#include <openbabel/xml.h>

Inheritance diagram for XMLConversion:

Public Types
typedef std::map< std::string, XMLBaseFormat * >	NsMapType

Public Member Functions
	XMLConversion (OBConversion *pConv)

	~XMLConversion ()

bool	SetupReader ()

bool	SetupWriter ()

bool	ReadXML (XMLBaseFormat pFormat, OBBase pOb)

int	SkipXML (const char *ctag)

bool	IsLast ()

int	GetOutputIndex ()

xmlTextReaderPtr	GetReader () const

xmlTextWriterPtr	GetWriter () const

void	OutputToStream ()

void	LookForNamespace ()

std::string	GetAttribute (const char *attrname)

std::string	GetContent ()

bool	GetContentInt (int &value)

bool	GetContentDouble (double &value)

void	CopyOptions (OBConversion *pSourceConv, Option_type typ=ALL)

Parameter get and set
These return a filtered stream for reading/writing (possible filters include compression, decompression, and newline transformation)
std::istream *	GetInStream () const

std::ostream *	GetOutStream () const

void	SetInStream (std::istream *pIn, bool takeOwnership=false)

void	SetOutStream (std::ostream *pOut, bool takeOwnership=false)

bool	SetInAndOutFormats (const char inID, const char outID, bool ingzip=false, bool outgzip=false)

bool	SetInAndOutFormats (OBFormat pIn, OBFormat pOut, bool ingzip=false, bool outgzip=false)

bool	SetInFormat (const char *inID, bool isgzip=false)

bool	SetInFormat (OBFormat *pIn, bool isgzip=false)

bool	SetOutFormat (const char *outID, bool isgzip=false)

bool	SetOutFormat (OBFormat *pOut, bool isgzip=false)

OBFormat *	GetInFormat () const

OBFormat *	GetOutFormat () const

bool	GetInGzipped () const

bool	GetOutGzipped () const

std::string	GetInFilename () const

std::string	GetOutFilename () const

std::streampos	GetInPos () const

size_t	GetInLen () const

const char *	GetTitle () const

OBConversion *	GetAuxConv () const

void	SetAuxConv (OBConversion *pConv)

Supported file format
std::vector< std::string >	GetSupportedInputFormat ()

std::vector< std::string >	GetSupportedOutputFormat ()

Conversion
int	Convert (std::istream is, std::ostream os)

int	Convert ()

int	FullConvert (std::vector< std::string > &FileList, std::string &OutputFileName, std::vector< std::string > &OutputFileList)

Conversion loop control
int	AddChemObject (OBBase *pOb)

OBBase *	GetChemObject ()

bool	IsFirstInput ()

void	SetFirstInput (bool b=true)

int	GetOutputIndex () const

void	SetOutputIndex (int indx)

void	SetMoreFilesToCome ()

void	SetOneObjectOnly (bool b=true)

void	SetLast (bool b)

bool	IsLastFile ()

int	GetCount () const

Static Public Member Functions
static NsMapType &	Namespaces ()

static void	RegisterXMLFormat (XMLBaseFormat pFormat, bool IsDefault=false, const char uri=NULL)

static XMLConversion *	GetDerived (OBConversion *pConv, bool ForReading=true)

static XMLBaseFormat *	GetDefaultXMLClass ()

static int	ReadStream (void context, char buffer, int len)

static int	WriteStream (void context, const char buffer, int len)

Collection of formats
static int	RegisterFormat (const char ID, OBFormat pFormat, const char *MIME=NULL)

static OBFormat *	FindFormat (const char *ID)

static OBFormat *	FindFormat (const std::string ID)

static OBFormat *	FormatFromExt (const char *filename)

static OBFormat *	FormatFromExt (const char *filename, bool &isgzip)

static OBFormat *	FormatFromExt (const std::string filename)

static OBFormat *	FormatFromExt (const std::string filename, bool &isgzip)

static OBFormat *	FormatFromMIME (const char *MIME)

static bool	GetNextFormat (Formatpos &itr, const char &str, OBFormat &pFormat)

Information
static const char *	Description ()

Public Attributes
bool	_SkipNextRead

Protected Types
typedef std::map< std::string, int >	OPAMapType

typedef FilteringInputStream< LineEndingExtractor >	LEInStream

Protected Member Functions
bool	SetStartAndEnd ()

bool	OpenAndSetFormat (bool SetFormat, std::ifstream is, std::stringstream ss=NULL)

Static Protected Member Functions
static OPAMapType &	OptionParamArray (Option_type typ)

Protected Attributes
std::string	InFilename

std::string	OutFilename

std::istream *	pInput

std::vector< std::istream * >	ownedInStreams

std::ostream *	pOutput

std::vector< std::ostream * >	ownedOutStreams

OBFormat *	pInFormat

OBFormat *	pOutFormat

std::map< std::string, std::string >	OptionsArray [3]

int	Index

unsigned int	StartNumber

unsigned int	EndNumber

int	Count

bool	m_IsFirstInput

bool	m_IsLast

bool	MoreFilesToCome

bool	OneObjectOnly

bool	ReadyToInput

bool	SkippedMolecules

bool	inFormatGzip

bool	outFormatGzip

OBBase *	pOb1

std::streampos	wInpos

std::streampos	rInpos

size_t	wInlen

size_t	rInlen

OBConversion *	pAuxConv

std::vector< std::string >	SupportedInputFormat

std::vector< std::string >	SupportedOutputFormat

Static Protected Attributes
static OBFormat *	pDefaultFormat

Option handling
Three types of Option provide information and control instructions to the conversion process, INOPTIONS, OUTOPTIONS, GENOPTIONS, and are stored in each OBConversion object in separate maps. Each option has an id and an optional text string. They are set individually by AddOption() or (rarely) collectively in SetOptions(). Options cannot be altered but can be replaced with AddOption() and deleted with RemoveOption(), which, however, should be used in an op derived from OBOp (because of iterator invalidation). If the "Convert" interface is used, the GENOPTIONS are acted upon in the OBBase::DoTransformations() functions (currently only OBMol has one). This happens after the object has been input but before it has been output. All the options are available to input and output formats, etc. via the IsOption() function, and the interpretation of any text string needs to be done subsequently. In the commandline interface, options with single character ids are are indicated like -s, and those with multiple character ids like –gen3D. An option may have one or more parameters which appear, space separated, in the option's text string. With babel, unless the option is at the end of the command, it is necessary for the number of its parameters to be exactly that specified in RegisterOptionParam(). The default is 0, but if it is more, and babel is likely to be used, this function should be called in the constructor of a format or op. With obabel (or the GUI), it is not necessary to call RegisterOptionParam(). New GENOPTIONS can be defined (as plugins) using the class OBOp. It is customary for a format or op to document any INOPTIONS or OUTPTIONS it uses in its Description() function. As well as providing documentation during use, this is also parsed by the GUI to construct its checkboxes,etc., so it is advisable to give new Descriptions the same form as existing ones. Some conversion options, such as -f, -l, -m, are unlikely to be used in programming, but are listed in OBConversion::Description(). The built-in GENOPTIONS for OBMol objects are listed in OBMol::ClassDescription() which is in transform.cpp and also in this documentation under AddOption().
enum	Option_type { INOPTIONS, OUTOPTIONS, GENOPTIONS, ALL }

const char *	IsOption (const char *opt, Option_type opttyp=OUTOPTIONS)

const std::map< std::string, std::string > *	GetOptions (Option_type opttyp)

void	AddOption (const char opt, Option_type opttyp=OUTOPTIONS, const char txt=NULL)

bool	RemoveOption (const char *opt, Option_type optype)

void	SetOptions (const char *options, Option_type opttyp)

static void	RegisterOptionParam (std::string name, OBFormat *pFormat, int numberParams=0, Option_type typ=OUTOPTIONS)

static int	GetOptionParams (std::string name, Option_type typ)

Convenience functions
bool	Write (OBBase pOb, std::ostream pout=NULL)

std::string	WriteString (OBBase *pOb, bool trimWhitespace=false)

bool	WriteFile (OBBase *pOb, std::string filePath)

void	CloseOutFile ()

bool	Read (OBBase pOb, std::istream pin=NULL)

bool	ReadString (OBBase *pOb, std::string input)

bool	ReadFile (OBBase *pOb, std::string filePath)

bool	OpenInAndOutFiles (std::string infilepath, std::string outfilepath)

void	ReportNumberConverted (int count, OBFormat *pFormat=NULL)

int	NumInputObjects ()

static OBFormat *	GetDefaultFormat ()

static std::string	BatchFileName (std::string &BaseName, std::string &InFile)

static std::string	IncrementedFileName (std::string &BaseName, const int Count)

static bool	CheckForUnintendedBatch (const std::string &infile, const std::string &outfile)

void	ClearInStreams ()

Detailed Description

A subclass for conversion of XML formats.

An extended OBConversion class which includes a libxml2 reader for use with XML formats. Copies an OBConversion and then extends it with a XML parser. Instances made on the heap are deleted when the original OBConversion object is.

This class is not intended to be used externally – instead use OBConversion which will find both XML and non-XML OBFormats.

Instead, this subclass also has support for handling specific needs in XML formats. For example, an XML file may include multiple namespaces, and the conversion should call appropriate XMLBaseFormat formats as needed.

Member Typedef Documentation

◆ NsMapType

typedef std::map<std::string, XMLBaseFormat*> NsMapType

◆ OPAMapType

typedef std::map<std::string,int> OPAMapType

protectedinherited

◆ LEInStream

typedef FilteringInputStream< LineEndingExtractor > LEInStream

protectedinherited

Member Enumeration Documentation

◆ Option_type

enum Option_type

inherited

Three types of options set on the the command line by -a? , -x? , or -?

Enumerator
INOPTIONS
OUTOPTIONS
GENOPTIONS
ALL

Constructor & Destructor Documentation

◆ XMLConversion()

XMLConversion ( OBConversion * pConv )

Existing OBConversion instance copied.

◆ ~XMLConversion()

~XMLConversion ( )

Frees reader and writer if necessary.

Member Function Documentation

◆ SetupReader()

bool SetupReader ( )

opens libxml2 reader

◆ SetupWriter()

bool SetupWriter ( )

opens libxml2 writer

◆ ReadXML()

bool ReadXML	(	XMLBaseFormat *	pFormat,
		OBBase *	pOb
	)

Parses the input xml stream and sends each element to the format's callback routines.

◆ SkipXML()

int SkipXML ( const char * ctag )

Read and discard XML text up to the next occurrence of the tag e.g."/molecule>" This is left as the current node. Returns 1 on success, 0 if not found, -1 if failed.

Referenced by XMLBaseFormat::SkipObjects().

◆ Namespaces()

static NsMapType& Namespaces ( )

inlinestatic

This static function returns a reference to the map Avoids "static initialization order fiasco"

◆ RegisterXMLFormat()

static void RegisterXMLFormat	(	XMLBaseFormat *	pFormat,
		bool	IsDefault = `false`,
		const char *	uri = `NULL`
	)

static

Referenced by XMLConversion::Namespaces().

◆ GetDerived()

static XMLConversion* GetDerived	(	OBConversion *	pConv,
		bool	ForReading = `true`
	)

static

Returns the extended OBConversion class, making it if necessary.

Referenced by XMLConversion::Namespaces(), XMLMoleculeFormat::ReadMolecule(), and XMLBaseFormat::SkipObjects().

◆ IsLast()

bool IsLast ( )

inline

Because OBConversion::Convert is still using the unextended OBConversion object we need to obtain the conversion paramters from it when requested

◆ GetOutputIndex() [1/2]

int GetOutputIndex ( )

inline

◆ GetReader()

xmlTextReaderPtr GetReader ( ) const

inline

Referenced by XMLBaseFormat::reader().

◆ GetWriter()

xmlTextWriterPtr GetWriter ( ) const

inline

Referenced by XMLBaseFormat::writer().

◆ OutputToStream()

void OutputToStream ( )

inline

Referenced by XMLBaseFormat::OutputToStream().

◆ GetDefaultXMLClass()

static XMLBaseFormat* GetDefaultXMLClass ( )

inlinestatic

◆ LookForNamespace()

void LookForNamespace ( )

inline

◆ ReadStream()

static int ReadStream	(	void *	context,
		char *	buffer,
		int	len
	)

static

Static callback functions for xmlReaderForIO()

Referenced by XMLConversion::LookForNamespace().

◆ WriteStream()

static int WriteStream	(	void *	context,
		const char *	buffer,
		int	len
	)

static

Referenced by XMLConversion::LookForNamespace().

◆ GetAttribute()

std::string GetAttribute ( const char * attrname )

Referenced by XMLConversion::LookForNamespace().

◆ GetContent()

std::string GetContent ( )

Sets value to element content. Returns false if there is no content.

Referenced by XMLConversion::LookForNamespace().

◆ GetContentInt()

bool GetContentInt ( int & value )

Sets value to element content as an integer. Returns false if there is no content.

Referenced by XMLConversion::LookForNamespace().

◆ GetContentDouble()

bool GetContentDouble ( double & value )

Sets value to element content as an double. Returns false if there is no content.

Referenced by XMLConversion::LookForNamespace().

◆ RegisterFormat()

int RegisterFormat	(	const char *	ID,
		OBFormat *	pFormat,
		const char *	MIME = `NULL`
	)

staticinherited

Called once by each format class.

Class information on formats is collected by making an instance of the class derived from OBFormat(only one is usually required). RegisterFormat() is called from its constructor.

If the compiled format is stored separately, like in a DLL or shared library, the initialization code makes an instance of the imported OBFormat class.

◆ FindFormat() [1/2]

OBFormat * FindFormat ( const char * ID )

staticinherited

Searches registered formats.

Referenced by OBConversion::FormatFromExt(), OBConversion::SetInFormat(), and OBConversion::SetOutFormat().

◆ FindFormat() [2/2]

OBFormat * FindFormat ( const std::string ID )

staticinherited

Searches registered formats.

Since: version 2.3

◆ FormatFromExt() [1/4]

OBFormat * FormatFromExt ( const char * filename )

staticinherited

Searches registered formats for an ID the same as the file extension.

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

Referenced by OBConversion::FormatFromExt(), OBConversion::OpenAndSetFormat(), OBConversion::OpenInAndOutFiles(), OBConversion::ReadFile(), and OBConversion::WriteFile().

◆ FormatFromExt() [2/4]

OBFormat * FormatFromExt	(	const char *	filename,
		bool &	isgzip
	)

staticinherited

◆ FormatFromExt() [3/4]

OBFormat * FormatFromExt ( const std::string filename )

staticinherited

Searches registered formats for an ID the same as the file extension.

Since: version 2.3

◆ FormatFromExt() [4/4]

OBFormat * FormatFromExt	(	const std::string	filename,
		bool &	isgzip
	)

staticinherited

◆ FormatFromMIME()

OBFormat * FormatFromMIME ( const char * MIME )

staticinherited

Searches registered formats for a MIME the same as the chemical MIME type passed.

◆ GetNextFormat()

bool GetNextFormat	(	Formatpos &	itr,
		const char *&	str,
		OBFormat *&	pFormat
	)

staticinherited

Deprecated!.Repeatedly called to recover available Formats.

◆ Description()

const char * Description ( )

staticinherited

◆ GetInStream()

std::istream* GetInStream ( ) const

inlineinherited

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

◆ GetOutStream()

std::ostream* GetOutStream ( ) const

inlineinherited

◆ SetInStream()

void SetInStream	(	std::istream *	pIn,
		bool	takeOwnership = `false`
	)

inherited

Set input stream. If takeOwnership is true, will deallocate when done. If isGzipped is true, will treat as a gzipped stream regardless of option settings,.

Set input stream, removing/deallocating previous stream if necessary. If takeOwnership is true, takes responsibility for freeing pIn

Referenced by OBConversion::Convert(), OBConversion::FullConvert(), OBConversion::OBConversion(), OBConversion::OpenInAndOutFiles(), OBConversion::operator=(), OBConversion::StreamState::popInput(), OBConversion::Read(), OBConversion::ReadFile(), OBConversion::ReadString(), and OBConversion::~OBConversion().

◆ SetOutStream()

void SetOutStream	(	std::ostream *	pOut,
		bool	takeOwnership = `false`
	)

inherited

Set output stream, removing/deallocating previous stream if necessary. If takeOwnership is true, takes responsibility for freeing pOut Be aware that if the output stream is gzipped format, then this outstream either needs to be replaced (e.g., SetOutStream(NULL)) or the OBConversion destroyed before the underlying outputstream is deallocated.

Referenced by OBConversion::CloseOutFile(), OBConversion::Convert(), OBConversion::FullConvert(), OBConversion::OBConversion(), OBConversion::OpenInAndOutFiles(), OBConversion::operator=(), OBConversion::StreamState::popOutput(), OBConversion::Write(), OBConversion::WriteFile(), OBConversion::WriteString(), and OBConversion::~OBConversion().

◆ SetInAndOutFormats() [1/2]

bool SetInAndOutFormats	(	const char *	inID,
		const char *	outID,
		bool	inzip = `false`,
		bool	outzip = `false`
	)

inherited

Sets the formats from their ids, e g CML.

Sets the formats from their ids, e g CML. If inID is NULL, the input format is left unchanged. Similarly for outID Returns true if both formats have been successfully set at sometime

Referenced by AliasData::Expand().

◆ SetInAndOutFormats() [2/2]

bool SetInAndOutFormats	(	OBFormat *	pIn,
		OBFormat *	pOut,
		bool	ingzip = `false`,
		bool	outgzip = `false`
	)

inherited

◆ SetInFormat() [1/2]

bool SetInFormat	(	const char *	inID,
		bool	isgzip = `false`
	)

inherited

Sets the input format from an id e.g. CML.

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

Referenced by OpenBabel::alternate(), OpenBabel::CompileSmilesQuery(), AliasData::Expand(), OBConversion::OpenAndSetFormat(), OBMoleculeFormat::ReadNameIndex(), and OBConversion::SetInAndOutFormats().

◆ SetInFormat() [2/2]

bool SetInFormat	(	OBFormat *	pIn,
		bool	isgzip = `false`
	)

inherited

◆ SetOutFormat() [1/2]

bool SetOutFormat	(	const char *	outID,
		bool	isgzip = `false`
	)

inherited

Sets the output format from an id e.g. CML.

Examples:: obconformersearch_default.cpp.

Referenced by OBBuilder::Build(), and OBConversion::SetInAndOutFormats().

◆ SetOutFormat() [2/2]

bool SetOutFormat	(	OBFormat *	pOut,
		bool	isgzip = `false`
	)

inherited

◆ GetInFormat()

OBFormat* GetInFormat ( ) const

inlineinherited

Referenced by OBConversion::NumInputObjects().

◆ GetOutFormat()

OBFormat* GetOutFormat ( ) const

inlineinherited

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

◆ GetInGzipped()

bool GetInGzipped ( ) const

inlineinherited

◆ GetOutGzipped()

bool GetOutGzipped ( ) const

inlineinherited

◆ GetInFilename()

std::string GetInFilename ( ) const

inlineinherited

◆ GetOutFilename()

std::string GetOutFilename ( ) const

inlineinherited

◆ GetInPos()

std::streampos GetInPos ( ) const

inlineinherited

Get the position in the input stream of the object being read.

◆ GetInLen()

size_t GetInLen ( ) const

inlineinherited

Get the length in the input stream of the object being read.

◆ GetTitle()

const char * GetTitle ( ) const

inherited

Returns: a default title which is the filename

◆ GetAuxConv()

OBConversion* GetAuxConv ( ) const

inlineinherited

Extension method: deleted in ~OBConversion()

◆ SetAuxConv()

void SetAuxConv ( OBConversion * pConv )

inlineinherited

◆ IsOption()

const char * IsOption	(	const char *	opt,
		Option_type	opttyp = `OUTOPTIONS`
	)

inherited

Determine whether an option is set.

Returns: NULL if option not and a pointer to the associated text if it is

Referenced by OBConversion::Convert(), OBMoleculeFormat::DoOutputOptions(), OBConversion::FullConvert(), OBConversion::NumInputObjects(), OBMoleculeFormat::ReadChemObjectImpl(), OBConversion::SetInStream(), OBConversion::SetOutStream(), OBConversion::SetStartAndEnd(), and OBMoleculeFormat::WriteChemObjectImpl().

◆ GetOptions()

const std::map<std::string,std::string>* GetOptions ( Option_type opttyp )

inlineinherited

Access the map with option name as key and any associated text as value.

Referenced by OBMoleculeFormat::DeleteDeferredMols(), OBMoleculeFormat::OutputDeferredMols(), and OBMoleculeFormat::ReadChemObjectImpl().

◆ AddOption()

void AddOption	(	const char *	opt,
		Option_type	opttyp = `OUTOPTIONS`,
		const char *	txt = `NULL`
	)

inherited

Set an option of specified type, with optional text.

Referenced by OBMoleculeFormat::DeferMolOutput(), and AliasData::Expand().

◆ RemoveOption()

bool RemoveOption	(	const char *	opt,
		Option_type	optype
	)

inherited

◆ SetOptions()

void SetOptions	(	const char *	options,
		Option_type	opttyp
	)

inherited

Set several single character options of specified type from string like ab"btext"c"ctext".

◆ RegisterOptionParam()

void RegisterOptionParam	(	std::string	name,
		OBFormat *	pFormat,
		int	numberParams = `0`,
		Option_type	typ = `OUTOPTIONS`
	)

staticinherited

For example -h takes 0 parameters; -f takes 1. Call in a format constructor.

Referenced by OBConversion::OBConversion(), and OBMoleculeFormat::OBMoleculeFormat().

◆ GetOptionParams()

int GetOptionParams	(	std::string	name,
		Option_type	typ
	)

staticinherited

Returns: the number of parameters registered for the option, or 0 if not found

◆ CopyOptions()

void CopyOptions	(	OBConversion *	pSourceConv,
		Option_type	typ = `ALL`
	)

inherited

Copies the options (by default of all types) from one OBConversion Object to another.

◆ GetSupportedInputFormat()

std::vector< std::string > GetSupportedInputFormat ( )

inherited

Returns the list of supported input format

◆ GetSupportedOutputFormat()

std::vector< std::string > GetSupportedOutputFormat ( )

inherited

Returns the list of supported output format

◆ Convert() [1/2]

int Convert	(	std::istream *	is,
		std::ostream *	os
	)

inherited

Conversion for single input and output stream.

Convert molecules from is into os. If either is null, uses existing streams. If streams are specified, they do not replace any existing streams.

Referenced by AliasData::Expand().

◆ Convert() [2/2]

int Convert ( )

inherited

Conversion with existing streams.

Actions the "convert" interface. Calls the OBFormat class's ReadMolecule() which

makes a new chemical object of its chosen type (e.g. OBMol)
reads an object from the input file
subjects the chemical object to 'transformations' as specified by the Options
calls AddChemObject to add it to a buffer. The previous object is first output via the output Format's WriteMolecule(). During the output process calling IsFirst() and GetIndex() (the number of objects including the current one already output. allows more control, for instance writing <cml> and </cml> tags for multiple molecule outputs only.

AddChemObject does not save the object passed to it if it is NULL (as a result of a DoTransformation()) or if the number of the object is outside the range defined by StartNumber and EndNumber.This means the start and end counts apply to all chemical objects found whether or not they are output.

If ReadMolecule returns false the input conversion loop is exited.

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

◆ FullConvert()

int FullConvert	(	std::vector< std::string > &	FileList,
		std::string &	OutputFileName,
		std::vector< std::string > &	OutputFileList
	)

inherited

Conversion with multiple input/output files: makes input and output streams, and carries out normal, batch, aggregation, and splitting conversion.

Makes input and output streams, and carries out normal, batch, aggregation, and splitting conversion.

Normal Done if FileList contains a single file name and OutputFileName does not contain a *.

Aggregation Done if FileList has more than one file name and OutputFileName does not contain * . All the chemical objects are converted and sent to the single output file.

Splitting Done if FileList contains a single file name and OutputFileName contains a * . Each chemical object in the input file is converted and sent to a separate file whose name is OutputFileName with the replaced by 1, 2, 3, etc. OutputFileName must have at least one character other than the * before the extension. For example, if OutputFileName is NEW*.smi then the output files are NEW1.smi, NEW2.smi, etc.

Batch Conversion Done if FileList has more than one file name and contains a * . Each input file is converted to an output file whose name is OutputFileName with the * replaced by the inputfile name without its path and extension. So if the input files were inpath/First.cml, inpath/Second.cml and OutputFileName was NEW*.mol, the output files would be NEWFirst.mol, NEWSecond.mol.

If FileList is empty, the input stream that has already been set (usually in the constructor) is used. If OutputFileName is empty, the output stream already set is used.

On exit, OutputFileList contains the names of the output files.

Returns the number of Chemical objects converted.

◆ AddChemObject()

int AddChemObject ( OBBase * pOb )

inherited

Adds to internal array during input.

Called by ReadMolecule() to deliver an object it has read from an input stream. Used in two modes:

When Count is negative it is left negative and the routine is just a store for an OBBase object. The negative value returned tells the calling routine that no more objects are required.
When count is >=0, probably set by Convert(), it acts as a queue of 2: writing the currently stored value before accepting the supplied one. This delay allows output routines to respond differently when the written object is the last. Count is incremented with each call, even if pOb=NULL. Objects are not added to the queue if the count is outside the range StartNumber to EndNumber. There is no upper limit if EndNumber is zero. The return value is Count ((>0) or 0 if WriteChemObject returned false.

Referenced by OBMoleculeFormat::ReadChemObjectImpl().

◆ GetChemObject()

OBBase * GetChemObject ( )

inherited

Retrieve from internal array during output.

Retrieves an object stored by AddChemObject() during output.

Referenced by OBMoleculeFormat::WriteChemObjectImpl().

◆ IsFirstInput()

bool IsFirstInput ( )

inherited

True if the first input object is being processed.

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

◆ SetFirstInput()

void SetFirstInput ( bool b = true )

inherited

Setwhether or not is the first input.

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

◆ GetOutputIndex() [2/2]

int GetOutputIndex ( ) const

inherited

Retrieves number of ChemObjects that have been actually output.

Returns the number of objects which have been output or are currently being output. The outputindex is incremented when an object for output is fetched by GetChemObject(). So the function will return 1 if called from WriteMolecule() during output of the first object.

Referenced by OBMoleculeFormat::DeleteDeferredMols(), OBMoleculeFormat::DoOutputOptions(), and XMLConversion::GetOutputIndex().

◆ SetOutputIndex()

void SetOutputIndex ( int indx )

inherited

Sets output index (maybe to control whether seen as first object)

Referenced by OBMoleculeFormat::DeleteDeferredMols(), OBConversion::FullConvert(), OBMoleculeFormat::OutputDeferredMols(), and OBMoleculeFormat::WriteChemObjectImpl().

◆ SetMoreFilesToCome()

void SetMoreFilesToCome ( )

inherited

Used with multiple input files. Off by default.

Referenced by OBConversion::FullConvert().

◆ SetOneObjectOnly()

void SetOneObjectOnly ( bool b = true )

inherited

Used with multiple input files. Off by default.

Referenced by OBConversion::FullConvert(), OBMoleculeFormat::OutputDeferredMols(), and OBConversion::Write().

◆ SetLast()

void SetLast ( bool b )

inlineinherited

Synonym for SetOneObjectOnly()

Referenced by OBMoleculeFormat::DeleteDeferredMols().

◆ IsLastFile()

bool IsLastFile ( )

inlineinherited

True if no more files to be read.

◆ GetCount()

int GetCount ( ) const

inlineinherited

Number of objects read and processed Incremented after options are processed, so 0 for first object. Returns -1 if Convert interface not used.

◆ GetDefaultFormat()

static OBFormat* GetDefaultFormat ( )

inlinestaticinherited

The default format is set in a single OBFormat class (generally it is OBMol)

◆ Write()

bool Write	(	OBBase *	pOb,
		std::ostream *	pout = `NULL`
	)

inherited

Outputs an object of a class derived from OBBase.

Part of "API" interface. The output stream can be specified and the change is retained in the OBConversion instance

Writes the object pOb but does not delete it afterwards. The output stream is lastingly changed if pos is not NULL Returns true if successful.

Examples:: obconformersearch_default.cpp.

Referenced by OBConversion::WriteFile(), and OBConversion::WriteString().

◆ WriteString()

std::string WriteString	(	OBBase *	pOb,
		bool	trimWhitespace = `false`
	)

inherited

Outputs an object of a class derived from OBBase as a string.

Part of "API" interface. The output stream is temporarily changed to the string and then restored This method is primarily intended for scripting languages without "stream" classes The optional "trimWhitespace" parameter allows trailing whitespace to be removed (e.g., in a SMILES string or InChI, etc.)

Writes the object pOb but does not delete it afterwards. The output stream not changed (since we cannot write to this string later) Returns true if successful.

Referenced by OBBuilder::Build().

◆ WriteFile()

bool WriteFile	(	OBBase *	pOb,
		std::string	filePath
	)

inherited

Outputs an object of a class derived from OBBase as a file (with the supplied path)

Part of "API" interface. The output stream is changed to the supplied file and the change is retained in the OBConversion instance. This method is primarily intended for scripting languages without "stream" classes

Writes the object pOb but does not delete it afterwards. The output stream is lastingly changed to point to the file Returns true if successful.

◆ CloseOutFile()

void CloseOutFile ( )

inherited

Manually closes and deletes the output stream The file is closed anyway when in the OBConversion destructor or when WriteFile is called again.

Since: version 2.1

◆ Read()

bool Read	(	OBBase *	pOb,
		std::istream *	pin = `NULL`
	)

inherited

Reads an object of a class derived from OBBase into pOb.

Part of "API" interface. The input stream can be specified and the change is retained in the OBConversion instance

Returns: false and pOb=NULL on error

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

Referenced by OpenBabel::alternate(), OBConversion::ReadFile(), OBMoleculeFormat::ReadNameIndex(), and OBConversion::ReadString().

◆ ReadString()

bool ReadString	(	OBBase *	pOb,
		std::string	input
	)

inherited

Reads an object of a class derived from OBBase into pOb from the supplied string.

Part of "API" interface. The input stream can be specified and the change is retained in the OBConversion instance

Returns: NULL on errorPart of "API" interface.; false and pOb=NULL on error This method is primarily intended for scripting languages without "stream" classes Any existing input stream will be replaced by stringstream.

Examples:: obconversion_readstring.cpp.

Referenced by OpenBabel::CompileSmilesQuery(), and AliasData::Expand().

◆ ReadFile()

bool ReadFile	(	OBBase *	pOb,
		std::string	filePath
	)

inherited

Reads an object of a class derived from OBBase into pOb from the file specified.

Part of "API" interface. The output stream is changed to the supplied file and the change is retained in the OBConversion instance. For multi-molecule files, the remaining molecules can be read by repeatedly calling the Read() method.

Returns: false and pOb=NULL on error This method is primarily intended for scripting languages without "stream" classes

◆ OpenInAndOutFiles()

bool OpenInAndOutFiles	(	std::string	infilepath,
		std::string	outfilepath
	)

inherited

Part of the "Convert" interface. Open the files and update the streams in the OBConversion object. This method is primarily intended for scripting languages without "stream" classes and will usually followed by a call to Convert(). Will set format from file extension if format has not already been set. Files will be opened even if format cannot be determined, but not if file path is empty.

Returns: false if unsucessful.

Referenced by OBConversion::OBConversion().

◆ ReportNumberConverted()

void ReportNumberConverted	(	int	count,
		OBFormat *	pFormat = `NULL`
	)

inherited

Sends a message like "2 molecules converted" to clog The type of object is taken from the TargetClassDescription of the specified class (or the output format if not specified)and is appropriately singular or plural.

◆ NumInputObjects()

int NumInputObjects ( )

inherited

Returns: the number of objects in the inputstream, or -1 if error or if SkipObjects for the input format is not implemented Adjusts for the value of -f and -l options (first and last objects).