generates protein ribbons More...

#include <vtkProteinRibbonFilter.h>

Inheritance diagram for vtkProteinRibbonFilter:

Collaboration diagram for vtkProteinRibbonFilter:

Public Types
typedef vtkPolyDataAlgorithm	Superclass

Public Types inherited from vtkPolyDataAlgorithm
typedef vtkAlgorithm	Superclass

Public Types inherited from vtkAlgorithm
typedef vtkObject	Superclass

enum	DesiredOutputPrecision { SINGLE_PRECISION, DOUBLE_PRECISION, DEFAULT_PRECISION }

Public Types inherited from vtkObject
typedef vtkObjectBase	Superclass

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

vtkProteinRibbonFilter *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent)


virtual float	GetCoilWidth ()

virtual void	SetCoilWidth (float)


virtual float	GetHelixWidth ()

virtual void	SetHelixWidth (float)


virtual int	GetSubdivideFactor ()

virtual void	SetSubdivideFactor (int)


virtual bool	GetDrawSmallMoleculesAsSpheres ()

virtual void	SetDrawSmallMoleculesAsSpheres (bool)


virtual int	GetSphereResolution ()

virtual void	SetSphereResolution (int)

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

vtkDataObject *	GetInput ()

vtkDataObject *	GetInput (int port)

vtkPolyData *	GetPolyDataInput (int port)

vtkPolyData *	GetOutput ()

vtkPolyData *	GetOutput (int)

virtual void	SetOutput (vtkDataObject *d)

virtual int	ProcessRequest (vtkInformation , vtkInformationVector , vtkInformationVector )

void	SetInputData (vtkDataObject *)

void	SetInputData (int, vtkDataObject *)

void	AddInputData (vtkDataObject *)

void	AddInputData (int, vtkDataObject *)

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

int	HasExecutive ()

vtkExecutive *	GetExecutive ()

virtual void	SetExecutive (vtkExecutive *executive)

virtual int	ModifyRequest (vtkInformation *request, int when)

vtkInformation *	GetInputPortInformation (int port)

vtkInformation *	GetOutputPortInformation (int port)

int	GetNumberOfInputPorts ()

int	GetNumberOfOutputPorts ()

void	UpdateProgress (double amount)

vtkInformation *	GetInputArrayInformation (int idx)

void	RemoveAllInputs ()

vtkDataObject *	GetOutputDataObject (int port)

virtual void	RemoveInputConnection (int port, vtkAlgorithmOutput *input)

virtual void	RemoveInputConnection (int port, int idx)

virtual void	RemoveAllInputConnections (int port)

int	GetNumberOfInputConnections (int port)

int	GetTotalNumberOfInputConnections ()

vtkAlgorithmOutput *	GetInputConnection (int port, int index)

vtkAlgorithm *	GetInputAlgorithm (int port, int index, int &algPort)

vtkAlgorithm *	GetInputAlgorithm (int port, int index)

vtkExecutive *	GetInputExecutive (int port, int index)

vtkInformation *	GetInputInformation (int port, int index)

vtkInformation *	GetOutputInformation (int port)

virtual void	UpdateInformation ()

virtual void	UpdateDataObject ()

virtual void	PropagateUpdateExtent ()

virtual void	UpdateWholeExtent ()

void	ConvertTotalInputToPortConnection (int ind, int &port, int &conn)

int	SetUpdateExtentToWholeExtent (int port)

int	SetUpdateExtentToWholeExtent ()

void	SetUpdateExtent (int port, int extent[6])

int	ProcessRequest (vtkInformation request, vtkCollection inInfo, vtkInformationVector *outInfo)

virtual int	ComputePipelineMTime (vtkInformation request, vtkInformationVector inInfoVec, vtkInformationVector outInfoVec, int requestFromOutputPort, unsigned long *mtime)

virtual vtkInformation *	GetInformation ()

virtual void	SetInformation (vtkInformation *)

virtual void	Register (vtkObjectBase *o)

virtual void	UnRegister (vtkObjectBase *o)

virtual void	SetAbortExecute (int)

virtual int	GetAbortExecute ()

virtual void	AbortExecuteOn ()

virtual void	AbortExecuteOff ()

virtual void	SetProgress (double)

virtual double	GetProgress ()

void	SetProgressText (const char *ptext)

virtual char *	GetProgressText ()

virtual unsigned long	GetErrorCode ()

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, const char *name)

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, int fieldAttributeType)

virtual void	SetInputArrayToProcess (int idx, vtkInformation *info)

virtual void	SetInputArrayToProcess (int idx, int port, int connection, const char fieldAssociation, const char attributeTypeorName)

vtkDataObject *	GetInputDataObject (int port, int connection)

virtual void	SetInputConnection (int port, vtkAlgorithmOutput *input)

virtual void	SetInputConnection (vtkAlgorithmOutput *input)

virtual void	AddInputConnection (int port, vtkAlgorithmOutput *input)

virtual void	AddInputConnection (vtkAlgorithmOutput *input)

virtual void	SetInputDataObject (int port, vtkDataObject *data)

virtual void	SetInputDataObject (vtkDataObject *data)

virtual void	AddInputDataObject (int port, vtkDataObject *data)

virtual void	AddInputDataObject (vtkDataObject *data)

vtkAlgorithmOutput *	GetOutputPort (int index)

vtkAlgorithmOutput *	GetOutputPort ()

vtkAlgorithm *	GetInputAlgorithm ()

vtkExecutive *	GetInputExecutive ()

vtkInformation *	GetInputInformation ()

virtual void	Update (int port)

virtual void	Update ()

virtual void	SetReleaseDataFlag (int)

virtual int	GetReleaseDataFlag ()

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

int	UpdateExtentIsEmpty (vtkInformation pinfo, vtkDataObject output)

int	UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)

void	SetUpdateExtent (int port, int piece, int numPieces, int ghostLevel)

void	SetUpdateExtent (int piece, int numPieces, int ghostLevel)

void	SetUpdateExtent (int extent[6])

int *	GetUpdateExtent ()

int *	GetUpdateExtent (int port)

void	GetUpdateExtent (int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)

void	GetUpdateExtent (int port, int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)

void	GetUpdateExtent (int extent[6])

void	GetUpdateExtent (int port, int extent[6])

int	GetUpdatePiece ()

int	GetUpdatePiece (int port)

int	GetUpdateNumberOfPieces ()

int	GetUpdateNumberOfPieces (int port)

int	GetUpdateGhostLevel ()

int	GetUpdateGhostLevel (int port)

void	SetProgressObserver (vtkProgressObserver *)

virtual vtkProgressObserver *	GetProgressObserver ()

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

virtual void	DebugOn ()

virtual void	DebugOff ()

bool	GetDebug ()

void	SetDebug (bool debugFlag)

virtual void	Modified ()

virtual unsigned long	GetMTime ()

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)

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 int	IsTypeOf (const char *type)

static vtkProteinRibbonFilter *	SafeDownCast (vtkObjectBase *o)

static vtkProteinRibbonFilter *	New ()

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

static int	IsTypeOf (const char *type)

static vtkPolyDataAlgorithm *	SafeDownCast (vtkObjectBase *o)

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

static int	IsTypeOf (const char *type)

static vtkAlgorithm *	SafeDownCast (vtkObjectBase *o)

static vtkInformationIntegerKey *	INPUT_IS_OPTIONAL ()

static vtkInformationIntegerKey *	INPUT_IS_REPEATABLE ()

static vtkInformationInformationVectorKey *	INPUT_REQUIRED_FIELDS ()

static vtkInformationStringVectorKey *	INPUT_REQUIRED_DATA_TYPE ()

static vtkInformationInformationVectorKey *	INPUT_ARRAYS_TO_PROCESS ()

static vtkInformationIntegerKey *	INPUT_PORT ()

static vtkInformationIntegerKey *	INPUT_CONNECTION ()

static vtkInformationIntegerKey *	CAN_PRODUCE_SUB_EXTENT ()

static vtkInformationIntegerKey *	CAN_HANDLE_PIECE_REQUEST ()

static void	SetDefaultExecutivePrototype (vtkExecutive *proto)

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

	vtkProteinRibbonFilter ()

	~vtkProteinRibbonFilter ()

int	FillInputPortInformation (int, vtkInformation *)

int	RequestData (vtkInformation , vtkInformationVector , vtkInformationVector )

void	CreateThinStrip (vtkPolyData poly, vtkUnsignedCharArray pointsColors, vtkPoints *p, std::vector< std::pair< vtkVector3f, bool > > &p1, std::vector< std::pair< vtkVector3f, bool > > &p2, std::vector< vtkColor3ub > &colors)

void	CreateAtomAsSphere (vtkPolyData poly, vtkUnsignedCharArray pointsColors, double *pos, const vtkColor3ub &color, float radius, float scale)

void	SetColorByAtom (std::vector< vtkColor3ub > &colors, vtkStringArray *atomTypes)

void	SetColorByStructure (std::vector< vtkColor3ub > &colors, vtkStringArray atomTypes, vtkUnsignedCharArray ss, const vtkColor3ub &helixColor, const vtkColor3ub &sheetColor)

Protected Member Functions inherited from vtkPolyDataAlgorithm
	vtkPolyDataAlgorithm ()

	~vtkPolyDataAlgorithm ()

virtual int	RequestInformation (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)

virtual int	FillOutputPortInformation (int port, vtkInformation *info)

virtual int	RequestUpdateExtent (vtkInformation , vtkInformationVector , vtkInformationVector )

Protected Member Functions inherited from vtkAlgorithm
	vtkAlgorithm ()

	~vtkAlgorithm ()

virtual void	SetNumberOfInputPorts (int n)

virtual void	SetNumberOfOutputPorts (int n)

int	InputPortIndexInRange (int index, const char *action)

int	OutputPortIndexInRange (int index, const char *action)

int	GetInputArrayAssociation (int idx, vtkInformationVector **inputVector)

virtual vtkExecutive *	CreateDefaultExecutive ()

virtual void	ReportReferences (vtkGarbageCollector *)

virtual void	SetNumberOfInputConnections (int port, int n)

int	GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector)

int	GetInputArrayAssociation (int idx, vtkDataObject *input)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input, int &association)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association)

vtkInformation *	GetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector)

virtual void	SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input)

void	SetInputDataInternal (int port, vtkDataObject *input)

void	AddInputDataInternal (int port, vtkDataObject *input)

virtual void	SetErrorCode (unsigned long)

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 &)

	vtkObjectBase (const vtkObjectBase &)

void	operator= (const vtkObjectBase &)

Static Protected Member Functions
static std::vector< vtkVector3f > *	Subdivide (std::vector< std::pair< vtkVector3f, bool > > &p, int div)

Static Protected Member Functions inherited from vtkAlgorithm
static vtkInformationIntegerKey *	PORT_REQUIREMENTS_FILLED ()

Protected Attributes
std::map< std::string, vtkColor3ub >	ElementColors

float	CoilWidth

float	HelixWidth

int	SphereResolution

int	SubdivideFactor

bool	DrawSmallMoleculesAsSpheres

Protected Attributes inherited from vtkAlgorithm
vtkInformation *	Information

double	Progress

char *	ProgressText

vtkProgressObserver *	ProgressObserver

unsigned long	ErrorCode

Protected Attributes inherited from vtkObject
bool	Debug

vtkTimeStamp	MTime

vtkSubjectHelper *	SubjectHelper

Protected Attributes inherited from vtkObjectBase
vtkAtomicInt32	ReferenceCount

vtkWeakPointerBase **	WeakPointers

Additional Inherited Members
Public Attributes inherited from vtkAlgorithm
int	AbortExecute

Static Protected Attributes inherited from vtkAlgorithm
static vtkExecutive *	DefaultExecutivePrototype

Detailed Description

generates protein ribbons

vtkProteinRibbonFilter is a polydata algorithm that generates protein ribbons.

Tests:: vtkProteinRibbonFilter (Tests)

Definition at line 38 of file vtkProteinRibbonFilter.h.

Member Typedef Documentation

typedef vtkPolyDataAlgorithm vtkProteinRibbonFilter::Superclass

Definition at line 42 of file vtkProteinRibbonFilter.h.

Constructor & Destructor Documentation

vtkProteinRibbonFilter::vtkProteinRibbonFilter ( )

protected

vtkProteinRibbonFilter::~vtkProteinRibbonFilter ( )

protected

Member Function Documentation

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

static

virtual int vtkProteinRibbonFilter::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 vtkPolyDataAlgorithm.

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

static

virtual vtkObjectBase* vtkProteinRibbonFilter::NewInstanceInternal ( ) const

protectedvirtual

Reimplemented from vtkPolyDataAlgorithm.

vtkProteinRibbonFilter* vtkProteinRibbonFilter::NewInstance ( ) const

void vtkProteinRibbonFilter::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 vtkPolyDataAlgorithm.

static vtkProteinRibbonFilter* vtkProteinRibbonFilter::New ( )

static

virtual float vtkProteinRibbonFilter::GetCoilWidth ( )

virtual

Width of the ribbon coil. Default is 0.3.

virtual void vtkProteinRibbonFilter::SetCoilWidth ( float )

virtual

Width of the ribbon coil. Default is 0.3.

virtual float vtkProteinRibbonFilter::GetHelixWidth ( )

virtual

Width of the helix part of the ribbon. Default is 1.3.

virtual void vtkProteinRibbonFilter::SetHelixWidth ( float )

virtual

Width of the helix part of the ribbon. Default is 1.3.

virtual int vtkProteinRibbonFilter::GetSubdivideFactor ( )

virtual

Smoothing factor of the ribbon. Default is 20.

virtual void vtkProteinRibbonFilter::SetSubdivideFactor ( int )

virtual

Smoothing factor of the ribbon. Default is 20.

virtual bool vtkProteinRibbonFilter::GetDrawSmallMoleculesAsSpheres ( )

virtual

If enabled, small molecules (HETATMs) are drawn as spheres. Default is true.

virtual void vtkProteinRibbonFilter::SetDrawSmallMoleculesAsSpheres ( bool )

virtual

If enabled, small molecules (HETATMs) are drawn as spheres. Default is true.

virtual int vtkProteinRibbonFilter::GetSphereResolution ( )

virtual

Resolution of the spheres for small molecules. Default is 20.

virtual void vtkProteinRibbonFilter::SetSphereResolution ( int )

virtual

Resolution of the spheres for small molecules. Default is 20.

int vtkProteinRibbonFilter::FillInputPortInformation	(	int	port,
		vtkInformation *	info
	)

protectedvirtual

Fill the input port information objects for this algorithm. This is invoked by the first call to GetInputPortInformation for each port so subclasses can specify what they can handle.

Reimplemented from vtkPolyDataAlgorithm.

int vtkProteinRibbonFilter::RequestData	(	vtkInformation *	request,
		vtkInformationVector **	inputVector,
		vtkInformationVector *	outputVector
	)

protectedvirtual

This is called by the superclass. This is the method you should override.

Reimplemented from vtkPolyDataAlgorithm.

void vtkProteinRibbonFilter::CreateThinStrip	(	vtkPolyData *	poly,
		vtkUnsignedCharArray *	pointsColors,
		vtkPoints *	p,
		std::vector< std::pair< vtkVector3f, bool > > &	p1,
		std::vector< std::pair< vtkVector3f, bool > > &	p2,
		std::vector< vtkColor3ub > &	colors
	)

protected

void vtkProteinRibbonFilter::CreateAtomAsSphere	(	vtkPolyData *	poly,
		vtkUnsignedCharArray *	pointsColors,
		double *	pos,
		const vtkColor3ub &	color,
		float	radius,
		float	scale
	)

protected

static std::vector<vtkVector3f>* vtkProteinRibbonFilter::Subdivide	(	std::vector< std::pair< vtkVector3f, bool > > &	p,
		int	div
	)

staticprotected

void vtkProteinRibbonFilter::SetColorByAtom	(	std::vector< vtkColor3ub > &	colors,
		vtkStringArray *	atomTypes
	)

protected

void vtkProteinRibbonFilter::SetColorByStructure	(	std::vector< vtkColor3ub > &	colors,
		vtkStringArray *	atomTypes,
		vtkUnsignedCharArray *	ss,
		const vtkColor3ub &	helixColor,
		const vtkColor3ub &	sheetColor
	)

protected

Member Data Documentation

std::map<std::string, vtkColor3ub> vtkProteinRibbonFilter::ElementColors

protected

Definition at line 107 of file vtkProteinRibbonFilter.h.

float vtkProteinRibbonFilter::CoilWidth

protected

Definition at line 109 of file vtkProteinRibbonFilter.h.

float vtkProteinRibbonFilter::HelixWidth

protected

Definition at line 110 of file vtkProteinRibbonFilter.h.

int vtkProteinRibbonFilter::SphereResolution

protected

Definition at line 111 of file vtkProteinRibbonFilter.h.

int vtkProteinRibbonFilter::SubdivideFactor

protected

Definition at line 112 of file vtkProteinRibbonFilter.h.

bool vtkProteinRibbonFilter::DrawSmallMoleculesAsSpheres

protected

Definition at line 113 of file vtkProteinRibbonFilter.h.

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

dox/Domains/Chemistry/vtkProteinRibbonFilter.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation