VTK
9.4.20241212
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class describing a molecule More...
#include <vtkMolecule.h>
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. | |
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:
Incremental:
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.
Definition at line 83 of file vtkMolecule.h.
Definition at line 87 of file vtkMolecule.h.
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overrideprotected |
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static |
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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.
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Reimplemented from vtkUndirectedGraph.
vtkMolecule * vtkMolecule::NewInstance | ( | ) | const |
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Initialize to an empty graph.
Reimplemented from vtkGraph.
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Return what type of dataset this is.
Reimplemented from vtkGraph.
Definition at line 94 of file vtkMolecule.h.
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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.
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.
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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.
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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.
Return a vtkAtom that refers to the atom with the specified id.
vtkIdType vtkMolecule::GetNumberOfAtoms | ( | ) |
Return the number of atoms in the molecule.
Add a bond between the specified atoms, optionally setting the bond order (default: 1).
Return a vtkBond object referring to the new bond.
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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.
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.
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Set the position of the atom with the specified id.
Definition at line 168 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.
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.
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Set/Get the AbstractElectronicData-subclassed object for this molecule.
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Set/Get the AbstractElectronicData-subclassed object for this molecule.
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Performs the same operation as ShallowCopy(), but instead of reporting an error for an incompatible graph, returns false.
Reimplemented from vtkGraph.
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Performs the same operation as DeepCopy(), but instead of reporting an error for an incompatible graph, returns false.
Reimplemented from vtkGraph.
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Shallow copies the data object into this molecule.
Reimplemented from vtkGraph.
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Deep copies the data object into this molecule.
Reimplemented from vtkGraph.
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Shallow copies the atoms and bonds from m into this.
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Deep copies the atoms and bonds from m into this.
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Shallow copies attributes (i.e.
everything besides atoms and bonds) from m into this.
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Deep copies attributes (i.e.
everything besides atoms and bonds) from m into this.
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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.
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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.
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.
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Get the unit cell origin (for rendering purposes).
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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.
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Overloads Initialize method.
Definition at line 371 of file vtkMolecule.h.
int vtkMolecule::Initialize | ( | vtkMolecule * | molecule | ) |
Use input molecule points, atomic number and atomic data to initialize the new molecule.
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Retrieve a molecule from an information vector.
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Retrieve a molecule from an information vector.
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Return the VertexData of the underlying graph.
Definition at line 392 of file vtkMolecule.h.
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Return the EdgeData of the underlying graph.
Definition at line 397 of file vtkMolecule.h.
Return the edge id from the underlying graph.
Definition at line 402 of file vtkMolecule.h.
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Get/Set the atomic number array name.
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Get/Set the atomic number array name.
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Get/Set the bond orders array name.
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Get/Set the bond orders array name.
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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.
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Copy bonds and atoms.
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Copy everything but bonds and atoms.
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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.
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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
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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
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friend |
Definition at line 456 of file vtkMolecule.h.
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friend |
Definition at line 457 of file vtkMolecule.h.
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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.
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Definition at line 459 of file vtkMolecule.h.
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Definition at line 460 of file vtkMolecule.h.
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Definition at line 461 of file vtkMolecule.h.
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Definition at line 463 of file vtkMolecule.h.
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Definition at line 464 of file vtkMolecule.h.
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Definition at line 466 of file vtkMolecule.h.
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Definition at line 467 of file vtkMolecule.h.