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vtkMoleculeReaderBase Class Referenceabstract

read Molecular Data files More...

#include <vtkMoleculeReaderBase.h>

Inheritance diagram for vtkMoleculeReaderBase:
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Collaboration diagram for vtkMoleculeReaderBase:
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Public Types

typedef vtkPolyDataAlgorithm Superclass
 
- Public Types inherited from vtkPolyDataAlgorithm
typedef vtkAlgorithm Superclass
 
- Public Types inherited from vtkAlgorithm
typedef vtkObject Superclass
 
- Public Types inherited from vtkObject
typedef vtkObjectBase Superclass
 

Public Member Functions

virtual const char * GetClassName ()
 
virtual int IsA (const char *type)
 
void PrintSelf (ostream &os, vtkIndent indent)
 
virtual void SetFileName (const char *)
 
virtual char * GetFileName ()
 
virtual int GetNumberOfAtoms ()
 
virtual void SetBScale (double)
 
virtual double GetBScale ()
 
virtual void SetHBScale (double)
 
virtual double GetHBScale ()
 
- Public Member Functions inherited from vtkPolyDataAlgorithm
vtkDataObjectGetInput ()
 
vtkDataObjectGetInput (int port)
 
vtkPolyDataGetPolyDataInput (int port)
 
vtkPolyDataGetOutput ()
 
vtkPolyDataGetOutput (int)
 
virtual void SetOutput (vtkDataObject *d)
 
virtual int ProcessRequest (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
 
void SetInput (vtkDataObject *)
 
void SetInput (int, vtkDataObject *)
 
void AddInput (vtkDataObject *)
 
void AddInput (int, vtkDataObject *)
 
- Public Member Functions inherited from vtkAlgorithm
int HasExecutive ()
 
vtkExecutiveGetExecutive ()
 
virtual void SetExecutive (vtkExecutive *executive)
 
virtual int ModifyRequest (vtkInformation *request, int when)
 
vtkInformationGetInputPortInformation (int port)
 
vtkInformationGetOutputPortInformation (int port)
 
int GetNumberOfInputPorts ()
 
int GetNumberOfOutputPorts ()
 
void UpdateProgress (double amount)
 
vtkInformationGetInputArrayInformation (int idx)
 
void RemoveAllInputs ()
 
vtkDataObjectGetOutputDataObject (int port)
 
virtual void RemoveInputConnection (int port, vtkAlgorithmOutput *input)
 
int GetNumberOfInputConnections (int port)
 
int GetTotalNumberOfInputConnections ()
 
vtkAlgorithmOutputGetInputConnection (int port, int index)
 
virtual void Update ()
 
virtual void UpdateInformation ()
 
virtual void UpdateWholeExtent ()
 
void ConvertTotalInputToPortConnection (int ind, int &port, int &conn)
 
virtual double ComputePriority ()
 
int ProcessRequest (vtkInformation *request, vtkCollection *inInfo, vtkInformationVector *outInfo)
 
virtual int ComputePipelineMTime (vtkInformation *request, vtkInformationVector **inInfoVec, vtkInformationVector *outInfoVec, int requestFromOutputPort, unsigned long *mtime)
 
virtual vtkInformationGetInformation ()
 
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)
 
vtkDataObjectGetInputDataObject (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)
 
vtkAlgorithmOutputGetOutputPort (int index)
 
vtkAlgorithmOutputGetOutputPort ()
 
virtual void SetReleaseDataFlag (int)
 
virtual int GetReleaseDataFlag ()
 
void ReleaseDataFlagOn ()
 
void ReleaseDataFlagOff ()
 
int UpdateExtentIsEmpty (vtkDataObject *output)
 
int UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)
 
- Public Member Functions inherited from vtkObject
virtual void DebugOn ()
 
virtual void DebugOff ()
 
unsigned char GetDebug ()
 
void SetDebug (unsigned char 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)
 
vtkCommandGetCommand (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)
 
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 &os)
 
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 vtkMoleculeReaderBaseSafeDownCast (vtkObject *o)
 
- Static Public Member Functions inherited from vtkPolyDataAlgorithm
static vtkPolyDataAlgorithmNew ()
 
static int IsTypeOf (const char *type)
 
static vtkPolyDataAlgorithmSafeDownCast (vtkObject *o)
 
- Static Public Member Functions inherited from vtkAlgorithm
static vtkAlgorithmNew ()
 
static int IsTypeOf (const char *type)
 
static vtkAlgorithmSafeDownCast (vtkObject *o)
 
static void SetDefaultExecutivePrototype (vtkExecutive *proto)
 
static vtkInformationIntegerKeyINPUT_IS_OPTIONAL ()
 
static vtkInformationIntegerKeyINPUT_IS_REPEATABLE ()
 
static
vtkInformationInformationVectorKey
INPUT_REQUIRED_FIELDS ()
 
static
vtkInformationStringVectorKey
INPUT_REQUIRED_DATA_TYPE ()
 
static
vtkInformationInformationVectorKey
INPUT_ARRAYS_TO_PROCESS ()
 
static vtkInformationIntegerKeyINPUT_PORT ()
 
static vtkInformationIntegerKeyINPUT_CONNECTION ()
 
static vtkInformationIntegerKeyPRESERVES_DATASET ()
 
static vtkInformationIntegerKeyPRESERVES_GEOMETRY ()
 
static vtkInformationIntegerKeyPRESERVES_BOUNDS ()
 
static vtkInformationIntegerKeyPRESERVES_TOPOLOGY ()
 
static vtkInformationIntegerKeyPRESERVES_ATTRIBUTES ()
 
static vtkInformationIntegerKeyPRESERVES_RANGES ()
 
- Static Public Member Functions inherited from vtkObject
static int IsTypeOf (const char *type)
 
static vtkObjectSafeDownCast (vtkObject *o)
 
static vtkObjectNew ()
 
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 vtkObjectBaseNew ()
 

Protected Member Functions

 vtkMoleculeReaderBase ()
 
 ~vtkMoleculeReaderBase ()
 
virtual int RequestData (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
 
int ReadMolecule (FILE *fp, vtkPolyData *output)
 
int MakeAtomType (const char *atype)
 
int MakeBonds (vtkPoints *, vtkIdTypeArray *, vtkCellArray *)
 
virtual void ReadSpecificMolecule (FILE *fp)=0
 
- 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 FillInputPortInformation (int port, vtkInformation *info)
 
virtual int RequestUpdateExtent (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
 
virtual void ExecuteData (vtkDataObject *output)
 
virtual void Execute ()
 
- 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 vtkExecutiveCreateDefaultExecutive ()
 
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)
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkInformationVector **inputVector)
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
 
vtkDataArrayGetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
 
vtkDataArrayGetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkDataObject *input)
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkDataObject *input, int &association)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, vtkDataObject *input)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association)
 
vtkInformationGetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector)
 
virtual void SetNthInputConnection (int port, int index, vtkAlgorithmOutput *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 &os)
 
 vtkObjectBase (const vtkObjectBase &)
 
void operator= (const vtkObjectBase &)
 

Protected Attributes

char * FileName
 
double BScale
 
double HBScale
 
int NumberOfAtoms
 
vtkPointsPoints
 
vtkUnsignedCharArrayRGB
 
vtkFloatArrayRadii
 
vtkIdTypeArrayAtomType
 

Additional Inherited Members

- Public Attributes inherited from vtkAlgorithm
int AbortExecute
 
- Static Protected Member Functions inherited from vtkAlgorithm
static vtkInformationIntegerKeyPORT_REQUIREMENTS_FILLED ()
 
- Static Protected Attributes inherited from vtkAlgorithm
static vtkExecutiveDefaultExecutivePrototype
 
- Friends inherited from vtkObject

Detailed Description

read Molecular Data files

vtkMoleculeReaderBase is a source object that reads Molecule files The FileName must be specified

Thanks:
Dr. Jean M. Favre who developed and contributed this class

Definition at line 37 of file vtkMoleculeReaderBase.h.

Member Typedef Documentation

Definition at line 40 of file vtkMoleculeReaderBase.h.

Constructor & Destructor Documentation

vtkMoleculeReaderBase::vtkMoleculeReaderBase ( )
protected
vtkMoleculeReaderBase::~vtkMoleculeReaderBase ( )
protected

Member Function Documentation

virtual const char* vtkMoleculeReaderBase::GetClassName ( )
virtual

Reimplemented from vtkPolyDataAlgorithm.

Reimplemented in vtkGaussianCubeReader, vtkPDBReader, and vtkXYZMolReader.

static int vtkMoleculeReaderBase::IsTypeOf ( const char *  type)
static
virtual int vtkMoleculeReaderBase::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.

Reimplemented in vtkGaussianCubeReader, vtkPDBReader, and vtkXYZMolReader.

static vtkMoleculeReaderBase* vtkMoleculeReaderBase::SafeDownCast ( vtkObject o)
static
void vtkMoleculeReaderBase::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.

Reimplemented in vtkPDBReader, and vtkXYZMolReader.

virtual void vtkMoleculeReaderBase::SetFileName ( const char *  )
virtual

Reimplemented in vtkGaussianCubeReader.

virtual char* vtkMoleculeReaderBase::GetFileName ( )
virtual

Reimplemented in vtkGaussianCubeReader.

virtual void vtkMoleculeReaderBase::SetBScale ( double  )
virtual

A scaling factor to compute bonds between non-hydrogen atoms

virtual double vtkMoleculeReaderBase::GetBScale ( )
virtual

A scaling factor to compute bonds between non-hydrogen atoms

virtual void vtkMoleculeReaderBase::SetHBScale ( double  )
virtual

A scaling factor to compute bonds with hydrogen atoms.

virtual double vtkMoleculeReaderBase::GetHBScale ( )
virtual

A scaling factor to compute bonds with hydrogen atoms.

virtual int vtkMoleculeReaderBase::GetNumberOfAtoms ( )
virtual
virtual int vtkMoleculeReaderBase::RequestData ( vtkInformation request,
vtkInformationVector **  inputVector,
vtkInformationVector outputVector 
)
protectedvirtual

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

Reimplemented from vtkPolyDataAlgorithm.

Reimplemented in vtkGaussianCubeReader.

int vtkMoleculeReaderBase::ReadMolecule ( FILE *  fp,
vtkPolyData output 
)
protected
int vtkMoleculeReaderBase::MakeAtomType ( const char *  atype)
protected
int vtkMoleculeReaderBase::MakeBonds ( vtkPoints ,
vtkIdTypeArray ,
vtkCellArray  
)
protected
virtual void vtkMoleculeReaderBase::ReadSpecificMolecule ( FILE *  fp)
protectedpure virtual

Member Data Documentation

char* vtkMoleculeReaderBase::FileName
protected

Definition at line 64 of file vtkMoleculeReaderBase.h.

double vtkMoleculeReaderBase::BScale
protected

Definition at line 65 of file vtkMoleculeReaderBase.h.

double vtkMoleculeReaderBase::HBScale
protected

Definition at line 66 of file vtkMoleculeReaderBase.h.

int vtkMoleculeReaderBase::NumberOfAtoms
protected

Definition at line 67 of file vtkMoleculeReaderBase.h.

vtkPoints* vtkMoleculeReaderBase::Points
protected

Definition at line 74 of file vtkMoleculeReaderBase.h.

vtkUnsignedCharArray* vtkMoleculeReaderBase::RGB
protected

Definition at line 75 of file vtkMoleculeReaderBase.h.

vtkFloatArray* vtkMoleculeReaderBase::Radii
protected

Definition at line 76 of file vtkMoleculeReaderBase.h.

vtkIdTypeArray* vtkMoleculeReaderBase::AtomType
protected

Definition at line 77 of file vtkMoleculeReaderBase.h.


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