OpenBabel::OBMoleculeFormat

OBMoleculeFormat Class Reference

An OBFormat convenience subclass for conversion to/from OBMol data. More...

#include <openbabel/obmolecformat.h>

Inheritance diagram for OBMoleculeFormat:

Inheritance graph
[legend]
List of all members.

Public Types

typedef std::map< std::string,
unsigned > 		NameIndexType

Public Member Functions

 OBMoleculeFormat ()
virtual bool ReadChemObject (OBConversion *pConv)
virtual bool WriteChemObject (OBConversion *pConv)
const std::type_info & GetType ()
virtual bool ReadMolecule (OBBase *, OBConversion *)
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 int SkipObjects (int, OBConversion *)
virtual OBFormat * MakeNewInstance ()

Static Public Member Functions

static bool ReadChemObjectImpl (OBConversion *pConv, OBFormat *)
static bool WriteChemObjectImpl (OBConversion *pConv, OBFormat *)
static bool ReadNameIndex (NameIndexType &index, const std::string &datafilename, OBFormat *pInFormat)
Routines to handle the -C option for combining data from several OBMols
static bool DeferMolOutput (OBMol *pmol, OBConversion *pConv, OBFormat *pF)
static bool OutputDeferredMols (OBConversion *pConv)
static bool DeleteDeferredMols ()
static OBMol * MakeCombinedMolecule (OBMol *pFirst, OBMol *pSecond)

Detailed Description

An OBFormat convenience subclass for conversion to/from OBMol data.

This class is not intended for direct use outside of Open Babel, unless you're writing a new format converting to or from an OBMol molecule. (e.g., see http://openbabel.sourceforge.net/wiki/HowTo:Add_A_New_File_Format).

An OBFormat which converts to and/or from OBMol can derive from this class to save duplicating the ReadChemObject() and/or WriteChemObject() methods. Derive directly from OBFormat if the object converted is not OBMol or if interaction with the framework is required during the execution of ReadMolecule() or WriteMolecule(), as for example in CMLFormat

Member Typedef Documentation

typedef std::map<std::string, unsigned> NameIndexType

Constructor & Destructor Documentation

OBMoleculeFormat (  )  [inline]

Member Function Documentation

static bool ReadChemObjectImpl ( OBConversion *  pConv,
OBFormat *   
) [static]

Static routine, which can be called from elsewhere.

static bool WriteChemObjectImpl ( OBConversion *  pConv,
OBFormat *   
) [static]

Static routine, which can be called from elsewhere.

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

The "Convert" interface for reading a new molecule.

Reimplemented from OBFormat.

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

The "Convert" interface for writing a new molecule.

Reimplemented from OBFormat.

static bool DeferMolOutput ( OBMol *  pmol,
OBConversion *  pConv,
OBFormat *  pF 
) [static]

Defer output of a molecule until later, so it can be combined with others

Returns:
Success, or false if no molecule was read.

static bool OutputDeferredMols ( OBConversion *  pConv  )  [static]

Write out all molecules queued with DeferMolOutput.

static bool DeleteDeferredMols (  )  [static]

Delete the list of queued molecules from DeferMolOutput.

static OBMol* MakeCombinedMolecule ( OBMol *  pFirst,
OBMol *  pSecond 
) [static]

Returns:
the OBMol which combines pFirst and pSecond (i.e.)

static bool ReadNameIndex ( NameIndexType &  index,
const std::string &  datafilename,
OBFormat *  pInFormat 
) [static]

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

Returns:
the type of data converted by this format (here, OBMol)

Reimplemented from OBFormat.

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

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.

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.

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.

const char * TargetClassDescription (  )  [virtual, inherited]

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

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

Web address where the format is defined.

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

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

Returns:
1 on success, -1 on error and 0 if not implemented

Reimplemented in XMLBaseFormat.

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.

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