class describing a molecule More...

#include <vtkMolecule.h>

Inheritance diagram for vtkMolecule:

Collaboration diagram for vtkMolecule:

Public Types
typedef vtkUndirectedGraph	Superclass

Public Types inherited from vtkUndirectedGraph
typedef vtkGraph	Superclass

Public Types inherited from vtkGraph
typedef vtkDataObject	Superclass

Public Types inherited from vtkDataObject
typedef vtkObject	Superclass

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 }

enum	AttributeTypes { POINT, CELL, FIELD, POINT_THEN_CELL, VERTEX, EDGE, ROW, NUMBER_OF_ATTRIBUTE_TYPES }

enum	FieldOperations { FIELD_OPERATION_PRESERVED, FIELD_OPERATION_REINTERPOLATED, FIELD_OPERATION_MODIFIED, FIELD_OPERATION_REMOVED }

Public Types inherited from vtkObject
typedef vtkObjectBase	Superclass

Public Member Functions
virtual int	IsA (const char *type)

vtkMolecule *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent)

virtual void	Initialize ()

virtual int	GetDataObjectType ()

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

vtkAtom	GetAtom (vtkIdType atomId)

vtkIdType	GetNumberOfAtoms ()

vtkIdType	GetNumberOfBonds ()

unsigned short	GetAtomAtomicNumber (vtkIdType atomId)

double	GetBondLength (vtkIdType bondId)

virtual void	ShallowCopy (vtkDataObject *obj)

virtual void	DeepCopy (vtkDataObject *obj)

virtual void	ShallowCopyStructure (vtkMolecule *m)

virtual void	DeepCopyStructure (vtkMolecule *m)

virtual void	ShallowCopyAttributes (vtkMolecule *m)

virtual void	DeepCopyAttributes (vtkMolecule *m)


vtkAtom	AppendAtom ()


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


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

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


vtkBond	GetBond (vtkIdType bondId)


void	SetAtomAtomicNumber (vtkIdType atomId, unsigned short atomicNum)


void	SetAtomPosition (vtkIdType atomId, const vtkVector3f &pos)

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


vtkVector3f	GetAtomPosition (vtkIdType atomId)

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


void	SetBondOrder (vtkIdType bondId, unsigned short order)

unsigned short	GetBondOrder (vtkIdType bondId)


vtkPoints *	GetAtomicPositionArray ()

vtkUnsignedShortArray *	GetAtomicNumberArray ()


virtual vtkAbstractElectronicData *	GetElectronicData ()

virtual void	SetElectronicData (vtkAbstractElectronicData *)

Public Member Functions inherited from vtkUndirectedGraph
vtkUndirectedGraph *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent)

virtual vtkIdType	GetInDegree (vtkIdType v)

virtual bool	IsStructureValid (vtkGraph *g)

virtual vtkInEdgeType	GetInEdge (vtkIdType v, vtkIdType i)

virtual void	GetInEdge (vtkIdType v, vtkIdType i, vtkGraphEdge *e)

virtual void	GetInEdges (vtkIdType v, vtkInEdgeIterator *it)

Public Member Functions inherited from vtkGraph
vtkGraph *	NewInstance () const

void	ComputeBounds ()

unsigned long int	GetMTime ()

virtual void	GetOutEdges (vtkIdType v, vtkOutEdgeIterator *it)

virtual vtkIdType	GetDegree (vtkIdType v)

virtual vtkIdType	GetOutDegree (vtkIdType v)

virtual void	GetOutEdge (vtkIdType v, vtkIdType index, vtkGraphEdge *e)

virtual void	GetAdjacentVertices (vtkIdType v, vtkAdjacentVertexIterator *it)

virtual void	GetEdges (vtkEdgeListIterator *it)

virtual vtkIdType	GetNumberOfEdges ()

virtual void	GetVertices (vtkVertexListIterator *it)

virtual vtkIdType	GetNumberOfVertices ()

void	SetDistributedGraphHelper (vtkDistributedGraphHelper *helper)

vtkIdType	FindVertex (const vtkVariant &pedigreeID)

virtual void	CopyStructure (vtkGraph *g)

virtual bool	CheckedShallowCopy (vtkGraph *g)

virtual bool	CheckedDeepCopy (vtkGraph *g)

virtual void	Squeeze ()

void	ReorderOutVertices (vtkIdType v, vtkIdTypeArray *vertices)

bool	IsSameStructure (vtkGraph *other)

vtkIdType	GetNumberOfEdgePoints (vtkIdType e)

double *	GetEdgePoint (vtkIdType e, vtkIdType i)

void	ClearEdgePoints (vtkIdType e)

vtkGraphInternals *	GetGraphInternals (bool modifying)

void	GetInducedEdges (vtkIdTypeArray verts, vtkIdTypeArray edges)

virtual vtkFieldData *	GetAttributesAsFieldData (int type)

virtual vtkIdType	GetNumberOfElements (int type)

void	Dump ()

vtkIdType	GetEdgeId (vtkIdType a, vtkIdType b)

bool	ToDirectedGraph (vtkDirectedGraph *g)

bool	ToUndirectedGraph (vtkUndirectedGraph *g)

virtual vtkDataSetAttributes *	GetVertexData ()

virtual vtkDataSetAttributes *	GetEdgeData ()

double *	GetPoint (vtkIdType ptId)

void	GetPoint (vtkIdType ptId, double x[3])

vtkPoints *	GetPoints ()

virtual void	SetPoints (vtkPoints *points)

double *	GetBounds ()

void	GetBounds (double bounds[6])

virtual vtkOutEdgeType	GetOutEdge (vtkIdType v, vtkIdType index)

vtkDistributedGraphHelper *	GetDistributedGraphHelper ()

vtkIdType	GetSourceVertex (vtkIdType e)

vtkIdType	GetTargetVertex (vtkIdType e)

void	SetEdgePoints (vtkIdType e, vtkIdType npts, double *pts)

void	GetEdgePoints (vtkIdType e, vtkIdType &npts, double *&pts)

void	SetEdgePoint (vtkIdType e, vtkIdType i, double x[3])

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

void	AddEdgePoint (vtkIdType e, double x[3])

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

void	ShallowCopyEdgePoints (vtkGraph *g)

void	DeepCopyEdgePoints (vtkGraph *g)

Public Member Functions inherited from vtkDataObject
vtkDataObject *	NewInstance () const

void	ReleaseData ()

unsigned long	GetUpdateTime ()

virtual unsigned long	GetActualMemorySize ()

virtual void	CopyInformationToPipeline (vtkInformation *vtkNotUsed(info))

void	DataHasBeenGenerated ()

virtual void	PrepareForNewData ()

virtual int	GetExtentType ()

virtual void	Crop (const int *updateExtent)

virtual vtkDataSetAttributes *	GetAttributes (int type)

virtual int	GetAttributeTypeForArray (vtkAbstractArray *arr)

virtual vtkInformation *	GetInformation ()

virtual void	SetInformation (vtkInformation *)

virtual int	GetDataReleased ()

virtual void	SetFieldData (vtkFieldData *)

virtual vtkFieldData *	GetFieldData ()

virtual void	CopyInformationFromPipeline (vtkInformation *vtkNotUsed(info))

void	GlobalReleaseDataFlagOn ()

void	GlobalReleaseDataFlagOff ()

Public Member Functions inherited from vtkObject
vtkObject *	NewInstance () const

virtual void	DebugOn ()

virtual void	DebugOff ()

bool	GetDebug ()

void	SetDebug (bool debugFlag)

virtual void	Modified ()

unsigned long	AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)

unsigned long	AddObserver (const char event, vtkCommand , float priority=0.0f)

vtkCommand *	GetCommand (unsigned long tag)

void	RemoveObserver (vtkCommand *)

void	RemoveObservers (unsigned long event, vtkCommand *)

void	RemoveObservers (const char event, vtkCommand )

int	HasObserver (unsigned long event, vtkCommand *)

int	HasObserver (const char event, vtkCommand )

void	RemoveObserver (unsigned long tag)

void	RemoveObservers (unsigned long event)

void	RemoveObservers (const char *event)

void	RemoveAllObservers ()

int	HasObserver (unsigned long event)

int	HasObserver (const char *event)

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::*callback)(), float priority=0.0f)

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, bool(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)

int	InvokeEvent (unsigned long event, void *callData)

int	InvokeEvent (const char event, void callData)

int	InvokeEvent (unsigned long event)

int	InvokeEvent (const char *event)

Public Member Functions inherited from vtkObjectBase
const char *	GetClassName () const

virtual void	Delete ()

virtual void	FastDelete ()

void	Print (ostream &os)

virtual void	Register (vtkObjectBase *o)

virtual void	UnRegister (vtkObjectBase *o)

void	SetReferenceCount (int)

void	PrintRevisions (ostream &)

virtual void	PrintHeader (ostream &os, vtkIndent indent)

virtual void	PrintTrailer (ostream &os, vtkIndent indent)

int	GetReferenceCount ()

Static Public Member Functions
static vtkMolecule *	New ()

static int	IsTypeOf (const char *type)

static vtkMolecule *	SafeDownCast (vtkObjectBase *o)


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

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

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

static int	IsTypeOf (const char *type)

static vtkUndirectedGraph *	SafeDownCast (vtkObjectBase *o)

static vtkUndirectedGraph *	GetData (vtkInformation *info)

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

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

static vtkGraph *	SafeDownCast (vtkObjectBase *o)

static vtkGraph *	GetData (vtkInformation *info)

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

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

static int	IsTypeOf (const char *type)

static vtkDataObject *	SafeDownCast (vtkObjectBase *o)

static const char *	GetAssociationTypeAsString (int associationType)

static int	GetAssociationTypeFromString (const char *associationType)

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 *	BOUNDING_BOX ()

static vtkInformationDataObjectKey *	SIL ()

static vtkInformation *	GetActiveFieldInformation (vtkInformation *info, int fieldAssociation, int attributeType)

static vtkInformation *	GetNamedFieldInformation (vtkInformation info, int fieldAssociation, const char name)

static void	RemoveNamedFieldInformation (vtkInformation info, int fieldAssociation, const char name)

static vtkInformation *	SetActiveAttribute (vtkInformation info, int fieldAssociation, const char attributeName, int attributeType)

static void	SetActiveAttributeInfo (vtkInformation info, int fieldAssociation, int attributeType, const char name, int arrayType, int numComponents, int numTuples)

static void	SetPointDataActiveScalarInfo (vtkInformation *info, int arrayType, int numComponents)

static vtkDataObject *	GetData (vtkInformation *info)

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

static void	SetGlobalReleaseDataFlag (int val)

static int	GetGlobalReleaseDataFlag ()

Static Public Member Functions inherited from vtkObject
static int	IsTypeOf (const char *type)

static vtkObject *	SafeDownCast (vtkObjectBase *o)

static vtkObject *	New ()

static void	BreakOnError ()

static void	SetGlobalWarningDisplay (int val)

static void	GlobalWarningDisplayOn ()

static void	GlobalWarningDisplayOff ()

static int	GetGlobalWarningDisplay ()

Static Public Member Functions inherited from vtkObjectBase
static int	IsTypeOf (const char *name)

static vtkObjectBase *	New ()

Protected Member Functions
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkMolecule ()

	~vtkMolecule ()

virtual void	CopyStructureInternal (vtkMolecule *m, bool deep)

virtual void	CopyAttributesInternal (vtkMolecule *m, bool deep)

Protected Member Functions inherited from vtkUndirectedGraph
	vtkUndirectedGraph ()

	~vtkUndirectedGraph ()

virtual void	GetInEdges (vtkIdType v, const vtkInEdgeType *&edges, vtkIdType &nedges)

Protected Member Functions inherited from vtkGraph
	vtkGraph ()

	~vtkGraph ()

void	AddVertexInternal (const vtkVariant &pedigree, vtkIdType *vertex)

void	RemoveVertexInternal (vtkIdType v, bool directed)

void	RemoveEdgeInternal (vtkIdType e, bool directed)

void	RemoveVerticesInternal (vtkIdTypeArray *arr, bool directed)

virtual void	CopyInternal (vtkGraph *g, bool deep)

void	SetInternals (vtkGraphInternals *internals)

void	SetEdgePoints (vtkGraphEdgePoints *edgePoints)

void	ForceOwnership ()

void	BuildEdgeList ()

void	AddVertexInternal (vtkVariantArray propertyArr=0, vtkIdType vertex=0)

void	AddEdgeInternal (vtkIdType u, vtkIdType v, bool directed, vtkVariantArray propertyArr, vtkEdgeType edge)

void	AddEdgeInternal (const vtkVariant &uPedigree, vtkIdType v, bool directed, vtkVariantArray propertyArr, vtkEdgeType edge)

void	AddEdgeInternal (vtkIdType u, const vtkVariant &vPedigree, bool directed, vtkVariantArray propertyArr, vtkEdgeType edge)

void	AddEdgeInternal (const vtkVariant &uPedigree, const vtkVariant &vPedigree, bool directed, vtkVariantArray propertyArr, vtkEdgeType edge)

void	RemoveEdgesInternal (vtkIdTypeArray *arr, bool directed)

virtual void	GetOutEdges (vtkIdType v, const vtkOutEdgeType *&edges, vtkIdType &nedges)

virtual vtkIdTypeArray *	GetEdgeList ()

virtual void	SetEdgeList (vtkIdTypeArray *list)

Protected Member Functions inherited from vtkDataObject
	vtkDataObject ()

	~vtkDataObject ()

Protected Member Functions inherited from vtkObject
	vtkObject ()

virtual	~vtkObject ()

virtual void	RegisterInternal (vtkObjectBase *, int check)

virtual void	UnRegisterInternal (vtkObjectBase *, int check)

void	InternalGrabFocus (vtkCommand mouseEvents, vtkCommand keypressEvents=NULL)

void	InternalReleaseFocus ()

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
vtkAbstractElectronicData *	ElectronicData

Protected Attributes inherited from vtkGraph
vtkGraphInternals *	Internals

vtkDistributedGraphHelper *	DistributedHelper

vtkGraphEdgePoints *	EdgePoints

double	Bounds [6]

vtkTimeStamp	ComputeTime

vtkDataSetAttributes *	VertexData

vtkDataSetAttributes *	EdgeData

vtkPoints *	Points

vtkIdTypeArray *	EdgeList

Protected Attributes inherited from vtkDataObject
vtkFieldData *	FieldData

int	DataReleased

vtkTimeStamp	UpdateTime

vtkInformation *	Information

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

void	SetBondListDirty ()

void	UpdateBondList ()

Additional Inherited Members
Static Protected Attributes inherited from vtkGraph
static double	DefaultPoint [3]

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 convience vtkAtom and vtkBond classes:

Single call:

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

Incremental:

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

Both of the above methods will produce the same molecule, two hydrogens connected with a 1.0 Angstrom single bond, aligned to the z-axis. The second example also demostrates 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 88 of file vtkMolecule.h.

Member Typedef Documentation

typedef vtkUndirectedGraph vtkMolecule::Superclass

Definition at line 92 of file vtkMolecule.h.

Constructor & Destructor Documentation

vtkMolecule::vtkMolecule ( )

protected

vtkMolecule::~vtkMolecule ( )

protected

Member Function Documentation

static vtkMolecule* vtkMolecule::New ( )

static

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

static

virtual int 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
	)

virtual

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.

virtual void vtkMolecule::Initialize ( )

virtual

Initialize to an empty graph.

Reimplemented from vtkGraph.

virtual int vtkMolecule::GetDataObjectType ( )

inlinevirtual

Return what type of dataset this is.

Reimplemented from vtkUndirectedGraph.

Definition at line 97 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 103 of file vtkMolecule.h.

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

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,
		double	x,
		double	y,
		double	z
	)

inline

Convenience methods to append a new atom with the specified atomic number and position.

Definition at line 116 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 134 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.

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::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

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.

virtual void vtkMolecule::ShallowCopy ( vtkDataObject * obj )

virtual

Shallow copies the data object into this molecule.

Reimplemented from vtkGraph.

virtual void vtkMolecule::DeepCopy ( vtkDataObject * obj )

virtual

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.

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 255 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

Friends And Related Function Documentation

friend class vtkAtom

friend

Definition at line 259 of file vtkMolecule.h.

friend class vtkBond

friend

Definition at line 260 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 254 of file vtkMolecule.h.

vtkAbstractElectronicData* vtkMolecule::ElectronicData

protected

Definition at line 262 of file vtkMolecule.h.

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

/home/boeckb/code/depot/group-kitware/vtk/build-release/Utilities/Doxygen/dox/Common/DataModel/vtkMolecule.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation