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 ()
virtual const char * GetMIMEType ()
virtual unsigned int Flags ()
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)

Protected Member Functions

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

Static Protected Member Functions

static PluginMapTypePluginMap ()
static void LoadAllPlugins ()
static PluginMapTypeGetTypeMap (const char *PluginID)
static OBPluginBaseFindType (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.


Member Typedef Documentation

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

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

Reimplemented from OBPlugin.

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::DoOutputOptions(), 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().

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

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), OBFormat::Display(), OBConversion::FullConvert(), OBConversion::GetNextFormat(), OBConversion::InstallStreamFilter(), OBConversion::OpenAndSetFormat(), OBMoleculeFormat::ReadChemObjectImpl(), 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]
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]

Member Data Documentation

OBMol* _pmol [protected]
std::string _prefix [protected, inherited]
int baseindent [protected, inherited]
int ind [protected, inherited]
std::string nsdecl [protected, inherited]
int _embedlevel [protected, inherited]

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