VTK
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Friends | List of all members
vtkMolecule Class Reference

class describing a molecule More...

#include <vtkMolecule.h>

Inheritance diagram for vtkMolecule:
[legend]
Collaboration diagram for vtkMolecule:
[legend]

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. More...
 
vtkMoleculeNewInstance () const
 
void PrintSelf (ostream &os, vtkIndent indent) override
 Methods invoked by print to print information about the object including superclasses. More...
 
void Initialize () override
 Initialize to an empty graph. More...
 
int GetDataObjectType () override
 Return what type of dataset this is. More...
 
vtkAtom AppendAtom ()
 Add new atom with atomic number 0 (dummy atom) at origin. More...
 
vtkAtom GetAtom (vtkIdType atomId)
 Return a vtkAtom that refers to the atom with the specified id. More...
 
vtkIdType GetNumberOfAtoms ()
 Return the number of atoms in the molecule. More...
 
vtkBond GetBond (vtkIdType bondId)
 Return a vtkAtom that refers to the bond with the specified id. More...
 
vtkIdType GetNumberOfBonds ()
 Return the number of bonds in the molecule. More...
 
unsigned short GetAtomAtomicNumber (vtkIdType atomId)
 Return the atomic number of the atom with the specified id. More...
 
void SetAtomAtomicNumber (vtkIdType atomId, unsigned short atomicNum)
 Set the atomic number of the atom with the specified id. More...
 
double GetBondLength (vtkIdType bondId)
 Get the bond length of the bond with the specified id. More...
 
bool CheckedShallowCopy (vtkGraph *g) override
 Performs the same operation as ShallowCopy(), but instead of reporting an error for an incompatible graph, returns false. More...
 
bool CheckedDeepCopy (vtkGraph *g) override
 Performs the same operation as DeepCopy(), but instead of reporting an error for an incompatible graph, returns false. More...
 
void ShallowCopy (vtkDataObject *obj) override
 Shallow copies the data object into this molecule. More...
 
void DeepCopy (vtkDataObject *obj) override
 Deep copies the data object into this molecule. More...
 
virtual void ShallowCopyStructure (vtkMolecule *m)
 Shallow copies the atoms and bonds from m into this. More...
 
virtual void DeepCopyStructure (vtkMolecule *m)
 Deep copies the atoms and bonds from m into this. More...
 
virtual void ShallowCopyAttributes (vtkMolecule *m)
 Shallow copies attributes (i.e. More...
 
virtual void DeepCopyAttributes (vtkMolecule *m)
 Deep copies attributes (i.e. More...
 
bool HasLattice ()
 Return true if a unit cell lattice is defined. More...
 
void ClearLattice ()
 Remove any unit cell lattice information from the molecule. More...
 
vtkMatrix3x3GetLattice ()
 Get the unit cell lattice vectors. More...
 
vtkUnsignedCharArrayGetAtomGhostArray ()
 Get the array that defines the ghost type of each atom. More...
 
void AllocateAtomGhostArray ()
 Allocate ghost array for atoms. More...
 
vtkUnsignedCharArrayGetBondGhostArray ()
 Get the array that defines the ghost type of each bond. More...
 
void AllocateBondGhostArray ()
 Allocate ghost array for bonds. More...
 
int Initialize (vtkPoints *atomPositions, vtkDataArray *atomicNumberArray, vtkDataSetAttributes *atomData)
 Initialize a molecule with an atom per input point. More...
 
int Initialize (vtkPoints *atomPositions, vtkDataSetAttributes *atomData)
 Overloads Initialize method. More...
 
int Initialize (vtkMolecule *molecule)
 Use input molecule points, atomic number and atomic data to initialize the new molecule. More...
 
vtkDataSetAttributesGetAtomData ()
 Return the VertexData of the underlying graph. More...
 
vtkDataSetAttributesGetBondData ()
 Return the EdgeData of the underlying graph. More...
 
vtkIdType GetBondId (vtkIdType a, vtkIdType b)
 Return the edge id from the underlying graph. More...
 
unsigned long GetActualMemorySize () override
 Return the actual size of the data in kibibytes (1024 bytes). More...
 
vtkAtom AppendAtom (unsigned short atomicNumber, double x, double y, double z)
 Add new atom with the specified atomic number and position. More...
 
vtkAtom AppendAtom (unsigned short atomicNumber, const vtkVector3f &pos)
 Add new atom with the specified atomic number and position. More...
 
vtkAtom AppendAtom (unsigned short atomicNumber, double pos[3])
 Add new atom with the specified atomic number and position. More...
 
vtkBond AppendBond (vtkIdType atom1, vtkIdType atom2, unsigned short order=1)
 Add a bond between the specified atoms, optionally setting the bond order (default: 1). More...
 
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). More...
 
void SetAtomPosition (vtkIdType atomId, const vtkVector3f &pos)
 Set the position of the atom with the specified id. More...
 
void SetAtomPosition (vtkIdType atomId, double x, double y, double z)
 Set the position of the atom with the specified id. More...
 
void SetAtomPosition (vtkIdType atomId, double pos[3])
 Set the position of the atom with the specified id. More...
 
vtkVector3f GetAtomPosition (vtkIdType atomId)
 Get the position of the atom with the specified id. More...
 
void GetAtomPosition (vtkIdType atomId, float pos[3])
 Get the position of the atom with the specified id. More...
 
void GetAtomPosition (vtkIdType atomId, double pos[3])
 Get the position of the atom with the specified id. More...
 
void SetBondOrder (vtkIdType bondId, unsigned short order)
 Get/Set the bond order of the bond with the specified id. More...
 
unsigned short GetBondOrder (vtkIdType bondId)
 Get/Set the bond order of the bond with the specified id. More...
 
vtkPointsGetAtomicPositionArray ()
 Access the raw arrays used in this vtkMolecule instance. More...
 
vtkUnsignedShortArrayGetAtomicNumberArray ()
 Access the raw arrays used in this vtkMolecule instance. More...
 
vtkUnsignedShortArrayGetBondOrdersArray ()
 Access the raw arrays used in this vtkMolecule instance. More...
 
virtual vtkAbstractElectronicDataGetElectronicData ()
 Set/Get the AbstractElectronicData-subclassed object for this molecule. More...
 
virtual void SetElectronicData (vtkAbstractElectronicData *)
 Set/Get the AbstractElectronicData-subclassed object for this molecule. More...
 
void SetLattice (vtkMatrix3x3 *matrix)
 The unit cell vectors. More...
 
void SetLattice (const vtkVector3d &a, const vtkVector3d &b, const vtkVector3d &c)
 The unit cell vectors. More...
 
void GetLattice (vtkVector3d &a, vtkVector3d &b, vtkVector3d &c)
 Get the unit cell lattice vectors, and optionally, the origin. More...
 
void GetLattice (vtkVector3d &a, vtkVector3d &b, vtkVector3d &c, vtkVector3d &origin)
 Get the unit cell lattice vectors, and optionally, the origin. More...
 
virtual vtkVector3d GetLatticeOrigin ()
 Get the unit cell origin (for rendering purposes). More...
 
virtual void SetLatticeOrigin (vtkVector3d)
 Get the unit cell origin (for rendering purposes). More...
 
virtual void SetAtomicNumberArrayName (const char *)
 Get/Set the atomic number array name. More...
 
virtual char * GetAtomicNumberArrayName ()
 Get/Set the atomic number array name. More...
 
virtual void SetBondOrdersArrayName (const char *)
 Get/Set the bond orders array name. More...
 
virtual char * GetBondOrdersArrayName ()
 Get/Set the bond orders array name. More...
 
- Public Member Functions inherited from vtkUndirectedGraph
vtkUndirectedGraphNewInstance () const
 
void PrintSelf (ostream &os, vtkIndent indent) override
 Methods invoked by print to print information about the object including superclasses. More...
 
int GetDataObjectType () override
 Return what type of dataset this is. More...
 
vtkIdType GetInDegree (vtkIdType v) override
 Returns the full degree of the vertex. More...
 
vtkInEdgeType GetInEdge (vtkIdType v, vtkIdType i) override
 Random-access method for retrieving the in edges of a vertex. More...
 
void GetInEdge (vtkIdType v, vtkIdType i, vtkGraphEdge *e) override
 Random-access method for retrieving incoming edges to vertex v. More...
 
void GetInEdges (vtkIdType v, vtkInEdgeIterator *it) override
 Initialize the iterator to get the incoming edges to a vertex. More...
 
bool IsStructureValid (vtkGraph *g) override
 Check the structure, and accept it if it is a valid undirected graph. More...
 
- Public Member Functions inherited from vtkGraph
vtkGraphNewInstance () const
 
void ComputeBounds ()
 Compute the bounds of the graph. More...
 
vtkMTimeType GetMTime () override
 The modified time of the graph. More...
 
virtual void GetOutEdges (vtkIdType v, vtkOutEdgeIterator *it)
 Initializes the out edge iterator to iterate over all outgoing edges of vertex v. More...
 
virtual vtkIdType GetDegree (vtkIdType v)
 The total of all incoming and outgoing vertices for vertex v. More...
 
virtual vtkIdType GetOutDegree (vtkIdType v)
 The number of outgoing edges from vertex v. More...
 
virtual vtkOutEdgeType GetOutEdge (vtkIdType v, vtkIdType index)
 Random-access method for retrieving outgoing edges from vertex v. More...
 
virtual void GetOutEdge (vtkIdType v, vtkIdType index, vtkGraphEdge *e)
 Random-access method for retrieving outgoing edges from vertex v. More...
 
virtual void GetAdjacentVertices (vtkIdType v, vtkAdjacentVertexIterator *it)
 Initializes the adjacent vertex iterator to iterate over all outgoing vertices from vertex v. More...
 
virtual void GetEdges (vtkEdgeListIterator *it)
 Initializes the edge list iterator to iterate over all edges in the graph. More...
 
virtual vtkIdType GetNumberOfEdges ()
 The number of edges in the graph. More...
 
virtual void GetVertices (vtkVertexListIterator *it)
 Initializes the vertex list iterator to iterate over all vertices in the graph. More...
 
virtual vtkIdType GetNumberOfVertices ()
 The number of vertices in the graph. More...
 
void SetDistributedGraphHelper (vtkDistributedGraphHelper *helper)
 Sets the distributed graph helper of this graph, turning it into a distributed graph. More...
 
vtkDistributedGraphHelperGetDistributedGraphHelper ()
 Retrieves the distributed graph helper for this graph. More...
 
vtkIdType FindVertex (const vtkVariant &pedigreeID)
 Retrieve the vertex with the given pedigree ID. More...
 
virtual void CopyStructure (vtkGraph *g)
 Does a shallow copy of the topological information, but not the associated attributes. More...
 
virtual void Squeeze ()
 Reclaim unused memory. More...
 
void ReorderOutVertices (vtkIdType v, vtkIdTypeArray *vertices)
 Reorder the outgoing vertices of a vertex. More...
 
bool IsSameStructure (vtkGraph *other)
 Returns true if both graphs point to the same adjacency structure. More...
 
vtkIdType GetNumberOfEdgePoints (vtkIdType e)
 Get the number of edge points associated with an edge. More...
 
doubleGetEdgePoint (vtkIdType e, vtkIdType i)
 Get the x,y,z location of a point along edge e. More...
 
void ClearEdgePoints (vtkIdType e)
 Clear all points associated with an edge. More...
 
void SetEdgePoint (vtkIdType e, vtkIdType i, const double x[3])
 Set an x,y,z location of a point along an edge. More...
 
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. More...
 
void AddEdgePoint (vtkIdType e, double x, double y, double z)
 
vtkGraphInternalsGetGraphInternals (bool modifying)
 Returns the internal representation of the graph. More...
 
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. More...
 
vtkFieldDataGetAttributesAsFieldData (int type) override
 Returns the attributes of the data object as a vtkFieldData. More...
 
vtkIdType GetNumberOfElements (int type) override
 Get the number of elements for a specific attribute type (VERTEX, EDGE, etc.). More...
 
void Dump ()
 Dump the contents of the graph to standard output. More...
 
vtkIdType GetEdgeId (vtkIdType a, vtkIdType b)
 Returns the Id of the edge between vertex a and vertex b. More...
 
bool ToDirectedGraph (vtkDirectedGraph *g)
 Convert the graph to a directed graph. More...
 
bool ToUndirectedGraph (vtkUndirectedGraph *g)
 Convert the graph to an undirected graph. More...
 
virtual vtkDataSetAttributesGetVertexData ()
 Get the vertex or edge data. More...
 
virtual vtkDataSetAttributesGetEdgeData ()
 Get the vertex or edge data. More...
 
doubleGetPoint (vtkIdType ptId)
 These methods return the point (0,0,0) until the points structure is created, when it returns the actual point position. More...
 
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. More...
 
vtkPointsGetPoints ()
 Returns the points array for this graph. More...
 
virtual void SetPoints (vtkPoints *points)
 Returns the points array for this graph. More...
 
doubleGetBounds ()
 Return a pointer to the geometry bounding box in the form (xmin,xmax, ymin,ymax, zmin,zmax). More...
 
void GetBounds (double bounds[6])
 Return a pointer to the geometry bounding box in the form (xmin,xmax, ymin,ymax, zmin,zmax). More...
 
vtkIdType GetSourceVertex (vtkIdType e)
 Retrieve the source and target vertices for an edge id. More...
 
vtkIdType GetTargetVertex (vtkIdType e)
 Retrieve the source and target vertices for an edge id. More...
 
void SetEdgePoints (vtkIdType e, vtkIdType npts, const double pts[])
 Get/Set the internal edge control points associated with each edge. More...
 
void GetEdgePoints (vtkIdType e, vtkIdType &npts, double *&pts)
 Get/Set the internal edge control points associated with each edge. More...
 
void ShallowCopyEdgePoints (vtkGraph *g)
 Copy the internal edge point data from another graph into this graph. More...
 
void DeepCopyEdgePoints (vtkGraph *g)
 Copy the internal edge point data from another graph into this graph. More...
 
- Public Member Functions inherited from vtkDataObject
vtkDataObjectNewInstance () const
 
void ReleaseData ()
 Release data back to system to conserve memory resource. More...
 
vtkMTimeType GetUpdateTime ()
 Used by Threaded ports to determine if they should initiate an asynchronous update (still in development). More...
 
virtual void CopyInformationFromPipeline (vtkInformation *vtkNotUsed(info))
 Copy from the pipeline information to the data object's own information. More...
 
virtual void CopyInformationToPipeline (vtkInformation *vtkNotUsed(info))
 Copy information from this data object to the pipeline information. More...
 
void DataHasBeenGenerated ()
 This method is called by the source when it executes to generate data. More...
 
virtual void PrepareForNewData ()
 make the output data ready for new data to be inserted. More...
 
virtual int GetExtentType ()
 The ExtentType will be left as VTK_PIECES_EXTENT for data objects such as vtkPolyData and vtkUnstructuredGrid. More...
 
virtual void Crop (const int *updateExtent)
 This method crops the data object (if necessary) so that the extent matches the update extent. More...
 
virtual vtkDataSetAttributesGetAttributes (int type)
 Returns the attributes of the data object of the specified attribute type. More...
 
virtual int GetAttributeTypeForArray (vtkAbstractArray *arr)
 Retrieves the attribute type that an array came from. More...
 
virtual vtkInformationGetInformation ()
 Set/Get the information object associated with this data object. More...
 
virtual void SetInformation (vtkInformation *)
 Set/Get the information object associated with this data object. More...
 
virtual int GetDataReleased ()
 Get the flag indicating the data has been released. More...
 
virtual void SetFieldData (vtkFieldData *)
 Assign or retrieve a general field data to this data object. More...
 
virtual vtkFieldDataGetFieldData ()
 Assign or retrieve a general field data to this data object. More...
 
void GlobalReleaseDataFlagOn ()
 Turn on/off flag to control whether every object releases its data after being used by a filter. More...
 
void GlobalReleaseDataFlagOff ()
 Turn on/off flag to control whether every object releases its data after being used by a filter. More...
 
- Public Member Functions inherited from vtkObject
 vtkBaseTypeMacro (vtkObject, vtkObjectBase)
 
virtual void DebugOn ()
 Turn debugging output on. More...
 
virtual void DebugOff ()
 Turn debugging output off. More...
 
bool GetDebug ()
 Get the value of the debug flag. More...
 
void SetDebug (bool debugFlag)
 Set the value of the debug flag. More...
 
virtual void Modified ()
 Update the modification time for this object. More...
 
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)
 
int InvokeEvent (unsigned long event)
 
int InvokeEvent (const char *event)
 
unsigned long AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)
 Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...
 
unsigned long AddObserver (const char *event, vtkCommand *, float priority=0.0f)
 Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...
 
vtkCommandGetCommand (unsigned long tag)
 Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...
 
void RemoveObserver (vtkCommand *)
 Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...
 
void RemoveObservers (unsigned long event, vtkCommand *)
 Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...
 
void RemoveObservers (const char *event, vtkCommand *)
 Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...
 
vtkTypeBool HasObserver (unsigned long event, vtkCommand *)
 Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...
 
vtkTypeBool HasObserver (const char *event, vtkCommand *)
 Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...
 
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. More...
 
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. More...
 
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. More...
 
int InvokeEvent (unsigned long event, void *callData)
 This method invokes an event and return whether the event was aborted or not. More...
 
int InvokeEvent (const char *event, void *callData)
 This method invokes an event and return whether the event was aborted or not. More...
 
- Public Member Functions inherited from vtkObjectBase
const char * GetClassName () const
 Return the class name as a string. More...
 
virtual void Delete ()
 Delete a VTK object. More...
 
virtual void FastDelete ()
 Delete a reference to this object. More...
 
void InitializeObjectBase ()
 
void Print (ostream &os)
 Print an object to an ostream. More...
 
virtual void Register (vtkObjectBase *o)
 Increase the reference count (mark as used by another object). More...
 
virtual void UnRegister (vtkObjectBase *o)
 Decrease the reference count (release by another object). More...
 
int GetReferenceCount ()
 Return the current reference count of this object. More...
 
void SetReferenceCount (int)
 Sets the reference count. More...
 
void PrintRevisions (ostream &)
 Legacy. More...
 
virtual void PrintHeader (ostream &os, vtkIndent indent)
 Methods invoked by print to print information about the object including superclasses. More...
 
virtual void PrintTrailer (ostream &os, vtkIndent indent)
 Methods invoked by print to print information about the object including superclasses. More...
 

Static Public Member Functions

static vtkMoleculeNew ()
 
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkMoleculeSafeDownCast (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. More...
 
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. More...
 
static vtkMoleculeGetData (vtkInformation *info)
 Retrieve a molecule from an information vector. More...
 
static vtkMoleculeGetData (vtkInformationVector *v, int i=0)
 Retrieve a molecule from an information vector. More...
 
- Static Public Member Functions inherited from vtkUndirectedGraph
static vtkUndirectedGraphNew ()
 
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkUndirectedGraphSafeDownCast (vtkObjectBase *o)
 
static vtkUndirectedGraphGetData (vtkInformation *info)
 Retrieve a graph from an information vector. More...
 
static vtkUndirectedGraphGetData (vtkInformationVector *v, int i=0)
 Retrieve a graph from an information vector. More...
 
- Static Public Member Functions inherited from vtkGraph
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkGraphSafeDownCast (vtkObjectBase *o)
 
static vtkGraphGetData (vtkInformation *info)
 Retrieve a graph from an information vector. More...
 
static vtkGraphGetData (vtkInformationVector *v, int i=0)
 Retrieve a graph from an information vector. More...
 
- Static Public Member Functions inherited from vtkDataObject
static vtkDataObjectNew ()
 
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkDataObjectSafeDownCast (vtkObjectBase *o)
 
static vtkInformationGetActiveFieldInformation (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) More...
 
static vtkInformationGetNamedFieldInformation (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. More...
 
static void RemoveNamedFieldInformation (vtkInformation *info, int fieldAssociation, const char *name)
 Remove the info associated with an array. More...
 
static vtkInformationSetActiveAttribute (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). More...
 
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). More...
 
static void SetPointDataActiveScalarInfo (vtkInformation *info, int arrayType, int numComponents)
 Convenience version of previous method for use (primarily) by the Imaging filters. More...
 
static const char * GetAssociationTypeAsString (int associationType)
 Given an integer association type, this static method returns a string type for the attribute (i.e. More...
 
static int GetAssociationTypeFromString (const char *associationType)
 Given an integer association type, this static method returns a string type for the attribute (i.e. More...
 
static vtkInformationStringKeyDATA_TYPE_NAME ()
 
static vtkInformationDataObjectKeyDATA_OBJECT ()
 
static vtkInformationIntegerKeyDATA_EXTENT_TYPE ()
 
static vtkInformationIntegerPointerKeyDATA_EXTENT ()
 
static vtkInformationIntegerVectorKeyALL_PIECES_EXTENT ()
 
static vtkInformationIntegerKeyDATA_PIECE_NUMBER ()
 
static vtkInformationIntegerKeyDATA_NUMBER_OF_PIECES ()
 
static vtkInformationIntegerKeyDATA_NUMBER_OF_GHOST_LEVELS ()
 
static vtkInformationDoubleKeyDATA_TIME_STEP ()
 
static vtkInformationInformationVectorKeyPOINT_DATA_VECTOR ()
 
static vtkInformationInformationVectorKeyCELL_DATA_VECTOR ()
 
static vtkInformationInformationVectorKeyVERTEX_DATA_VECTOR ()
 
static vtkInformationInformationVectorKeyEDGE_DATA_VECTOR ()
 
static vtkInformationIntegerKeyFIELD_ARRAY_TYPE ()
 
static vtkInformationIntegerKeyFIELD_ASSOCIATION ()
 
static vtkInformationIntegerKeyFIELD_ATTRIBUTE_TYPE ()
 
static vtkInformationIntegerKeyFIELD_ACTIVE_ATTRIBUTE ()
 
static vtkInformationIntegerKeyFIELD_NUMBER_OF_COMPONENTS ()
 
static vtkInformationIntegerKeyFIELD_NUMBER_OF_TUPLES ()
 
static vtkInformationIntegerKeyFIELD_OPERATION ()
 
static vtkInformationDoubleVectorKeyFIELD_RANGE ()
 
static vtkInformationIntegerVectorKeyPIECE_EXTENT ()
 
static vtkInformationStringKeyFIELD_NAME ()
 
static vtkInformationDoubleVectorKeyORIGIN ()
 
static vtkInformationDoubleVectorKeySPACING ()
 
static vtkInformationDoubleVectorKeyBOUNDING_BOX ()
 
static vtkInformationDataObjectKeySIL ()
 
static vtkDataObjectGetData (vtkInformation *info)
 Retrieve an instance of this class from an information object. More...
 
static vtkDataObjectGetData (vtkInformationVector *v, int i=0)
 Retrieve an instance of this class from an information object. More...
 
static void SetGlobalReleaseDataFlag (int val)
 Turn on/off flag to control whether every object releases its data after being used by a filter. More...
 
static int GetGlobalReleaseDataFlag ()
 Turn on/off flag to control whether every object releases its data after being used by a filter. More...
 
- Static Public Member Functions inherited from vtkObject
static vtkObjectNew ()
 Create an object with Debug turned off, modified time initialized to zero, and reference counting on. More...
 
static void BreakOnError ()
 This method is called when vtkErrorMacro executes. More...
 
static void SetGlobalWarningDisplay (int val)
 This is a global flag that controls whether any debug, warning or error messages are displayed. More...
 
static void GlobalWarningDisplayOn ()
 This is a global flag that controls whether any debug, warning or error messages are displayed. More...
 
static void GlobalWarningDisplayOff ()
 This is a global flag that controls whether any debug, warning or error messages are displayed. More...
 
static int GetGlobalWarningDisplay ()
 This is a global flag that controls whether any debug, warning or error messages are displayed. More...
 
- 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. More...
 
static vtkObjectBaseNew ()
 Create an object with Debug turned off, modified time initialized to zero, and reference counting on. More...
 

Protected Member Functions

virtual vtkObjectBaseNewInstanceInternal () const
 
 vtkMolecule ()
 
 ~vtkMolecule () override
 
virtual void CopyStructureInternal (vtkMolecule *m, bool deep)
 Copy bonds and atoms. More...
 
virtual void CopyAttributesInternal (vtkMolecule *m, bool deep)
 Copy everything but bonds and atoms. More...
 
- Protected Member Functions inherited from vtkUndirectedGraph
 vtkUndirectedGraph ()
 
 ~vtkUndirectedGraph () override
 
void GetInEdges (vtkIdType v, const vtkInEdgeType *&edges, vtkIdType &nedges) override
 For iterators, returns the same edge list as GetOutEdges(). More...
 
- Protected Member Functions inherited from vtkGraph
 vtkGraph ()
 
 ~vtkGraph () override
 
void AddVertexInternal (vtkVariantArray *propertyArr=nullptr, vtkIdType *vertex=nullptr)
 Protected method for adding vertices, optionally with properties, used by mutable subclasses. More...
 
void AddVertexInternal (const vtkVariant &pedigree, vtkIdType *vertex)
 Adds a vertex with the given pedigree ID to the graph. More...
 
void RemoveVertexInternal (vtkIdType v, bool directed)
 Removes a vertex from the graph, along with any adjacent edges. More...
 
void RemoveEdgeInternal (vtkIdType e, bool directed)
 Removes an edge from the graph. More...
 
void RemoveVerticesInternal (vtkIdTypeArray *arr, bool directed)
 Removes a collection of vertices from the graph, along with any adjacent edges. More...
 
void RemoveEdgesInternal (vtkIdTypeArray *arr, bool directed)
 Removes a collection of edges from the graph. More...
 
virtual void CopyInternal (vtkGraph *g, bool deep)
 Copy internal data structure. More...
 
void SetInternals (vtkGraphInternals *internals)
 Private method for setting internals. More...
 
void SetEdgePoints (vtkGraphEdgePoints *edgePoints)
 Private method for setting edge points. More...
 
void ForceOwnership ()
 If this instance does not own its internals, it makes a copy of the internals. More...
 
void BuildEdgeList ()
 Builds a mapping from edge id to source/target vertex id. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
virtual void GetOutEdges (vtkIdType v, const vtkOutEdgeType *&edges, vtkIdType &nedges)
 Fast access functions for iterators. More...
 
virtual vtkIdTypeArrayGetEdgeList ()
 The optional mapping from edge id to source/target ids. More...
 
virtual void SetEdgeList (vtkIdTypeArray *list)
 The optional mapping from edge id to source/target ids. More...
 
- Protected Member Functions inherited from vtkDataObject
 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. More...
 
void InternalReleaseFocus ()
 These methods allow a command to exclusively grab all events. More...
 
- Protected Member Functions inherited from vtkObjectBase
 vtkObjectBase ()
 
virtual ~vtkObjectBase ()
 
virtual void CollectRevisions (ostream &)
 
virtual void ReportReferences (vtkGarbageCollector *)
 
 vtkObjectBase (const vtkObjectBase &)
 
void operator= (const vtkObjectBase &)
 

Protected Attributes

vtkAbstractElectronicDataElectronicData
 
vtkSmartPointer< vtkMatrix3x3Lattice
 
vtkVector3d LatticeOrigin
 
vtkUnsignedCharArrayAtomGhostArray
 
vtkUnsignedCharArrayBondGhostArray
 
char * AtomicNumberArrayName
 
char * BondOrdersArrayName
 
- Protected Attributes inherited from vtkGraph
vtkGraphInternalsInternals
 The adjacency list internals of this graph. More...
 
vtkDistributedGraphHelperDistributedHelper
 The distributed graph helper. More...
 
vtkGraphEdgePoints * EdgePoints
 The structure for holding the edge points. More...
 
double Bounds [6]
 (xmin,xmax, ymin,ymax, zmin,zmax) geometric bounds. More...
 
vtkTimeStamp ComputeTime
 Time at which bounds were computed. More...
 
vtkDataSetAttributesVertexData
 The vertex and edge data. More...
 
vtkDataSetAttributesEdgeData
 The vertex and edge data. More...
 
vtkPointsPoints
 The vertex locations. More...
 
vtkIdTypeArrayEdgeList
 The optional mapping from edge id to source/target ids. More...
 
- Protected Attributes inherited from vtkDataObject
vtkFieldDataFieldData
 
int DataReleased
 
vtkTimeStamp UpdateTime
 
vtkInformationInformation
 
- Protected Attributes inherited from vtkObject
bool Debug
 
vtkTimeStamp MTime
 
vtkSubjectHelper * SubjectHelper
 
- Protected Attributes inherited from vtkObjectBase
vtkAtomicInt32 ReferenceCount
 
vtkWeakPointerBase ** WeakPointers
 

Friends

class vtkAtom
 
class vtkBond
 
bool BondListIsDirty
 The graph superclass does not provide fast random access to the edge (bond) data. More...
 
void SetBondListDirty ()
 The graph superclass does not provide fast random access to the edge (bond) data. More...
 
void UpdateBondList ()
 The graph superclass does not provide fast random access to the edge (bond) data. More...
 
vtkIdTypeArrayGetBondList ()
 The graph superclass does not provide fast random access to the edge (bond) data. More...
 

Additional Inherited Members

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

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:

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:

vtkAtom h1 = mol->AppendAtom();
h1.SetPosition(0.0, 0.0, -0.5);
vtkAtom h2 = mol->AppendAtom();
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 94 of file vtkMolecule.h.

Member Typedef Documentation

Definition at line 98 of file vtkMolecule.h.

Constructor & Destructor Documentation

vtkMolecule::vtkMolecule ( )
protected
vtkMolecule::~vtkMolecule ( )
overrideprotected

Member Function Documentation

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

static vtkMolecule* vtkMolecule::SafeDownCast ( vtkObjectBase o)
static
virtual vtkObjectBase* vtkMolecule::NewInstanceInternal ( ) const
protectedvirtual

Reimplemented from vtkUndirectedGraph.

vtkMolecule* vtkMolecule::NewInstance ( ) const
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.

void vtkMolecule::Initialize ( )
overridevirtual

Initialize to an empty graph.

Reimplemented from vtkGraph.

int vtkMolecule::GetDataObjectType ( )
inlineoverridevirtual

Return what type of dataset this is.

Reimplemented from vtkGraph.

Definition at line 105 of file vtkMolecule.h.

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 111 of file vtkMolecule.h.

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.

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 122 of file vtkMolecule.h.

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 127 of file vtkMolecule.h.

vtkAtom vtkMolecule::GetAtom ( vtkIdType  atomId)

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

vtkIdType vtkMolecule::GetNumberOfAtoms ( )

Return the number of atoms in the molecule.

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.

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 151 of file vtkMolecule.h.

vtkBond vtkMolecule::GetBond ( vtkIdType  bondId)

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

vtkIdType vtkMolecule::GetNumberOfBonds ( )

Return the number of bonds in the molecule.

unsigned short vtkMolecule::GetAtomAtomicNumber ( vtkIdType  atomId)

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

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

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

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

Set the position of the atom with the specified id.

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

Set the position of the atom with the specified id.

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

Set the position of the atom with the specified id.

Definition at line 185 of file vtkMolecule.h.

vtkVector3f vtkMolecule::GetAtomPosition ( vtkIdType  atomId)

Get the position of the atom with the specified id.

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

Get the position of the atom with the specified id.

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

Get the position of the atom with the specified id.

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

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

unsigned short vtkMolecule::GetBondOrder ( vtkIdType  bondId)

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

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()
vtkPoints* vtkMolecule::GetAtomicPositionArray ( )

Access the raw arrays used in this vtkMolecule instance.

vtkUnsignedShortArray* vtkMolecule::GetAtomicNumberArray ( )

Access the raw arrays used in this vtkMolecule instance.

vtkUnsignedShortArray* vtkMolecule::GetBondOrdersArray ( )

Access the raw arrays used in this vtkMolecule instance.

virtual vtkAbstractElectronicData* vtkMolecule::GetElectronicData ( )
virtual

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

virtual void vtkMolecule::SetElectronicData ( vtkAbstractElectronicData )
virtual

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

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.

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.

void vtkMolecule::ShallowCopy ( vtkDataObject obj)
overridevirtual

Shallow copies the data object into this molecule.

Reimplemented from vtkGraph.

void vtkMolecule::DeepCopy ( vtkDataObject obj)
overridevirtual

Deep copies the data object into this molecule.

Reimplemented from vtkGraph.

virtual void vtkMolecule::ShallowCopyStructure ( vtkMolecule m)
virtual

Shallow copies the atoms and bonds from m into this.

virtual void vtkMolecule::DeepCopyStructure ( vtkMolecule m)
virtual

Deep copies the atoms and bonds from m into this.

virtual void vtkMolecule::ShallowCopyAttributes ( vtkMolecule m)
virtual

Shallow copies attributes (i.e.

everything besides atoms and bonds) from m into this.

virtual void vtkMolecule::DeepCopyAttributes ( vtkMolecule m)
virtual

Deep copies attributes (i.e.

everything besides atoms and bonds) from m into this.

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.

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.

bool vtkMolecule::HasLattice ( )

Return true if a unit cell lattice is defined.

void vtkMolecule::ClearLattice ( )

Remove any unit cell lattice information from the molecule.

void vtkMolecule::SetLattice ( vtkMatrix3x3 matrix)

The unit cell vectors.

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

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.

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

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

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

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

virtual vtkVector3d vtkMolecule::GetLatticeOrigin ( )
virtual

Get the unit cell origin (for rendering purposes).

virtual void vtkMolecule::SetLatticeOrigin ( vtkVector3d  )
virtual

Get the unit cell origin (for rendering purposes).

vtkUnsignedCharArray* vtkMolecule::GetAtomGhostArray ( )

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

void vtkMolecule::AllocateAtomGhostArray ( )

Allocate ghost array for atoms.

vtkUnsignedCharArray* vtkMolecule::GetBondGhostArray ( )

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

void vtkMolecule::AllocateBondGhostArray ( )

Allocate ghost array for bonds.

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.

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

Overloads Initialize method.

Definition at line 393 of file vtkMolecule.h.

int vtkMolecule::Initialize ( vtkMolecule molecule)

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

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

Retrieve a molecule from an information vector.

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

Retrieve a molecule from an information vector.

vtkDataSetAttributes* vtkMolecule::GetAtomData ( )
inline

Return the VertexData of the underlying graph.

Definition at line 415 of file vtkMolecule.h.

vtkDataSetAttributes* vtkMolecule::GetBondData ( )
inline

Return the EdgeData of the underlying graph.

Definition at line 423 of file vtkMolecule.h.

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

Return the edge id from the underlying graph.

Definition at line 431 of file vtkMolecule.h.

virtual void vtkMolecule::SetAtomicNumberArrayName ( const char *  )
virtual

Get/Set the atomic number array name.

virtual char* vtkMolecule::GetAtomicNumberArrayName ( )
virtual

Get/Set the atomic number array name.

virtual void vtkMolecule::SetBondOrdersArrayName ( const char *  )
virtual

Get/Set the bond orders array name.

virtual char* vtkMolecule::GetBondOrdersArrayName ( )
virtual

Get/Set the bond orders array name.

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.

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

Copy bonds and atoms.

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

Copy everything but bonds and atoms.

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 483 of file vtkMolecule.h.

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

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 Function Documentation

friend class vtkAtom
friend

Definition at line 488 of file vtkMolecule.h.

friend class vtkBond
friend

Definition at line 489 of file vtkMolecule.h.

Member Data Documentation

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 482 of file vtkMolecule.h.

vtkAbstractElectronicData* vtkMolecule::ElectronicData
protected

Definition at line 491 of file vtkMolecule.h.

vtkSmartPointer<vtkMatrix3x3> vtkMolecule::Lattice
protected

Definition at line 492 of file vtkMolecule.h.

vtkVector3d vtkMolecule::LatticeOrigin
protected

Definition at line 493 of file vtkMolecule.h.

vtkUnsignedCharArray* vtkMolecule::AtomGhostArray
protected

Definition at line 495 of file vtkMolecule.h.

vtkUnsignedCharArray* vtkMolecule::BondGhostArray
protected

Definition at line 496 of file vtkMolecule.h.

char* vtkMolecule::AtomicNumberArrayName
protected

Definition at line 498 of file vtkMolecule.h.

char* vtkMolecule::BondOrdersArrayName
protected

Definition at line 499 of file vtkMolecule.h.


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