPoints *	Points
	The vertex locations.

vtkIdTypeArray *	EdgeList
	The optional mapping from edge id to source/target ids.

Protected Attributes inherited from vtkDataObject
vtkFieldData *	FieldData

vtkTypeBool	DataReleased

vtkTimeStamp	UpdateTime

vtkInformation *	Information

Protected Attributes inherited from vtkObject
bool	Debug

vtkTimeStamp	MTime

vtkSubjectHelper *	SubjectHelper

std::string	ObjectName

Protected Attributes inherited from vtkObjectBase
std::atomic< int32_t >	ReferenceCount

vtkWeakPointerBase **	WeakPointers

Friends
class	vtkAtom

class	vtkBond

bool	BondListIsDirty
	The graph superclass does not provide fast random access to the edge (bond) data.

void	SetBondListDirty ()
	The graph superclass does not provide fast random access to the edge (bond) data.

void	UpdateBondList ()
	The graph superclass does not provide fast random access to the edge (bond) data.

vtkIdTypeArray *	GetBondList ()
	The graph superclass does not provide fast random access to the edge (bond) data.

Additional Inherited Members
Static Protected Member Functions inherited from vtkObjectBase
static vtkMallocingFunction	GetCurrentMallocFunction ()

static vtkReallocingFunction	GetCurrentReallocFunction ()

static vtkFreeingFunction	GetCurrentFreeFunction ()

static vtkFreeingFunction	GetAlternateFreeFunction ()

Static Protected Attributes inherited from vtkGraph
static double	DefaultPoint [3]
	The vertex locations.

Detailed Description

class describing a molecule

vtkMolecule and the convenience classes vtkAtom and vtkBond describe the geometry and connectivity of a molecule. The molecule can be constructed using the AppendAtom() and AppendBond() methods in one of two ways; either by fully specifying the atom/bond in a single call, or by incrementally setting the various attributes using the convenience vtkAtom and vtkBond classes:

Single call:

vtkMolecule *mol = vtkMolecule::New();
vtkAtom h1 = mol->AppendAtom(1, 0.0, 0.0, -0.5);
vtkAtom h2 = mol->AppendAtom(1, 0.0, 0.0,  0.5);
vtkBond b  = mol->AppendBond(h1, h2, 1);

Incremental:

vtkMolecule *mol = vtkMolecule::New();
 
vtkAtom h1 = mol->AppendAtom();
h1.SetAtomicNumber(1);
h1.SetPosition(0.0, 0.0, -0.5);
 
vtkAtom h2 = mol->AppendAtom();
h2.SetAtomicNumber(1);
vtkVector3d displacement (0.0, 0.0, 1.0);
h2.SetPosition(h1.GetPositionAsVector3d() + displacement);
 
vtkBond b  = mol->AppendBond(h1, h2, 1);

Both of the above methods will produce the same molecule, two hydrogens connected with a 1.0 Angstrom single bond, aligned to the z-axis. The second example also demonstrates the use of VTK's vtkVector class, which is fully supported by the Chemistry kit.

The vtkMolecule object is intended to be used with the vtkMoleculeMapper class for visualizing molecular structure using common rendering techniques.

Warning: While direct use of the underlying vtkUndirectedGraph structure is possible due to vtkMolecule's public inheritance, this should not be relied upon and may change in the future.

See also: vtkAtom vtkBond vtkMoleculeMapper vtkPeriodicTable

Tests:: vtkMolecule (Tests)

Definition at line 83 of file vtkMolecule.h.

Member Typedef Documentation

◆ Superclass

typedef vtkUndirectedGraph vtkMolecule::Superclass

Definition at line 87 of file vtkMolecule.h.

Constructor & Destructor Documentation

◆ vtkMolecule()

vtkMolecule::vtkMolecule ( )

protected

◆ ~vtkMolecule()

vtkMolecule::~vtkMolecule ( )

overrideprotected

Member Function Documentation

◆ New()

static vtkMolecule * vtkMolecule::New ( )

static

◆ IsTypeOf()

static vtkTypeBool vtkMolecule::IsTypeOf ( const char * type )

static

◆ IsA()

virtual vtkTypeBool vtkMolecule::IsA ( const char * name )

virtual

Return 1 if this class is the same type of (or a subclass of) the named class.

Returns 0 otherwise. This method works in combination with vtkTypeMacro found in vtkSetGet.h.

Reimplemented from vtkUndirectedGraph.

◆ SafeDownCast()

static vtkMolecule * vtkMolecule::SafeDownCast ( vtkObjectBase * o )

static

◆ NewInstanceInternal()

virtual vtkObjectBase * vtkMolecule::NewInstanceInternal ( ) const

protectedvirtual

Reimplemented from vtkUndirectedGraph.

◆ NewInstance()

vtkMolecule * vtkMolecule::NewInstance ( ) const

◆ PrintSelf()

void vtkMolecule::PrintSelf	(	ostream &	os,
		vtkIndent	indent
	)

overridevirtual

Methods invoked by print to print information about the object including superclasses.

Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from vtkGraph.

◆ Initialize() [1/4]

void vtkMolecule::Initialize ( )

overridevirtual

Initialize to an empty graph.

Reimplemented from vtkGraph.

◆ GetDataObjectType()

int vtkMolecule::GetDataObjectType ( )

inlineoverridevirtual

Return what type of dataset this is.

Reimplemented from vtkGraph.

Definition at line 94 of file vtkMolecule.h.

◆ AppendAtom() [1/4]

vtkAtom vtkMolecule::AppendAtom ( )

inline

Add new atom with atomic number 0 (dummy atom) at origin.

Return a vtkAtom that refers to the new atom.

Definition at line 100 of file vtkMolecule.h.

◆ AppendAtom() [2/4]

vtkAtom vtkMolecule::AppendAtom	(	unsigned short	atomicNumber,
		double	x,
		double	y,
		double	z
	)

Add new atom with the specified atomic number and position.

Return a vtkAtom that refers to the new atom.

◆ AppendAtom() [3/4]

vtkAtom vtkMolecule::AppendAtom	(	unsigned short	atomicNumber,
		const vtkVector3f &	pos
	)

inline

Add new atom with the specified atomic number and position.

Return a vtkAtom that refers to the new atom.

Definition at line 108 of file vtkMolecule.h.

◆ AppendAtom() [4/4]

vtkAtom vtkMolecule::AppendAtom	(	unsigned short	atomicNumber,
		double	pos[3]
	)

inline

Add new atom with the specified atomic number and position.

Return a vtkAtom that refers to the new atom.

Definition at line 113 of file vtkMolecule.h.

◆ GetAtom()

vtkAtom vtkMolecule::GetAtom ( vtkIdType atomId )

Return a vtkAtom that refers to the atom with the specified id.

◆ GetNumberOfAtoms()

vtkIdType vtkMolecule::GetNumberOfAtoms ( )

Return the number of atoms in the molecule.

◆ AppendBond() [1/2]

vtkBond vtkMolecule::AppendBond	(	vtkIdType	atom1,
		vtkIdType	atom2,
		unsigned short	order = `1`
	)

Add a bond between the specified atoms, optionally setting the bond order (default: 1).

Return a vtkBond object referring to the new bond.

◆ AppendBond() [2/2]

vtkBond vtkMolecule::AppendBond	(	const vtkAtom &	atom1,
		const vtkAtom &	atom2,
		unsigned short	order = `1`
	)

inline

Add a bond between the specified atoms, optionally setting the bond order (default: 1).

Return a vtkBond object referring to the new bond.

Definition at line 136 of file vtkMolecule.h.

◆ GetBond()

vtkBond vtkMolecule::GetBond ( vtkIdType bondId )

Return a vtkAtom that refers to the bond with the specified id.

◆ GetNumberOfBonds()

vtkIdType vtkMolecule::GetNumberOfBonds ( )

Return the number of bonds in the molecule.

◆ GetAtomAtomicNumber()

unsigned short vtkMolecule::GetAtomAtomicNumber ( vtkIdType atomId )

Return the atomic number of the atom with the specified id.

◆ SetAtomAtomicNumber()

void vtkMolecule::SetAtomAtomicNumber	(	vtkIdType	atomId,
		unsigned short	atomicNum
	)

Set the atomic number of the atom with the specified id.

◆ SetAtomPosition() [1/3]

void vtkMolecule::SetAtomPosition	(	vtkIdType	atomId,
		const vtkVector3f &	pos
	)

Set the position of the atom with the specified id.

◆ SetAtomPosition() [2/3]

void vtkMolecule::SetAtomPosition	(	vtkIdType	atomId,
		double	x,
		double	y,
		double	z
	)

Set the position of the atom with the specified id.

◆ SetAtomPosition() [3/3]

void vtkMolecule::SetAtomPosition	(	vtkIdType	atomId,
		double	pos[3]
	)

inline

Set the position of the atom with the specified id.

Definition at line 168 of file vtkMolecule.h.

◆ GetAtomPosition() [1/3]

vtkVector3f vtkMolecule::GetAtomPosition ( vtkIdType atomId )

Get the position of the atom with the specified id.

◆ GetAtomPosition() [2/3]

void vtkMolecule::GetAtomPosition	(	vtkIdType	atomId,
		float	pos[3]
	)

Get the position of the atom with the specified id.

◆ GetAtomPosition() [3/3]

void vtkMolecule::GetAtomPosition	(	vtkIdType	atomId,
		double	pos[3]
	)

Get the position of the atom with the specified id.

◆ SetBondOrder()

void vtkMolecule::SetBondOrder	(	vtkIdType	bondId,
		unsigned short	order
	)

Get/Set the bond order of the bond with the specified id.

◆ GetBondOrder()

unsigned short vtkMolecule::GetBondOrder ( vtkIdType bondId )

Get/Set the bond order of the bond with the specified id.

◆ GetBondLength()

double vtkMolecule::GetBondLength ( vtkIdType bondId )

Get the bond length of the bond with the specified id.

Note: If the associated vtkBond object is already available, vtkBond::GetBondLength is potentially much faster than this function, as a list of all bonds may need to be constructed to locate the appropriate bond.

See also: UpdateBondList()

◆ GetAtomicPositionArray()

vtkPoints * vtkMolecule::GetAtomicPositionArray ( )

Access the raw arrays used in this vtkMolecule instance.

◆ GetAtomicNumberArray()

vtkUnsignedShortArray * vtkMolecule::GetAtomicNumberArray ( )

Access the raw arrays used in this vtkMolecule instance.

◆ GetBondOrdersArray()

vtkUnsignedShortArray * vtkMolecule::GetBondOrdersArray ( )

Access the raw arrays used in this vtkMolecule instance.

◆ GetElectronicData()

virtual vtkAbstractElectronicData * vtkMolecule::GetElectronicData ( )

virtual

Set/Get the AbstractElectronicData-subclassed object for this molecule.

◆ SetElectronicData()

virtual void vtkMolecule::SetElectronicData ( vtkAbstractElectronicData * )

virtual

Set/Get the AbstractElectronicData-subclassed object for this molecule.

◆ CheckedShallowCopy()

bool vtkMolecule::CheckedShallowCopy ( vtkGraph * g )

overridevirtual

Performs the same operation as ShallowCopy(), but instead of reporting an error for an incompatible graph, returns false.

Reimplemented from vtkGraph.

◆ CheckedDeepCopy()

bool vtkMolecule::CheckedDeepCopy ( vtkGraph * g )

overridevirtual

Performs the same operation as DeepCopy(), but instead of reporting an error for an incompatible graph, returns false.

Reimplemented from vtkGraph.

◆ ShallowCopy()

void vtkMolecule::ShallowCopy ( vtkDataObject * obj )

overridevirtual

Shallow copies the data object into this molecule.

Reimplemented from vtkGraph.

◆ DeepCopy()

void vtkMolecule::DeepCopy ( vtkDataObject * obj )

overridevirtual

Deep copies the data object into this molecule.

Reimplemented from vtkGraph.

◆ ShallowCopyStructure()

virtual void vtkMolecule::ShallowCopyStructure ( vtkMolecule * m )

virtual

Shallow copies the atoms and bonds from m into this.

◆ DeepCopyStructure()

virtual void vtkMolecule::DeepCopyStructure ( vtkMolecule * m )

virtual

Deep copies the atoms and bonds from m into this.

◆ ShallowCopyAttributes()

virtual void vtkMolecule::ShallowCopyAttributes ( vtkMolecule * m )

virtual

Shallow copies attributes (i.e.

everything besides atoms and bonds) from m into this.

◆ DeepCopyAttributes()

virtual void vtkMolecule::DeepCopyAttributes ( vtkMolecule * m )

virtual

Deep copies attributes (i.e.

everything besides atoms and bonds) from m into this.

◆ GetPlaneFromBond() [1/2]

static bool vtkMolecule::GetPlaneFromBond	(	const vtkBond &	bond,
		const vtkVector3f &	normal,
		vtkPlane *	plane
	)

static

Obtain the plane that passes through the indicated bond with the given normal.

If the plane is set successfully, the function returns true.

If the normal is not orthogonal to the bond, a new normal will be constructed in such a way that the plane will be orthogonal to the plane spanned by the bond vector and the input normal vector.

This ensures that the plane passes through the bond, and the normal is more of a "hint" indicating the orientation of the plane.

The new normal (n) is defined as the input normal vector (n_i) minus the projection of itself (proj[n_i]_v) onto the bond vector (v):

* v ^
* |  n = (n_i - proj[n_j]_v)
* proj[n_i]_v ^  |----x
* |  |   /
* |  |  / n_i
* |  | /
* |  |/
*

If n_i is parallel to v, a warning will be printed and no plane will be added. Obviously, n_i must not be parallel to v.

◆ GetPlaneFromBond() [2/2]

static bool vtkMolecule::GetPlaneFromBond	(	const vtkAtom &	atom1,
		const vtkAtom &	atom2,
		const vtkVector3f &	normal,
		vtkPlane *	plane
	)

static

Obtain the plane that passes through the indicated bond with the given normal.

If the plane is set successfully, the function returns true.

If the normal is not orthogonal to the bond, a new normal will be constructed in such a way that the plane will be orthogonal to the plane spanned by the bond vector and the input normal vector.

This ensures that the plane passes through the bond, and the normal is more of a "hint" indicating the orientation of the plane.

The new normal (n) is defined as the input normal vector (n_i) minus the projection of itself (proj[n_i]_v) onto the bond vector (v):

* v ^
* |  n = (n_i - proj[n_j]_v)
* proj[n_i]_v ^  |----x
* |  |   /
* |  |  / n_i
* |  | /
* |  |/
*

If n_i is parallel to v, a warning will be printed and no plane will be added. Obviously, n_i must not be parallel to v.

◆ HasLattice()

bool vtkMolecule::HasLattice ( )

Return true if a unit cell lattice is defined.

◆ ClearLattice()

void vtkMolecule::ClearLattice ( )

Remove any unit cell lattice information from the molecule.

◆ SetLattice() [1/2]

void vtkMolecule::SetLattice ( vtkMatrix3x3 * matrix )

The unit cell vectors.

The matrix is stored using a row-major layout, with the vectors encoded as columns.

◆ SetLattice() [2/2]

void vtkMolecule::SetLattice	(	const vtkVector3d &	a,
		const vtkVector3d &	b,
		const vtkVector3d &	c
	)

The unit cell vectors.

The matrix is stored using a row-major layout, with the vectors encoded as columns.

◆ GetLattice() [1/3]

vtkMatrix3x3 * vtkMolecule::GetLattice ( )

Get the unit cell lattice vectors.

The matrix is stored using a row-major layout, with the vectors encoded as columns. Will return nullptr if no unit cell information is available.

See also: GetLatticeOrigin

◆ GetLattice() [2/3]

void vtkMolecule::GetLattice	(	vtkVector3d &	a,
		vtkVector3d &	b,
		vtkVector3d &	c
	)

Get the unit cell lattice vectors, and optionally, the origin.

◆ GetLattice() [3/3]

void vtkMolecule::GetLattice	(	vtkVector3d &	a,
		vtkVector3d &	b,
		vtkVector3d &	c,
		vtkVector3d &	origin
	)

Get the unit cell lattice vectors, and optionally, the origin.

◆ GetLatticeOrigin()

virtual vtkVector3d vtkMolecule::GetLatticeOrigin ( )

virtual

Get the unit cell origin (for rendering purposes).

◆ SetLatticeOrigin()

virtual void vtkMolecule::SetLatticeOrigin ( vtkVector3d )

virtual

Get the unit cell origin (for rendering purposes).

◆ GetAtomGhostArray()

vtkUnsignedCharArray * vtkMolecule::GetAtomGhostArray ( )

Get the array that defines the ghost type of each atom.

◆ AllocateAtomGhostArray()

void vtkMolecule::AllocateAtomGhostArray ( )

Allocate ghost array for atoms.

◆ GetBondGhostArray()

vtkUnsignedCharArray * vtkMolecule::GetBondGhostArray ( )

Get the array that defines the ghost type of each bond.

◆ AllocateBondGhostArray()

void vtkMolecule::AllocateBondGhostArray ( )

Allocate ghost array for bonds.

◆ Initialize() [2/4]

int vtkMolecule::Initialize	(	vtkPoints *	atomPositions,
		vtkDataArray *	atomicNumberArray,
		vtkDataSetAttributes *	atomData
	)

Initialize a molecule with an atom per input point.

Parameters atomPositions and atomicNumberArray should have the same size.

◆ Initialize() [3/4]

int vtkMolecule::Initialize	(	vtkPoints *	atomPositions,
		vtkDataSetAttributes *	atomData
	)

inline

Overloads Initialize method.

Definition at line 371 of file vtkMolecule.h.

◆ Initialize() [4/4]

int vtkMolecule::Initialize ( vtkMolecule * molecule )

Use input molecule points, atomic number and atomic data to initialize the new molecule.

◆ GetData() [1/2]

static vtkMolecule * vtkMolecule::GetData ( vtkInformation * info )

static

Retrieve a molecule from an information vector.

◆ GetData() [2/2]

static vtkMolecule * vtkMolecule::GetData	(	vtkInformationVector *	v,
		int	i = `0`
	)

static

Retrieve a molecule from an information vector.

◆ GetAtomData()

vtkDataSetAttributes * vtkMolecule::GetAtomData ( )

inline

Return the VertexData of the underlying graph.

Definition at line 392 of file vtkMolecule.h.

◆ GetBondData()

vtkDataSetAttributes * vtkMolecule::GetBondData ( )

inline

Return the EdgeData of the underlying graph.

Definition at line 397 of file vtkMolecule.h.

◆ GetBondId()

vtkIdType vtkMolecule::GetBondId	(	vtkIdType	a,
		vtkIdType	b
	)

inline

Return the edge id from the underlying graph.

Definition at line 402 of file vtkMolecule.h.

◆ SetAtomicNumberArrayName()

virtual void vtkMolecule::SetAtomicNumberArrayName ( const char * )

virtual

Get/Set the atomic number array name.

◆ GetAtomicNumberArrayName()

virtual char * vtkMolecule::GetAtomicNumberArrayName ( )

virtual

Get/Set the atomic number array name.

◆ SetBondOrdersArrayName()

virtual void vtkMolecule::SetBondOrdersArrayName ( const char * )

virtual

Get/Set the bond orders array name.

◆ GetBondOrdersArrayName()

virtual char * vtkMolecule::GetBondOrdersArrayName ( )

virtual

Get/Set the bond orders array name.

◆ GetActualMemorySize()

unsigned long vtkMolecule::GetActualMemorySize ( )

overridevirtual

Return the actual size of the data in kibibytes (1024 bytes).

This number is valid only after the pipeline has updated. The memory size returned is guaranteed to be greater than or equal to the memory required to represent the data (e.g., extra space in arrays, etc. are not included in the return value).

Reimplemented from vtkGraph.

◆ CopyStructureInternal()

virtual void vtkMolecule::CopyStructureInternal	(	vtkMolecule *	m,
		bool	deep
	)

protectedvirtual

Copy bonds and atoms.

◆ CopyAttributesInternal()

virtual void vtkMolecule::CopyAttributesInternal	(	vtkMolecule *	m,
		bool	deep
	)

protectedvirtual

Copy everything but bonds and atoms.

◆ SetBondListDirty()

void vtkMolecule::SetBondListDirty ( )

inlineprotected

The graph superclass does not provide fast random access to the edge (bond) data.

All random access is performed using a lookup table that must be rebuilt periodically. These allow for lazy building of the lookup table

Definition at line 451 of file vtkMolecule.h.

◆ UpdateBondList()

void vtkMolecule::UpdateBondList ( )

protected

The graph superclass does not provide fast random access to the edge (bond) data.

All random access is performed using a lookup table that must be rebuilt periodically. These allow for lazy building of the lookup table

◆ GetBondList()

vtkIdTypeArray * vtkMolecule::GetBondList ( )

protected

The graph superclass does not provide fast random access to the edge (bond) data.

All random access is performed using a lookup table that must be rebuilt periodically. These allow for lazy building of the lookup table

Friends And Related Symbol Documentation

◆ vtkAtom

friend class vtkAtom

friend

Definition at line 456 of file vtkMolecule.h.

◆ vtkBond

friend class vtkBond

friend

Definition at line 457 of file vtkMolecule.h.

Member Data Documentation

◆ BondListIsDirty

bool vtkMolecule::BondListIsDirty

protected

The graph superclass does not provide fast random access to the edge (bond) data.

All random access is performed using a lookup table that must be rebuilt periodically. These allow for lazy building of the lookup table

Definition at line 450 of file vtkMolecule.h.

◆ ElectronicData

vtkAbstractElectronicData* vtkMolecule::ElectronicData

protected

Definition at line 459 of file vtkMolecule.h.

◆ Lattice

vtkSmartPointer<vtkMatrix3x3> vtkMolecule::Lattice

protected

Definition at line 460 of file vtkMolecule.h.

◆ LatticeOrigin

vtkVector3d vtkMolecule::LatticeOrigin

protected

Definition at line 461 of file vtkMolecule.h.

◆ AtomGhostArray

vtkUnsignedCharArray* vtkMolecule::AtomGhostArray

protected

Definition at line 463 of file vtkMolecule.h.

◆ BondGhostArray

vtkUnsignedCharArray* vtkMolecule::BondGhostArray

protected

Definition at line 464 of file vtkMolecule.h.

◆ AtomicNumberArrayName

char* vtkMolecule::AtomicNumberArrayName

protected

Definition at line 466 of file vtkMolecule.h.

◆ BondOrdersArrayName

char* vtkMolecule::BondOrdersArrayName

protected

Definition at line 467 of file vtkMolecule.h.

The documentation for this class was generated from the following file:

Common/DataModel/vtkMolecule.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Superclass

Constructor & Destructor Documentation

◆ vtkMolecule()

◆ ~vtkMolecule()

Member Function Documentation

◆ New()

◆ IsTypeOf()

◆ IsA()

◆ SafeDownCast()

◆ NewInstanceInternal()

◆ NewInstance()

◆ PrintSelf()

◆ Initialize() [1/4]

◆ GetDataObjectType()

◆ AppendAtom() [1/4]

◆ AppendAtom() [2/4]

◆ AppendAtom() [3/4]

◆ AppendAtom() [4/4]

◆ GetAtom()

◆ GetNumberOfAtoms()

◆ AppendBond() [1/2]

◆ AppendBond() [2/2]

◆ GetBond()

◆ GetNumberOfBonds()

◆ GetAtomAtomicNumber()

◆ SetAtomAtomicNumber()

◆ SetAtomPosition() [1/3]

◆ SetAtomPosition() [2/3]

◆ SetAtomPosition() [3/3]

◆ GetAtomPosition() [1/3]

◆ GetAtomPosition() [2/3]

◆ GetAtomPosition() [3/3]

◆ SetBondOrder()

◆ GetBondOrder()

◆ GetBondLength()

◆ GetAtomicPositionArray()

◆ GetAtomicNumberArray()

◆ GetBondOrdersArray()

◆ GetElectronicData()

◆ SetElectronicData()

◆ CheckedShallowCopy()

◆ CheckedDeepCopy()

◆ ShallowCopy()

◆ DeepCopy()

◆ ShallowCopyStructure()

◆ DeepCopyStructure()

◆ ShallowCopyAttributes()

◆ DeepCopyAttributes()

◆ GetPlaneFromBond() [1/2]

◆ GetPlaneFromBond() [2/2]

◆ HasLattice()

◆ ClearLattice()

◆ SetLattice() [1/2]

◆ SetLattice() [2/2]

◆ GetLattice() [1/3]

◆ GetLattice() [2/3]

◆ GetLattice() [3/3]

◆ GetLatticeOrigin()

◆ SetLatticeOrigin()

◆ GetAtomGhostArray()

◆ AllocateAtomGhostArray()

◆ GetBondGhostArray()

◆ AllocateBondGhostArray()

◆ Initialize() [2/4]

◆ Initialize() [3/4]

◆ Initialize() [4/4]

◆ GetData() [1/2]

◆ GetData() [2/2]

◆ GetAtomData()

◆ GetBondData()

◆ GetBondId()