#include <openbabel/obconversion.h>

Inheritance diagram for OBFormat:

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

typedef PluginMapType::const_iterator	PluginIterator

Public Member Functions
	OBFormat ()

const char *	TypeID ()

virtual bool	ReadMolecule (OBBase , OBConversion )

virtual bool	ReadChemObject (OBConversion *)

virtual bool	WriteMolecule (OBBase , OBConversion )

virtual bool	WriteChemObject (OBConversion *)

virtual const char *	Description ()=0

virtual const char *	TargetClassDescription ()

virtual const std::type_info &	GetType ()

virtual const char *	SpecificationURL ()

virtual const char *	GetMIMEType ()

virtual unsigned int	Flags ()

virtual int	SkipObjects (int, OBConversion *)

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 ()

Static Protected Member Functions
static PluginMapType &	PluginMap ()

static PluginMapType &	GetTypeMap (const char *PluginID)

static OBPlugin *	BaseFindType (PluginMapType &Map, const char *ID)

Protected Attributes
const char *	_id

Static Protected Attributes
static int	AllPluginsLoaded = 0

Detailed Description

Base class for file formats.

Two sets of Read and Write functions are specified for each format to handle two different requirements. The "Convert" interface is for use in file format conversion applications. The user interface, a console, a GUI, or another program is kept unaware of the details of the chemistry and does not need to #include mol.h. It is then necessary to manipulate only pointers to OBBase in OBConversion and the user interface, with all the construction and deletion of OBMol etc objects being done in the Format classes or the OB core. The convention with "Covert" interface functions is that chemical objects are made on the heap with new in the ReadChemicalObject() functions and and deleted in WriteChemicalObject() functions

The "API" interface is for programatic use of the OB routines in application programs where mol.h is #included. There is generally no creation or destruction of objects in ReadMolecule() and WriteMolecule() and no restriction on whether the pointers are to the heap or the stack.

Examples:: obconformersearch_default.cpp, and obforcefield_energy.cpp.

Constructor & Destructor Documentation

◆ OBFormat()

OBFormat ( )

inline

Default constructor. Registration via RegisterFormat(), not via constructor as in other plugins.

Member Function Documentation

◆ TypeID()

const char* TypeID ( )

inlinevirtual

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

Reimplemented from OBPlugin.

◆ 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 in XMLMoleculeFormat.

Referenced by OBMoleculeFormat::DeferMolOutput(), OBConversion::Read(), and OBMoleculeFormat::ReadChemObjectImpl().

◆ 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 in XMLMoleculeFormat, and OBMoleculeFormat.

Referenced by OBConversion::Convert().

◆ WriteMolecule()

virtual bool WriteMolecule	(	OBBase *	,
		OBConversion *
	)

inlinevirtual

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().

◆ 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 in XMLMoleculeFormat, and OBMoleculeFormat.

Referenced by OBConversion::AddChemObject(), and OBConversion::Convert().

◆ Description()

virtual const char* Description ( )

pure virtual

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 ( )

virtual

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().

◆ GetType()

const type_info & GetType ( )

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 in XMLMoleculeFormat, and OBMoleculeFormat.

◆ SpecificationURL()

virtual const char* SpecificationURL ( )

inlinevirtual

Web address where the format is defined.

◆ GetMIMEType()

virtual const char* GetMIMEType ( )

inlinevirtual

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

◆ Flags()

virtual unsigned int Flags ( )

inlinevirtual

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().

◆ SkipObjects()

virtual int SkipObjects	(	int	,
		OBConversion *
	)

inlinevirtual

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 in XMLBaseFormat.

Referenced by OBConversion::Convert(), OBConversion::NumInputObjects(), and OBConversion::SetStartAndEnd().

◆ MakeNewInstance()

virtual OBFormat* MakeNewInstance ( )

inlinevirtual

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`
	)

Referenced by OBConversion::RegisterFormat().

◆ Display()

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

virtual

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 )

static

Referenced by OBConversion::FormatFromMIME().

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

Public Types

Public Member Functions

Static Public Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ OBFormat()

Member Function Documentation

◆ TypeID()

◆ ReadMolecule()

◆ ReadChemObject()

◆ WriteMolecule()

◆ WriteChemObject()

◆ Description()

◆ TargetClassDescription()

◆ GetType()

◆ SpecificationURL()

◆ GetMIMEType()

◆ Flags()

◆ SkipObjects()

◆ MakeNewInstance()

◆ RegisterFormat()

◆ Display()

◆ FormatFromMIME()