Mapper that draws vtkMolecule objects. More...

#include <vtkMoleculeMapper.h>

Inheritance diagram for vtkMoleculeMapper:

Collaboration diagram for vtkMoleculeMapper:

Public Types
enum	{ CovalentRadius = 0, VDWRadius, UnitRadius }
enum	{ SingleColor = 0, DiscreteByAtom }
typedef vtkMapper	Superclass
Public Member Functions
virtual int	IsA (const char *type)
vtkMoleculeMapper *	NewInstance () const
void	PrintSelf (ostream &os, vtkIndent indent)
void	UseBallAndStickSettings ()
void	UseVDWSpheresSettings ()
void	UseLiquoriceStickSettings ()
void	UseFastSettings ()

void	SetInputData (vtkMolecule *in)
vtkMolecule *	GetInput ()

virtual bool	GetRenderAtoms ()
virtual void	SetRenderAtoms (bool)
virtual void	RenderAtomsOn ()
virtual void	RenderAtomsOff ()

virtual bool	GetRenderBonds ()
virtual void	SetRenderBonds (bool)
virtual void	RenderBondsOn ()
virtual void	RenderBondsOff ()

virtual int	GetAtomicRadiusType ()
virtual void	SetAtomicRadiusType (int)
const char *	GetAtomicRadiusTypeAsString ()
void	SetAtomicRadiusTypeToCovalentRadius ()
void	SetAtomicRadiusTypeToVDWRadius ()
void	SetAtomicRadiusTypeToUnitRadius ()

virtual float	GetAtomicRadiusScaleFactor ()
virtual void	SetAtomicRadiusScaleFactor (float)

virtual bool	GetUseMultiCylindersForBonds ()
virtual void	SetUseMultiCylindersForBonds (bool)
virtual void	UseMultiCylindersForBondsOn ()
virtual void	UseMultiCylindersForBondsOff ()

virtual int	GetBondColorMode ()
virtual void	SetBondColorMode (int)
const char *	GetBondColorModeAsString ()
void	SetBondColorModeToSingleColor ()
void	SetBondColorModeToDiscreteByAtom ()

virtual unsigned char *	GetBondColor ()
virtual void	GetBondColor (unsigned char &, unsigned char &, unsigned char &)
virtual void	GetBondColor (unsigned char[3])
virtual void	SetBondColor (unsigned char, unsigned char, unsigned char)
virtual void	SetBondColor (unsigned char[3])

virtual float	GetBondRadius ()
virtual void	SetBondRadius (float)

virtual void	GetSelectedAtomsAndBonds (vtkSelection selection, vtkIdTypeArray atomIds, vtkIdTypeArray *bondIds)
virtual void	GetSelectedAtoms (vtkSelection selection, vtkIdTypeArray atomIds)
virtual void	GetSelectedBonds (vtkSelection selection, vtkIdTypeArray bondIds)

virtual void	Render (vtkRenderer , vtkActor )
virtual void	ReleaseGraphicsResources (vtkWindow *)
double *	GetBounds ()
void	GetBounds (double bounds[6])
virtual int	FillInputPortInformation (int port, vtkInformation *info)
virtual bool	GetSupportsSelection ()
Static Public Member Functions
static vtkMoleculeMapper *	New ()
static int	IsTypeOf (const char *type)
static vtkMoleculeMapper *	SafeDownCast (vtkObjectBase *o)
Protected Member Functions
virtual vtkObjectBase *	NewInstanceInternal () const
	vtkMoleculeMapper ()
	~vtkMoleculeMapper ()
void	GlyphRender (vtkRenderer ren, vtkActor act)
Protected Attributes
vtkNew< vtkPeriodicTable >	PeriodicTable

bool	RenderAtoms
int	AtomicRadiusType
float	AtomicRadiusScaleFactor

bool	RenderBonds
int	BondColorMode
bool	UseMultiCylindersForBonds
float	BondRadius
unsigned char	BondColor [3]

vtkNew< vtkGlyph3DMapper >	AtomGlyphMapper
vtkNew< vtkGlyph3DMapper >	BondGlyphMapper
vtkNew< vtkPolyData >	AtomGlyphPolyData
vtkNew< vtkTrivialProducer >	AtomGlyphPointOutput
vtkNew< vtkPolyData >	BondGlyphPolyData
vtkNew< vtkTrivialProducer >	BondGlyphPointOutput
bool	GlyphDataInitialized
void	UpdateGlyphPolyData ()
void	UpdateAtomGlyphPolyData ()
void	UpdateBondGlyphPolyData ()

Detailed Description

Mapper that draws vtkMolecule objects.

vtkMoleculeMapper uses glyphs (display lists) to quickly render a molecule.

Tests:: vtkMoleculeMapper (Tests)

Definition at line 44 of file vtkMoleculeMapper.h.

Member Typedef Documentation

typedef vtkMapper vtkMoleculeMapper::Superclass

Reimplemented from vtkMapper.

Definition at line 48 of file vtkMoleculeMapper.h.

Member Enumeration Documentation

anonymous enum

Enumerator:

CovalentRadius
VDWRadius
UnitRadius

Definition at line 101 of file vtkMoleculeMapper.h.

anonymous enum

Enumerator:

SingleColor
DiscreteByAtom

Definition at line 142 of file vtkMoleculeMapper.h.

Constructor & Destructor Documentation

vtkMoleculeMapper::vtkMoleculeMapper ( ) [protected]

vtkMoleculeMapper::~vtkMoleculeMapper ( ) [protected]

Member Function Documentation

static vtkMoleculeMapper* vtkMoleculeMapper::New ( ) [static]

Create an object with Debug turned off, modified time initialized to zero, and reference counting on.

Reimplemented from vtkAlgorithm.

static int vtkMoleculeMapper::IsTypeOf ( const char * name ) [static]

Return 1 if this class type 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 vtkMapper.

virtual int vtkMoleculeMapper::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 vtkMapper.

static vtkMoleculeMapper* vtkMoleculeMapper::SafeDownCast ( vtkObjectBase * o ) [static]

Reimplemented from vtkMapper.

virtual vtkObjectBase* vtkMoleculeMapper::NewInstanceInternal ( ) const [protected, virtual]

Reimplemented from vtkMapper.

vtkMoleculeMapper* vtkMoleculeMapper::NewInstance ( ) const

Reimplemented from vtkMapper.

void vtkMoleculeMapper::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 vtkMapper.

void vtkMoleculeMapper::SetInputData ( vtkMolecule * in )

Get/Set the input vtkMolecule.

vtkMolecule* vtkMoleculeMapper::GetInput ( )

Get/Set the input vtkMolecule.

Reimplemented from vtkMapper.

void vtkMoleculeMapper::UseBallAndStickSettings ( )

Set ivars to default ball-and-stick settings. This is equivalent to the following: - SetRenderAtoms( true ) - SetRenderBonds( true ) - SetAtomicRadiusType( VDWRadius ) - SetAtomicRadiusScaleFactor( 0.3 )

SetBondColorMode( DiscreteByAtom ) - SetUseMultiCylindersForBonds( true ) - SetBondRadius( 0.075 )

void vtkMoleculeMapper::UseVDWSpheresSettings ( )

Set ivars to default van der Waals spheres settings. This is equivalent to the following: - SetRenderAtoms( true ) - SetRenderBonds( true ) - SetAtomicRadiusType( VDWRadius ) - SetAtomicRadiusScaleFactor( 1.0 ) - SetBondColorMode( DiscreteByAtom ) - SetUseMultiCylindersForBonds( true ) - SetBondRadius( 0.075 )

void vtkMoleculeMapper::UseLiquoriceStickSettings ( )

Set ivars to default liquorice stick settings. This is equivalent to the following: - SetRenderAtoms( true ) - SetRenderBonds( true ) - SetAtomicRadiusType( UnitRadius ) - SetAtomicRadiusScaleFactor( 0.1 )

SetBondColorMode( DiscreteByAtom ) - SetUseMultiCylindersForBonds( false ) - SetBondRadius( 0.1 )

void vtkMoleculeMapper::UseFastSettings ( )

Set ivars to use fast settings that may be useful for rendering extremely large molecules where the overall shape is more important than the details of the atoms/bond. This is equivalent to the following: - SetRenderAtoms( true ) - SetRenderBonds( true ) - SetAtomicRadiusType( UnitRadius ) - SetAtomicRadiusScaleFactor( 0.60 ) - SetBondColorMode( SingleColor ) - SetBondColor( 50, 50, 50 ) - SetUseMultiCylindersForBonds( false ) - SetBondRadius( 0.075 )

virtual bool vtkMoleculeMapper::GetRenderAtoms ( ) [virtual]

Get/Set whether or not to render atoms. Default: On.

virtual void vtkMoleculeMapper::SetRenderAtoms ( bool ) [virtual]

Get/Set whether or not to render atoms. Default: On.

virtual void vtkMoleculeMapper::RenderAtomsOn ( ) [virtual]

Get/Set whether or not to render atoms. Default: On.

virtual void vtkMoleculeMapper::RenderAtomsOff ( ) [virtual]

Get/Set whether or not to render atoms. Default: On.

virtual bool vtkMoleculeMapper::GetRenderBonds ( ) [virtual]

Get/Set whether or not to render bonds. Default: On.

virtual void vtkMoleculeMapper::SetRenderBonds ( bool ) [virtual]

Get/Set whether or not to render bonds. Default: On.

virtual void vtkMoleculeMapper::RenderBondsOn ( ) [virtual]

Get/Set whether or not to render bonds. Default: On.

virtual void vtkMoleculeMapper::RenderBondsOff ( ) [virtual]

Get/Set whether or not to render bonds. Default: On.

virtual int vtkMoleculeMapper::GetAtomicRadiusType ( ) [virtual]

Get/Set the type of radius used to generate the atoms. Default: VDWRadius.

virtual void vtkMoleculeMapper::SetAtomicRadiusType ( int ) [virtual]

Get/Set the type of radius used to generate the atoms. Default: VDWRadius.

const char* vtkMoleculeMapper::GetAtomicRadiusTypeAsString ( )

Get/Set the type of radius used to generate the atoms. Default: VDWRadius.

void vtkMoleculeMapper::SetAtomicRadiusTypeToCovalentRadius ( ) [inline]

Get/Set the type of radius used to generate the atoms. Default: VDWRadius.

Definition at line 113 of file vtkMoleculeMapper.h.

void vtkMoleculeMapper::SetAtomicRadiusTypeToVDWRadius ( ) [inline]

Get/Set the type of radius used to generate the atoms. Default: VDWRadius.

Definition at line 117 of file vtkMoleculeMapper.h.

void vtkMoleculeMapper::SetAtomicRadiusTypeToUnitRadius ( ) [inline]

Get/Set the type of radius used to generate the atoms. Default: VDWRadius.

Definition at line 121 of file vtkMoleculeMapper.h.

virtual float vtkMoleculeMapper::GetAtomicRadiusScaleFactor ( ) [virtual]

Get/Set the uniform scaling factor applied to the atoms. Default: 0.3.

virtual void vtkMoleculeMapper::SetAtomicRadiusScaleFactor ( float ) [virtual]

Get/Set the uniform scaling factor applied to the atoms. Default: 0.3.

virtual bool vtkMoleculeMapper::GetUseMultiCylindersForBonds ( ) [virtual]

Get/Set whether multicylinders will be used to represent multiple bonds. Default: On.

virtual void vtkMoleculeMapper::SetUseMultiCylindersForBonds ( bool ) [virtual]

Get/Set whether multicylinders will be used to represent multiple bonds. Default: On.

virtual void vtkMoleculeMapper::UseMultiCylindersForBondsOn ( ) [virtual]

Get/Set whether multicylinders will be used to represent multiple bonds. Default: On.

virtual void vtkMoleculeMapper::UseMultiCylindersForBondsOff ( ) [virtual]

Get/Set whether multicylinders will be used to represent multiple bonds. Default: On.

virtual int vtkMoleculeMapper::GetBondColorMode ( ) [virtual]

Get/Set the method by which bonds are colored. If 'SingleColor' is used, all bonds will be the same color. Use SetBondColor to set the rgb values used. If 'DiscreteByAtom' is selected, each bond is colored using the same lookup table as the atoms at each end, with a sharp color boundary at the bond center.

virtual void vtkMoleculeMapper::SetBondColorMode ( int ) [virtual]

Get/Set the method by which bonds are colored. If 'SingleColor' is used, all bonds will be the same color. Use SetBondColor to set the rgb values used. If 'DiscreteByAtom' is selected, each bond is colored using the same lookup table as the atoms at each end, with a sharp color boundary at the bond center.

const char* vtkMoleculeMapper::GetBondColorModeAsString ( )

Get/Set the method by which bonds are colored. If 'SingleColor' is used, all bonds will be the same color. Use SetBondColor to set the rgb values used. If 'DiscreteByAtom' is selected, each bond is colored using the same lookup table as the atoms at each end, with a sharp color boundary at the bond center.

void vtkMoleculeMapper::SetBondColorModeToSingleColor ( ) [inline]

Get/Set the method by which bonds are colored. If 'SingleColor' is used, all bonds will be the same color. Use SetBondColor to set the rgb values used. If 'DiscreteByAtom' is selected, each bond is colored using the same lookup table as the atoms at each end, with a sharp color boundary at the bond center.

Definition at line 156 of file vtkMoleculeMapper.h.

void vtkMoleculeMapper::SetBondColorModeToDiscreteByAtom ( ) [inline]

Get/Set the method by which bonds are colored. If 'SingleColor' is used, all bonds will be the same color. Use SetBondColor to set the rgb values used. If 'DiscreteByAtom' is selected, each bond is colored using the same lookup table as the atoms at each end, with a sharp color boundary at the bond center.

Definition at line 160 of file vtkMoleculeMapper.h.

virtual unsigned char* vtkMoleculeMapper::GetBondColor ( ) [virtual]

Get/Set the color of the bonds as an rgb tuple. Default: {50, 50, 50} (dark grey)

virtual void vtkMoleculeMapper::GetBondColor	(	unsigned char &	,
		unsigned char &	,
		unsigned char &
	)		`[virtual]`

Get/Set the color of the bonds as an rgb tuple. Default: {50, 50, 50} (dark grey)

virtual void vtkMoleculeMapper::GetBondColor ( unsigned char[3] ) [virtual]

Get/Set the color of the bonds as an rgb tuple. Default: {50, 50, 50} (dark grey)

virtual void vtkMoleculeMapper::SetBondColor	(	unsigned	char,
		unsigned	char,
		unsigned	char
	)		`[virtual]`

Get/Set the color of the bonds as an rgb tuple. Default: {50, 50, 50} (dark grey)

virtual void vtkMoleculeMapper::SetBondColor ( unsigned char[3] ) [virtual]

Get/Set the color of the bonds as an rgb tuple. Default: {50, 50, 50} (dark grey)

virtual float vtkMoleculeMapper::GetBondRadius ( ) [virtual]

Get/Set the radius of the bond cylinders. Default: 0.075

virtual void vtkMoleculeMapper::SetBondRadius ( float ) [virtual]

Get/Set the radius of the bond cylinders. Default: 0.075

virtual void vtkMoleculeMapper::GetSelectedAtomsAndBonds	(	vtkSelection *	selection,
		vtkIdTypeArray *	atomIds,
		vtkIdTypeArray *	bondIds
	)		`[virtual]`

Extract the ids atoms and/or bonds rendered by this molecule from a vtkSelection object. The vtkIdTypeArray

virtual void vtkMoleculeMapper::GetSelectedAtoms	(	vtkSelection *	selection,
		vtkIdTypeArray *	atomIds
	)		`[inline, virtual]`

Extract the ids atoms and/or bonds rendered by this molecule from a vtkSelection object. The vtkIdTypeArray

Definition at line 185 of file vtkMoleculeMapper.h.

virtual void vtkMoleculeMapper::GetSelectedBonds	(	vtkSelection *	selection,
		vtkIdTypeArray *	bondIds
	)		`[inline, virtual]`

Extract the ids atoms and/or bonds rendered by this molecule from a vtkSelection object. The vtkIdTypeArray

Definition at line 190 of file vtkMoleculeMapper.h.

virtual void vtkMoleculeMapper::Render	(	vtkRenderer *	,
		vtkActor *
	)		`[virtual]`

Reimplemented from base class

Implements vtkMapper.

virtual void vtkMoleculeMapper::ReleaseGraphicsResources ( vtkWindow * ) [virtual]

Reimplemented from base class

Reimplemented from vtkMapper.

double* vtkMoleculeMapper::GetBounds ( ) [virtual]

Reimplemented from base class

Reimplemented from vtkMapper.

void vtkMoleculeMapper::GetBounds ( double bounds[6] ) [inline, virtual]

Reimplemented from base class

Reimplemented from vtkMapper.

Definition at line 202 of file vtkMoleculeMapper.h.

virtual int vtkMoleculeMapper::FillInputPortInformation	(	int	port,
		vtkInformation *	info
	)		`[virtual]`

Reimplemented from base class

Reimplemented from vtkAlgorithm.

virtual bool vtkMoleculeMapper::GetSupportsSelection ( ) [inline, virtual]

Reimplemented from base class

Reimplemented from vtkMapper.

Definition at line 204 of file vtkMoleculeMapper.h.

void vtkMoleculeMapper::GlyphRender	(	vtkRenderer *	ren,
		vtkActor *	act
	)		`[protected]`

Internal render methods

void vtkMoleculeMapper::UpdateGlyphPolyData ( ) [protected]

Cached variables and update methods

void vtkMoleculeMapper::UpdateAtomGlyphPolyData ( ) [protected]

Cached variables and update methods

void vtkMoleculeMapper::UpdateBondGlyphPolyData ( ) [protected]

Cached variables and update methods

Member Data Documentation

bool vtkMoleculeMapper::RenderAtoms [protected]

Customize atom rendering

Definition at line 213 of file vtkMoleculeMapper.h.

int vtkMoleculeMapper::AtomicRadiusType [protected]

Customize atom rendering

Definition at line 214 of file vtkMoleculeMapper.h.

float vtkMoleculeMapper::AtomicRadiusScaleFactor [protected]

Customize atom rendering

Definition at line 215 of file vtkMoleculeMapper.h.

bool vtkMoleculeMapper::RenderBonds [protected]

Customize bond rendering

Definition at line 220 of file vtkMoleculeMapper.h.

int vtkMoleculeMapper::BondColorMode [protected]

Customize bond rendering

Definition at line 221 of file vtkMoleculeMapper.h.

bool vtkMoleculeMapper::UseMultiCylindersForBonds [protected]

Customize bond rendering

Definition at line 222 of file vtkMoleculeMapper.h.

float vtkMoleculeMapper::BondRadius [protected]

Customize bond rendering

Definition at line 223 of file vtkMoleculeMapper.h.

unsigned char vtkMoleculeMapper::BondColor[3] [protected]

Customize bond rendering

Definition at line 224 of file vtkMoleculeMapper.h.

vtkNew<vtkPolyData> vtkMoleculeMapper::AtomGlyphPolyData [protected]

Cached variables and update methods

Definition at line 232 of file vtkMoleculeMapper.h.

vtkNew<vtkTrivialProducer> vtkMoleculeMapper::AtomGlyphPointOutput [protected]

Cached variables and update methods

Definition at line 233 of file vtkMoleculeMapper.h.

vtkNew<vtkPolyData> vtkMoleculeMapper::BondGlyphPolyData [protected]

Cached variables and update methods

Definition at line 234 of file vtkMoleculeMapper.h.

vtkNew<vtkTrivialProducer> vtkMoleculeMapper::BondGlyphPointOutput [protected]

Cached variables and update methods

Definition at line 235 of file vtkMoleculeMapper.h.

bool vtkMoleculeMapper::GlyphDataInitialized [protected]

Cached variables and update methods

Definition at line 236 of file vtkMoleculeMapper.h.

vtkNew<vtkGlyph3DMapper> vtkMoleculeMapper::AtomGlyphMapper [protected]

Internal mappers

Definition at line 244 of file vtkMoleculeMapper.h.

vtkNew<vtkGlyph3DMapper> vtkMoleculeMapper::BondGlyphMapper [protected]

Internal mappers

Definition at line 245 of file vtkMoleculeMapper.h.

vtkNew<vtkPeriodicTable> vtkMoleculeMapper::PeriodicTable [protected]

Periodic table for lookups

Definition at line 249 of file vtkMoleculeMapper.h.

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

dox/Domains/Chemistry/vtkMoleculeMapper.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation