OBFormat Class Reference

Base class for file formats. More...

#include <openbabel/obconversion.h>

Inheritance diagram for OBFormat:
OBPlugin OBMoleculeFormat XMLBaseFormat XMLMoleculeFormat

List of all members.

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 OBFormatMakeNewInstance ()
int RegisterFormat (const char *ID, const char *MIME=NULL)
virtual bool Display (std::string &txt, const char *param, const char *ID=NULL)
virtual OBPluginMakeInstance (const std::vector< std::string > &)
virtual void Init ()
const char * GetID () const
virtual PluginMapTypeGetMap () const =0

Static Public Member Functions

static OBFormatFormatFromMIME (const char *MIME)
static OBPluginGetPlugin (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 Protected Member Functions

static PluginMapTypePluginMap ()
static PluginMapTypeGetTypeMap (const char *PluginID)
static OBPluginBaseFindType (PluginMapType &Map, const char *ID)

Protected Attributes

const char * _id

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.


Member Typedef Documentation

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

Constructor & Destructor Documentation

OBFormat (  ) [inline]

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


Member Function Documentation

const char* TypeID (  ) [inline, virtual]

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

Reimplemented from OBPlugin.

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 in XMLMoleculeFormat.

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

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 in OBMoleculeFormat, and XMLMoleculeFormat.

Referenced by OBConversion::Convert().

virtual bool WriteMolecule ( OBBase ,
OBConversion  
) [inline, virtual]

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

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 in OBMoleculeFormat, and XMLMoleculeFormat.

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

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(), OBMoleculeFormat::ReadChemObjectImpl(), OBConversion::RegisterOptionParam(), and OBMoleculeFormat::WriteChemObjectImpl().

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().

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 OBMoleculeFormat, and XMLMoleculeFormat.

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

Web address where the format is defined.

virtual const char* GetMIMEType (  ) [inline, virtual]

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

virtual unsigned int Flags (  ) [inline, virtual]

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

virtual int SkipObjects ( int  ,
OBConversion  
) [inline, virtual]

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().

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

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

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