XMLMoleculeFormat Class Reference

Abstract class for XML formats which represent molecules. More...

#include <openbabel/xml.h>

Inheritance diagram for XMLMoleculeFormat:

List of all members.

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 ()

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 > &)

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)

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

Detailed Description

Abstract class for XML formats which represent molecules.

Member Typedef Documentation

typedef std::map<const char*, OBPlugin*, CharPtrLess> PluginMapType [inherited]

typedef PluginMapType::const_iterator PluginIterator [inherited]

Constructor & Destructor Documentation

~XMLMoleculeFormat ( ) [inline]

Member Function Documentation

virtual bool ReadChemObject ( OBConversion * ) [inline, virtual]

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.

virtual bool WriteChemObject ( OBConversion * ) [inline, virtual]

The "Convert" interface Write function.

Writes a single object Deletes the object after writing

Returns:: false on error

Reimplemented from OBFormat.

virtual bool ReadMolecule	(	OBBase *	,
		OBConversion *
	)			`[inline, virtual]`

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.

const std::type_info& GetType ( void ) [inline, virtual]

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.

virtual const char* NamespaceURI ( ) const [pure virtual, inherited]

virtual bool DoElement ( const std::string & ElName ) [inline, virtual, inherited]

virtual bool EndElement ( const std::string & ElName ) [inline, virtual, inherited]

virtual const char* EndTag ( ) [inline, virtual, inherited]

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

Referenced by XMLBaseFormat::SkipObjects().

xmlTextReaderPtr reader ( ) const [inline, protected, inherited]

xmlTextWriterPtr writer ( ) const [inline, protected, inherited]

void OutputToStream ( ) [inline, protected, inherited]

virtual int SkipObjects	(	int	n,
		OBConversion *	pConv
	)			`[inline, protected, virtual, inherited]`

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.

const char* TypeID ( ) [inline, inherited]

Referenced by OBFormat::RegisterFormat().

virtual bool WriteMolecule	(	OBBase *	,
		OBConversion *
	)			`[inline, virtual, inherited]`

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::OutputDeferredMols(), OBConversion::Write(), and OBMoleculeFormat::WriteChemObjectImpl().

virtual const char* Description ( ) [pure virtual, inherited]

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 OBFormat::Display(), OBConversion::GetNextFormat(), OBMoleculeFormat::OutputDeferredMols(), OBMoleculeFormat::ReadChemObjectImpl(), OBConversion::RegisterOptionParam(), and OBMoleculeFormat::WriteChemObjectImpl().

const char * TargetClassDescription ( ) [virtual, inherited]

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().

virtual const char* SpecificationURL ( ) [inline, virtual, inherited]

Web address where the format is defined.

Referenced by OBFormat::Display().

const char* GetMIMEType ( ) [inline, inherited]

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

virtual unsigned int Flags ( ) [inline, virtual, inherited]

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(), OBFormat::Display(), OBConversion::FullConvert(), OBConversion::GetNextFormat(), OBConversion::InstallStreamFilter(), OBConversion::OpenAndSetFormat(), OBMoleculeFormat::ReadChemObjectImpl(), OBConversion::ReadFile(), OBFormat::RegisterFormat(), OBConversion::SetInFormat(), OBConversion::SetOutFormat(), and OBConversion::WriteFile().

virtual OBFormat* MakeNewInstance ( ) [inline, virtual, inherited]

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.

int RegisterFormat	(	const char *	ID,
		const char *	MIME = `NULL`
	)			`[inherited]`

Referenced by OBConversion::RegisterFormat().

bool Display	(	std::string &	txt,
		const char *	param,
		const char *	ID = `NULL`
	)			`[virtual, inherited]`

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.

OBFormat * FormatFromMIME ( const char * MIME ) [static, inherited]

Referenced by OBConversion::FormatFromMIME().

virtual OBPlugin* MakeInstance ( const std::vector< std::string > & ) [inline, virtual, inherited]

Make a new instance of the class. See OpTransform, OBGroupContrib, SmartsDescriptor classes for derived versions. Usually, the first parameter is the classname, the next three are parameters(ID, filename, description) for a constructor, and the rest data.

Reimplemented in OBGroupContrib, and OpTransform.

Referenced by OBConversion::LoadFormatFiles().

static OBPlugin* GetPlugin	(	const char *	Type,
		const char *	ID
	)			`[inline, static, inherited]`

Get a pointer to a plugin from its type and ID. Return NULL if not found. Not cast to Type*.

Referenced by OBConversion::LoadFormatFiles().

const char* GetID ( ) const [inline, inherited]

Return the ID of the sub-type instance.

Referenced by OBPlugin::Display(), OBFormat::Display(), and OBDescriptor::PredictAndSave().

bool ListAsVector	(	const char *	PluginID,
		const char *	param,
		std::vector< std::string > &	vlist
	)			`[static, inherited]`

Output a list of sub-type classes of the the type PluginID, or, if PluginID is "plugins" or empty, a list of the base types. If PluginID is not recognized or is NULL, the base types are output and the return is false.

Referenced by OBConversion::GetSupportedInputFormat(), OBConversion::GetSupportedOutputFormat(), and OBPlugin::List().

void List	(	const char *	PluginID,
		const char *	param = `NULL`,
		std::ostream *	os = `&std::cout`
	)			`[static, inherited]`

As ListAsVector but sent to an ostream with a default of cout if not specified.

Referenced by OBPlugin::ListAsString().

string ListAsString	(	const char *	PluginID,
		const char *	param = `NULL`
	)			`[static, inherited]`

As ListAsVector but returns a string containing the list.

string FirstLine ( const char * txt ) [static, inherited]

Utility function to return only the first line of a string.

Referenced by OBPlugin::Display(), OBFormat::Display(), and OBOp::OpOptions().

static PluginIterator Begin ( const char * PluginID ) [inline, static, inherited]

Return an iterator at the start of the map of the plugin types PluginID or, if there is no such map, the end of the top level plugin map.

Referenced by OBConversion::GetNextFormat(), and OBOp::OpOptions().

static PluginIterator End ( const char * PluginID ) [inline, static, inherited]

Referenced by OBConversion::GetNextFormat(), and OBOp::OpOptions().

virtual PluginMapType& GetMap ( ) const [pure virtual, inherited]

Returns the map of the subtypes.

Referenced by OBFormat::RegisterFormat().

static PluginMapType& PluginMap ( ) [inline, static, protected, inherited]

Returns a reference to the map of the plugin types. Is a function rather than a static member variable to avoid initialization problems.

Referenced by OBPlugin::GetTypeMap(), OBPlugin::ListAsVector(), and OBFormat::RegisterFormat().

OBPlugin::PluginMapType & GetTypeMap ( const char * PluginID ) [static, protected, inherited]

Returns the map of a particular plugin type, e.g. GetMapType("fingerprints").

static OBPlugin* BaseFindType	(	PluginMapType &	Map,
		const char *	ID
	)			`[inline, static, protected, inherited]`

Returns the type with the specified ID, or NULL if not found. Will be cast to the appropriate class in the calling routine.

Member Data Documentation

OBMol* _pmol [protected]

Referenced by XMLMoleculeFormat::ReadMolecule().

XMLConversion* _pxmlConv [protected, inherited]

Referenced by XMLBaseFormat::OutputToStream(), XMLBaseFormat::reader(), XMLMoleculeFormat::ReadMolecule(), XMLBaseFormat::SkipObjects(), and XMLBaseFormat::writer().

std::string _prefix [protected, inherited]

int baseindent [protected, inherited]

int ind [protected, inherited]

std::string nsdecl [protected, inherited]

int _embedlevel [protected, inherited]

Referenced by XMLMoleculeFormat::ReadMolecule().

const char* _id [protected, inherited]

Referenced by OBFormat::RegisterFormat().

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

xml.h


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 ()
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 > &)
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)
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