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vtkXYZMolReader Class Reference

read Molecular Data files More...

#include <vtkXYZMolReader.h>

Inheritance diagram for vtkXYZMolReader:
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Collaboration diagram for vtkXYZMolReader:
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Public Types

typedef vtkMoleculeReaderBase Superclass
- Public Types inherited from vtkMoleculeReaderBase
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 int CanReadFile (const char *name)
virtual void SetTimeStep (int)
virtual int GetTimeStep ()
virtual int GetMaxTimeStep ()
- Public Member Functions inherited from vtkMoleculeReaderBase
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 vtkXYZMolReaderSafeDownCast (vtkObject *o)
static vtkXYZMolReaderNew ()

Protected Member Functions

 vtkXYZMolReader ()
 ~vtkXYZMolReader ()
void ReadSpecificMolecule (FILE *fp)
char * GetNextLine (FILE *fp, char *line, int maxlen)
int GetLine1 (const char *line, int *cnt)
int GetLine2 (const char *line, char *name)
int GetAtom (const char *line, char *atom, float *x)
void InsertAtom (const char *atom, float *pos)
virtual void SetMaxTimeStep (int)
- Protected Member Functions inherited from vtkMoleculeReaderBase
 vtkMoleculeReaderBase ()
 ~vtkMoleculeReaderBase ()
virtual int RequestData (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
int ReadMolecule (FILE *fp, vtkPolyData *output)
int MakeAtomType (const char *atype)
int MakeBonds (vtkPoints *, vtkIdTypeArray *, vtkCellArray *)
- 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

int TimeStep
int MaxTimeStep
- Protected Attributes inherited from vtkMoleculeReaderBase
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

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

Thanks:
Dr. Jean M. Favre who developed and contributed this class
Tests:
vtkXYZMolReader (Tests)

Definition at line 34 of file vtkXYZMolReader.h.

Member Typedef Documentation

Definition at line 37 of file vtkXYZMolReader.h.

Constructor & Destructor Documentation

vtkXYZMolReader::vtkXYZMolReader ( )
protected
vtkXYZMolReader::~vtkXYZMolReader ( )
protected

Member Function Documentation

virtual const char* vtkXYZMolReader::GetClassName ( )
virtual

Reimplemented from vtkMoleculeReaderBase.

static int vtkXYZMolReader::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 vtkMoleculeReaderBase.

virtual int vtkXYZMolReader::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 vtkMoleculeReaderBase.

static vtkXYZMolReader* vtkXYZMolReader::SafeDownCast ( vtkObject o)
static

Reimplemented from vtkMoleculeReaderBase.

void vtkXYZMolReader::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 vtkMoleculeReaderBase.

static vtkXYZMolReader* vtkXYZMolReader::New ( )
static

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

Reimplemented from vtkPolyDataAlgorithm.

virtual int vtkXYZMolReader::CanReadFile ( const char *  name)
virtual

Test whether the file with the given name can be read by this reader.

virtual void vtkXYZMolReader::SetTimeStep ( int  )
virtual

Set the current time step. It should be greater than 0 and smaller than MaxTimeStep.

virtual int vtkXYZMolReader::GetTimeStep ( )
virtual

Set the current time step. It should be greater than 0 and smaller than MaxTimeStep.

virtual int vtkXYZMolReader::GetMaxTimeStep ( )
virtual

Get the maximum time step.

void vtkXYZMolReader::ReadSpecificMolecule ( FILE *  fp)
protectedvirtual

Implements vtkMoleculeReaderBase.

char* vtkXYZMolReader::GetNextLine ( FILE *  fp,
char *  line,
int  maxlen 
)
protected

Get next line that is not a comment. It returns the beginning of data on line (skips empty spaces)

int vtkXYZMolReader::GetLine1 ( const char *  line,
int *  cnt 
)
protected
int vtkXYZMolReader::GetLine2 ( const char *  line,
char *  name 
)
protected
int vtkXYZMolReader::GetAtom ( const char *  line,
char *  atom,
float *  x 
)
protected
void vtkXYZMolReader::InsertAtom ( const char *  atom,
float *  pos 
)
protected
virtual void vtkXYZMolReader::SetMaxTimeStep ( int  )
protectedvirtual

Member Data Documentation

int vtkXYZMolReader::TimeStep
protected

Definition at line 73 of file vtkXYZMolReader.h.

int vtkXYZMolReader::MaxTimeStep
protected

Definition at line 76 of file vtkXYZMolReader.h.


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