XMLMoleculeFormat Class Reference

#include <openbabel/xml.h>

Inheritance diagram for XMLMoleculeFormat:

Public Types
typedef std::map< const char *, OBPlugin *, CharPtrLess >	PluginMapType
typedef PluginMapType::const_iterator	PluginIterator

Public Member Functions
	~XMLMoleculeFormat ()
virtual bool	ReadChemObject (OBConversion *pConv)
virtual bool	WriteChemObject (OBConversion *pConv)
virtual bool	ReadMolecule (OBBase *pOb, OBConversion *pConv)
const std::type_info &	GetType ()
virtual const char *	NamespaceURI () const =0
virtual bool	DoElement (const std::string &ElName)
virtual bool	EndElement (const std::string &ElName)
virtual const char *	EndTag ()
const char *	TypeID ()
virtual bool	WriteMolecule (OBBase *, OBConversion *)
virtual const char *	Description ()=0
virtual const char *	TargetClassDescription ()
virtual const char *	SpecificationURL ()
virtual const char *	GetMIMEType ()
virtual unsigned int	Flags ()
virtual OBFormat *	MakeNewInstance ()
int	RegisterFormat (const char *ID, const char *MIME=NULL)
virtual bool	Display (std::string &txt, const char *param, const char *ID=NULL)
virtual OBPlugin *	MakeInstance (const std::vector< std::string > &)
virtual void	Init ()
const char *	GetID () const
virtual PluginMapType &	GetMap () const =0

Static Public Member Functions
static OBFormat *	FormatFromMIME (const char *MIME)
static OBPlugin *	GetPlugin (const char *Type, const char *ID)
static bool	ListAsVector (const char *PluginID, const char *param, std::vector< std::string > &vlist)
static void	List (const char *PluginID, const char *param=NULL, std::ostream *os=&std::cout)
static std::string	ListAsString (const char *PluginID, const char *param=NULL)
static std::string	FirstLine (const char *txt)
static PluginIterator	Begin (const char *PluginID)
static PluginIterator	End (const char *PluginID)
static void	LoadAllPlugins ()

Protected Member Functions
xmlTextReaderPtr	reader () const
xmlTextWriterPtr	writer () const
void	OutputToStream ()
virtual int	SkipObjects (int n, OBConversion *pConv)

Static Protected Member Functions
static PluginMapType &	PluginMap ()
static PluginMapType &	GetTypeMap (const char *PluginID)
static OBPlugin *	BaseFindType (PluginMapType &Map, const char *ID)

Protected Attributes
OBMol *	_pmol
XMLConversion *	_pxmlConv
std::string	_prefix
int	baseindent
int	ind
std::string	nsdecl
int	_embedlevel
const char *	_id

Static Protected Attributes
static int	AllPluginsLoaded = 0

Detailed Description

Abstract class for XML formats which represent molecules.

Constructor & Destructor Documentation

~XMLMoleculeFormat()

~XMLMoleculeFormat ( )

inline

Member Function Documentation

ReadChemObject()

virtual bool ReadChemObject ( OBConversion *  )

inlinevirtual

The "Convert" interface Read function.

Possibly reads multiple new objects on the heap and subjects them to its DoTransformations() function, which may delete them again. Sends result to pConv->AddChemObject()

Reimplemented from OBFormat.

WriteChemObject()

virtual bool WriteChemObject ( OBConversion *  )

inlinevirtual

The "Convert" interface Write function.

Writes a single object Deletes the object after writing

Returns

false on error

Reimplemented from OBFormat.

ReadMolecule()

virtual bool ReadMolecule ( OBBase *  , OBConversion *    )

inlinevirtual

The "API" interface Read function.

Reads a single object. Does not make a new object on the heap; can be used with a pointer to an chem object on the heap or the stack.

Reimplemented from OBFormat.

GetType()

const std::type_info& GetType ( )

inlinevirtual

Returns

the type of chemical object used by the format. Defaults to that used by the default format. Useful for checking that a format can handle a particular object.

Reimplemented from OBFormat.

NamespaceURI()

virtual const char* NamespaceURI ( ) const

pure virtualinherited

DoElement()

virtual bool DoElement ( const std::string &  ElName )

inlinevirtualinherited

EndElement()

virtual bool EndElement ( const std::string &  ElName )

inlinevirtualinherited

EndTag()

virtual const char* EndTag ( )

inlinevirtualinherited

The tag at the end of the chemical object e.g. "/molecule>".

reader()

xmlTextReaderPtr reader ( ) const

inlineprotectedinherited

writer()

xmlTextWriterPtr writer ( ) const

inlineprotectedinherited

OutputToStream()

void OutputToStream ( )

inlineprotectedinherited

SkipObjects()

virtual int SkipObjects ( int  n, OBConversion *  pConv  )

inlineprotectedvirtualinherited

Skip past first n objects in input stream (or current one with n=0) Returns 1 on success, -1 on error and 0 if not implemented

Reimplemented from OBFormat.

TypeID()

const char* TypeID ( )

inlinevirtualinherited

Redefined by each plugin type: "formats", "fingerprints", etc.

Reimplemented from OBPlugin.

WriteMolecule()

virtual bool WriteMolecule ( OBBase *  , OBConversion *    )

inlinevirtualinherited

The "API" interface Write function.

Writes a single object Does not delete the object; can be used with a pointer to an chem object on the heap or the stack.

Returns

false on error.

Referenced by OBMoleculeFormat::DeleteDeferredMols(), OBMoleculeFormat::DoOutputOptions(), OBMoleculeFormat::OutputDeferredMols(), OBConversion::Write(), and OBMoleculeFormat::WriteChemObjectImpl().

Description()

virtual const char* Description ( )

pure virtualinherited

Information on this format. Printed out in response to -Hxxx option where xxx id the id of the format.

Must be provided by each format class. Can include a list of command line Options. These may be used to construction check boxes, radio buttons etc for GUI interface.

Reimplemented from OBPlugin.

Referenced by OBConversion::GetNextFormat(), and OBConversion::RegisterOptionParam().

TargetClassDescription()

const char * TargetClassDescription ( )

virtualinherited

A decription of the chemical object converted by this format.

If not provided, the object type used by the default format is used (usually OBMol).

Referenced by OBConversion::ReportNumberConverted().

SpecificationURL()

virtual const char* SpecificationURL ( )

inlinevirtualinherited

Web address where the format is defined.

GetMIMEType()

virtual const char* GetMIMEType ( )

inlinevirtualinherited

Chemical MIME type associated with this file type (if any)

Flags()

virtual unsigned int Flags ( )

inlinevirtualinherited

Decribes the capabilities of the format (Read only etc.)

Currently, can be a bitwise OR of any of the following NOTREADABLE READONEONLY NOTWRITABLE WRITEONEONLY DEFAULTFORMAT READBINARY WRITEBINARY READXML

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), OBMoleculeFormat::DeleteDeferredMols(), OBConversion::GetNextFormat(), OBMoleculeFormat::ReadChemObjectImpl(), OBConversion::SetInFormat(), OBConversion::SetInStream(), and OBConversion::SetOutFormat().

MakeNewInstance()

virtual OBFormat* MakeNewInstance ( )

inlinevirtualinherited

Returns

a pointer to a new instance of the format, or NULL if fails. Normally a single global instance is used but this may cause problems if there are member variables and the format is used in more than one place in the program.

RegisterFormat()

int RegisterFormat ( const char *  ID, const char *  MIME = NULL  )

inherited

Referenced by OBConversion::RegisterFormat().

Display()

bool Display ( std::string &  txt, const char *  param, const char *  ID = NULL  )

virtualinherited

Provides a description in txt of the format specified by itr. If param starts with "in", "read", "out" or "write" only the appropriate formats are output. The others return false. If param contains "verbose", the whole description is output.

Reimplemented from OBPlugin.

FormatFromMIME()

OBFormat * FormatFromMIME ( const char *  MIME )

staticinherited

Referenced by OBConversion::FormatFromMIME().

Member Data Documentation

_pmol

OBMol* _pmol

protected

_pxmlConv

XMLConversion* _pxmlConv

protectedinherited

_prefix

std::string _prefix

protectedinherited

baseindent

int baseindent

protectedinherited

ind

int ind

protectedinherited

nsdecl

std::string nsdecl

protectedinherited

_embedlevel

int _embedlevel

protectedinherited

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

• xml.h