OBMoleculeFormat Class Reference

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

#include <openbabel/obmolecformat.h>

Inheritance diagram for OBMoleculeFormat:

List of all members.

Public Types

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

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

typedef
PluginMapType::const_iterator PluginIterator

Public Member Functions

OBMoleculeFormat ()

virtual bool ReadChemObject (OBConversion *pConv)

virtual bool WriteChemObject (OBConversion *pConv)

const std::type_info & GetType ()

const char * TypeID ()

virtual bool ReadMolecule (OBBase *, OBConversion *)

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 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 > &)

const char * GetID () const

virtual PluginMapType & GetMap () const =0

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)

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)

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)

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

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

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

typedef PluginMapType::const_iterator PluginIterator [inherited]

Constructor & Destructor Documentation

OBMoleculeFormat ( ) [inline]

Member Function Documentation

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

Static routine, which can be called from elsewhere.

Referenced by XMLMoleculeFormat::ReadChemObject().

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

Static routine, which can be called from elsewhere.

Referenced by XMLMoleculeFormat::WriteChemObject().

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.

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.

Instead of sending molecules for output via AddChemObject(), they are saved in here in OBMoleculeFormat or discarded. By default they are saved only if they are in the first input file. Parts of subsequent molecules, such as chemical structure, coordinates and OBGenericData can replace the parts in molecules with the same title that have already been stored, subject to a set of rules. After all input files have been read, the stored molecules (possibly now having augmented properties) are sent to the output format.

Is a static function with *this as parameter so that it can be called from other format classes like XMLMoleculeFormat which are not derived from OBMoleculeFormat.

Referenced by OBMoleculeFormat::ReadChemObjectImpl().

bool OutputDeferredMols ( OBConversion * pConv ) [static]

Write out all molecules queued with DeferMolOutput.

Referenced by OBMoleculeFormat::WriteChemObjectImpl().

bool DeleteDeferredMols ( ) [static]

Delete the list of queued molecules from DeferMolOutput.

Referenced by OBMoleculeFormat::DeferMolOutput(), and OBMoleculeFormat::OutputDeferredMols().

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

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

Makes a new OBMol on the heap by combining two molecules according to the rule below. If both have OBGenericData of the same type, or OBPairData with the same attribute, the version from pFirst is used. Returns a pointer to a new OBMol which will need deleting by the calling program (probably by being sent to an output format). If the molecules cannot be regarded as being the same structure a NULL pointer is returned and an error message logged.

pFirst and pSecond and the objects they point to are not changed. (const modifiers difficult because class OBMol not designed appropriately)

Combining molecules: rules for each of the three parts Title: Use the title of pFirst unless it has none, when use that of pSecond. Warning if neither molecule has a title.

Structure

a structure with atoms replaces one with no atoms
a structure with bonds replaces one with no bonds, provided the formula is the same, else an error.
structures with atoms and bonds are compared by InChI; error if not the same.
a structure with 3D coordinates replaces one with 2D coordinates
a structure with 2D coordinates replace one with 0D coordinates

OBGenericData OBPairData

Referenced by OBMoleculeFormat::DeferMolOutput().

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

Attempts to read the index file datafilename.obindx successively from the following directories:

the current directory
that in the environment variable BABEL_DATADIR or in the macro BABEL_DATADIR if the environment variable is not set
in a subdirectory of the BABEL_DATADIR directory with the version of OpenBabel as its name An index of type NameIndexType is then constructed. NameIndexType is defined in obmolecformat.h and may be a std::tr1::unordered_map (a hash_map) or std::map. In any case it is searched by
```
      NameIndexType::iterator itr = index.find(molecule_name);
      if(itr!=index.end())
      unsigned pos_in_datafile = itr->second;
```
pos_in_datafile is used as a parameter in seekg() to read from the datafile

If no index is found, it is constructed from the datafile by reading all of it using the format pInFormat, and written to the directory containing the datafile. This means that this function can be used without worrying whether there is an index. It will be slow to execute the first time, but subsequent uses get the speed benefit of indexed access to the datafile.

The serialization and de-serialization of the NameIndexType is entirely in this routine and could possibly be improved. Currently re-hashing is done every time the index is read.

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

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

Reimplemented from OBFormat.

const char* TypeID ( ) [inline, inherited]

Referenced by OBFormat::RegisterFormat().

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.

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

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 int SkipObjects	(	int	,
		OBConversion *
	)			`[inline, 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 in XMLBaseFormat.

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

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

const char* _id [protected, inherited]

Referenced by OBFormat::RegisterFormat().

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


Public Types
typedef std::map< std::string, unsigned >	NameIndexType
typedef std::map< const char , OBPlugin , CharPtrLess >	PluginMapType
typedef PluginMapType::const_iterator	PluginIterator
Public Member Functions
	OBMoleculeFormat ()
virtual bool	ReadChemObject (OBConversion *pConv)
virtual bool	WriteChemObject (OBConversion *pConv)
const std::type_info &	GetType ()
const char *	TypeID ()
virtual bool	ReadMolecule (OBBase , OBConversion )
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 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 > &)
const char *	GetID () const
virtual PluginMapType &	GetMap () const =0
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)
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)
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)
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