src/openbabel/obconversion.hpp

/**********************************************************************
obconversion.h - Handle file conversions. Declaration of OBFormat, OBConversion

Copyright (C) 2004-2005 by Chris Morley

This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#ifndef OB_CONV_H
#define OB_CONV_H

#include "config.h"

#if HAVE_IOSTREAM
#include <iostream>
#elif HAVE_IOSTREAM_H
#include <iostream.h>
#endif
#if HAVE_FSTREAM
#include <fstream>
#elif HAVE_FSTREAM_H
#include <fstream.h>
#endif

#if HAVE_SSTREAM
        #include <sstream>
#elif
        #include <sstream.h>
#endif

#include <string>
#include <vector>
#include <map>
#include <typeinfo>

//#include "dlhandler.h"

// These macros are used in DLL builds. If they have not
// been set in babelconfig.h, define them as nothing.
#ifndef OBCONV
        #define OBCONV
#endif
#ifndef OBDLL
        #define OBDLL
#endif

//using namespace std;
namespace OpenBabel {


class OBBase;
class OBConversion;
//*************************************************

/// @brief 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.
/// 
class OBCONV OBFormat
{
public:
        /// @brief 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.
        virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv)
                { std::cerr << "Not a valid input format"; return false;}

        /// @brief 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()
        virtual bool ReadChemObject(OBConversion* pConv)
                { std::cerr << "Not a valid input format"; return false;}

        /// @brief 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 bool WriteMolecule(OBBase* pOb, OBConversion* pConv)
                { std::cerr << "Not a valid output format"; return false;}

        /// @brief The "Convert" interface Write function.

        /// Writes a single object
        /// Deletes the object after writing 
        /// Returns false on error
        virtual bool WriteChemObject(OBConversion* pConv)
                { std::cerr << "Not a valid output format"; return false;}

        /// @brief 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.
        virtual const char* Description()=0;
        
        /// @brief 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). 
        virtual const char* TargetClassDescription();

        /// @brief 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.
        virtual const std::type_info& GetType();
        
        /// @brief Web address where the format is defined.
        virtual const char* SpecificationURL() { return ""; }

        /// @brief Chemical MIME type associated with this file type (if any)
        virtual const char* GetMIMEType() { return ""; }

/// @brief 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
        virtual unsigned int Flags() { return 0;}; 

        /// @brief 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 
        virtual int SkipObjects(int n, OBConversion* pConv)
        {
                return 0; //shows not implemented in the format class
        };

        /// @brief 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.
        virtual OBFormat* MakeNewInstance()
        {
                return NULL; //shows not implemented in the format class
        }

        /// @brief Format classes do not have a destructor
        virtual ~OBFormat(){};
};

//*************************************************
/// @brief Case insensitive string comparison for FormatsMap key.
        struct CharPtrLess : public std::binary_function<const char*,const char*, bool>
        {
                bool operator()(const char* p1,const char* p2) const
                { return strcasecmp(p1,p2)<0; }
        };

        typedef std::map<const char*,OBFormat*,CharPtrLess > FMapType;
        typedef FMapType::iterator Formatpos;

//*************************************************

/// Class to convert from one format to another.
class OBCONV OBConversion
{
        /// @nosubgrouping
public:
        /// @name Construction
        //@{
                                                        OBConversion(std::istream* is=NULL, std::ostream* os=NULL);
        /// @brief Copy constructor
                                                        OBConversion(const OBConversion& o);
        virtual     ~OBConversion(); 
        //@}    
        /// @name Collection of formats
        //@{
        /// @brief Called once by each format class
        static int                              RegisterFormat(const char* ID, OBFormat* pFormat, const char* MIME = NULL);
        /// @brief Searches registered formats
        static OBFormat*        FindFormat(const char* ID);
        /// @brief Searches registered formats for an ID the same as the file extension
        static OBFormat*        FormatFromExt(const char* filename);
        /// @brief Searches registered formats for a MIME the same as the chemical MIME type passed
        static OBFormat*        FormatFromMIME(const char* MIME);

        ///Repeatedly called to recover available Formats
        static bool             GetNextFormat(Formatpos& itr, const char*& str,OBFormat*& pFormat);
        //@}
                
        /// @name Information
        //@{
        static const char* Description(); //generic conversion options
        //@}

        /// @name Parameter get and set
        //@{
        std::istream* GetInStream() const {return pInStream;};
        std::ostream* GetOutStream() const {return pOutStream;};
        void          SetInStream(std::istream* pIn){pInStream=pIn;};
        void          SetOutStream(std::ostream* pOut){pOutStream=pOut;};
        bool          SetInAndOutFormats(const char* inID, const char* outID);///< Sets the formats from their ids, e g CML
        bool          SetInAndOutFormats(OBFormat* pIn, OBFormat* pOut);
        bool          SetInFormat(const char* inID);
        bool          SetInFormat(OBFormat* pIn);
        bool          SetOutFormat(const char* outID);
        bool          SetOutFormat(OBFormat* pOut);

        OBFormat*   GetInFormat() const{return pInFormat;};
        OBFormat*   GetOutFormat() const{return pOutFormat;};
        std::string GetInFilename() const{return InFilename;};
        
        ///Get the position in the input stream of the object being read
        std::streampos GetInPos()const{return wInpos;}; 

        ///Get the length in the input stream of the object being read
        size_t GetInLen()const{return wInlen;}; 

        ///@brief Returns a default title which is the filename
        const char* GetTitle() const;

        ///@brief Extension method: deleted in ~OBConversion()
        OBConversion* GetAuxConv() const {return pAuxConv;};
        void          SetAuxConv(OBConversion* pConv) {pAuxConv=pConv;};
        //@}
        /// @name Option handling
        //@{
        ///@brief Three types of options set on the the command line by -a? , -x? , or -?
        enum Option_type { INOPTIONS, OUTOPTIONS, GENOPTIONS };

        ///@brief Determine whether an option is set. Returns NULL if option not and a pointer to the associated text if it is 
        const char* IsOption(const char* opt,Option_type opttyp=OUTOPTIONS);
        
        ///@brief Access the map with option name as key and any associated text as value
        const std::map<std::string,std::string>* GetOptions(Option_type opttyp)
        { return &OptionsArray[opttyp];};

        ///@brief Set an option of specified type, with optional text
        void AddOption(const char* opt, Option_type opttyp, const char* txt=NULL);
        
        bool RemoveOption(const char* opt, Option_type optype);

        ///@brief Set several single character options of specified type from string like ab"btext"c"ctext"
        void SetOptions(const char* options, Option_type opttyp);

        ///@brief For example -h takes 0 parameters; -f takes 1. Call in a format constructor.
        static void RegisterOptionParam(std::string name, OBFormat* pFormat,
                                              int numberParams=0, Option_type typ=OUTOPTIONS);

        ///@brief Returns the number of parameters registered for the option, or 0 if not found
        static int GetOptionParams(std::string name, Option_type typ);
        //@}

        /// @name Conversion
        //@{
        /// @brief Conversion for single input and output stream
        int         Convert(std::istream* is, std::ostream* os);

        /// @brief Conversion with existing streams
        int         Convert();

        /// @brief Conversion with multiple input/output files:
        /// makes input and output streams, and carries out normal, batch, aggregation, and splitting conversion.
        int                                     FullConvert(std::vector<std::string>& FileList,
                                                                                std::string& OutputFileName, std::vector<std::string>& OutputFileList);
        //@}

        /// @name Conversion loop control
        //@{
        int                                     AddChemObject(OBBase* pOb);///< @brief Adds to internal array during input
        OBBase*                 GetChemObject(); ///< @brief Retrieve from internal array during output
        bool                            IsLast();///< @brief True if no more objects to be output
        bool                            IsFirstInput();///< @brief True if the first input object is being processed
        int         GetOutputIndex() const ;///< @brief Retrieves number of ChemObjects that have been actually output
        void                            SetOutputIndex(int indx);///< @brief Sets ouput index (maybe to control whether seen as first object)
        void                            SetMoreFilesToCome();///<@brief Used with multiple input files. Off by default.
        void                            SetOneObjectOnly();///<@brief Used with multiple input files. Off by default.
        //@}
        /// @name Convenience functions
        //@{
        ///The default format is set in a single OBFormat class (generally it is OBMol) 
        static OBFormat* GetDefaultFormat(){return pDefaultFormat;};

        /// @brief 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
        bool                            Write(OBBase* pOb, std::ostream* pout=NULL);

        /// @brief 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
        std::string                     WriteString(OBBase* pOb);

        /// @brief 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
        bool                            WriteFile(OBBase* pOb, std::string filePath);

        /// @brief 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 
        bool    Read(OBBase* pOb, std::istream* pin=NULL);

        /// @brief Reads an object of a class derived from OBBase into pOb from the supplied string
        
        /// Part of "API" interface. 
        /// Returns false and pOb=NULL on error
        /// This method is primarily intended for scripting languages without "stream" classes
          bool  ReadString(OBBase* pOb, std::string input);

        /// @brief 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.
        /// Returns false and pOb=NULL on error 
        /// This method is primarily intended for scripting languages without "stream" classes
          bool  ReadFile(OBBase* pOb, std::string filePath);


        ///Replaces * in BaseName by InFile without extension and path
        static std::string BatchFileName(std::string& BaseName, std::string& InFile);
        ///Replaces * in BaseName by Count
        static std::string IncrementedFileName(std::string& BaseName, const int Count);
        //@}

protected:
        bool             SetStartAndEnd();
        static FMapType& FormatsMap();///<contains ID and pointer to all OBFormat classes
        static FMapType& FormatsMIMEMap();///<contains MIME and pointer to all OBFormat classes
        typedef std::map<std::string,int> OPAMapType;
        static OPAMapType& OptionParamArray(Option_type typ);
        static int       LoadFormatFiles();
        bool             OpenAndSetFormat(bool SetFormat, std::ifstream* is);

        std::string       InFilename;
        std::istream*     pInStream;
        std::ostream*     pOutStream;
        static OBFormat*  pDefaultFormat;
        OBFormat*         pInFormat;
        OBFormat*         pOutFormat;

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

        int               Index;
        unsigned int      StartNumber;
        unsigned int      EndNumber;
        int               Count;
        bool              m_IsLast;
        bool              MoreFilesToCome;
        bool              OneObjectOnly;
        bool              ReadyToInput;
        static int FormatFilesLoaded;
        OBBase*           pOb1;
        std::streampos wInpos; ///<position in the input stream of the object being written
        std::streampos rInpos; ///<position in the input stream of the object being read
        size_t wInlen; ///<length in the input stream of the object being written
        size_t rInlen; ///<length in the input stream of the object being read
        
        OBConversion* pAuxConv;///<Way to extend OBConversion
};

///For OBFormat::Flags()
#define NOTREADABLE     0x01
#define READONEONLY     0x02
#define READBINARY      0x04
#define NOTWRITABLE     0x10
#define WRITEONEONLY    0x20
#define WRITEBINARY     0x40
#define DEFAULTFORMAT 0x4000

} //namespace OpenBabel
#endif //OB_CONV_H

//! \file
//! \brief Handle file conversions. Declaration of OBFormat, OBConversion.

 
Revision:	809
Committed:	Mon Dec 12 19:32:50 2005 UTC (19 years, 10 months ago) by gezelter
File size:	15516 byte(s)
Log Message:	made some minor changes to allow compilation with the portland group compilers
#	User	Rev	Content
1	tim	741	/**********************************************************************
2			obconversion.h - Handle file conversions. Declaration of OBFormat, OBConversion
3
4			Copyright (C) 2004-2005 by Chris Morley
5
6			This file is part of the Open Babel project.
7			For more information, see <http://openbabel.sourceforge.net/>
8
9			This program is free software; you can redistribute it and/or modify
10			it under the terms of the GNU General Public License as published by
11			the Free Software Foundation version 2 of the License.
12
13			This program is distributed in the hope that it will be useful,
14			but WITHOUT ANY WARRANTY; without even the implied warranty of
15			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16			GNU General Public License for more details.
17			***********************************************************************/
18
19			#ifndef OB_CONV_H
20			#define OB_CONV_H
21
22	gezelter	751	#include "config.h"
23	tim	741
24			#if HAVE_IOSTREAM
25			#include <iostream>
26			#elif HAVE_IOSTREAM_H
27			#include <iostream.h>
28			#endif
29			#if HAVE_FSTREAM
30			#include <fstream>
31			#elif HAVE_FSTREAM_H
32			#include <fstream.h>
33			#endif
34
35			#if HAVE_SSTREAM
36			#include <sstream>
37			#elif
38			#include <sstream.h>
39			#endif
40
41			#include <string>
42			#include <vector>
43			#include <map>
44	gezelter	809	#include <typeinfo>
45	tim	741
46			//#include "dlhandler.h"
47
48			// These macros are used in DLL builds. If they have not
49			// been set in babelconfig.h, define them as nothing.
50			#ifndef OBCONV
51			#define OBCONV
52			#endif
53			#ifndef OBDLL
54			#define OBDLL
55			#endif
56
57			//using namespace std;
58			namespace OpenBabel {
59
60
61			class OBBase;
62			class OBConversion;
63			//*************************************************
64
65			/// @brief Base class for file formats.
66
67			/// Two sets of Read and Write functions are specified for each format
68			/// to handle two different requirements.
69			/// The "Convert" interface is for use in file format conversion applications. The
70			/// user interface, a console, a GUI, or another program is kept unaware of the
71			/// details of the chemistry and does not need to \#include mol.h. It is then
72			/// necessary to manipulate only pointers to OBBase in OBConversion and the user
73			/// interface, with all the construction and deletion of OBMol etc objects being
74			/// done in the Format classes or the OB core. The convention with "Covert"
75			/// interface functions is that chemical objects are made on the heap with new
76			/// in the ReadChemicalObject() functions and and deleted in WriteChemicalObject()
77			/// functions
78			///
79			/// The "API" interface is for programatic use of the OB routines in application
80			/// programs where mol.h is \#included. There is generally no creation or
81			/// destruction of objects in ReadMolecule() and WriteMolecule() and no restriction
82			/// on whether the pointers are to the heap or the stack.
83			///
84			class OBCONV OBFormat
85			{
86			public:
87			/// @brief The "API" interface Read function.
88
89			/// Reads a single object.
90			/// Does not make a new object on the heap;
91			/// can be used with a pointer to an chem object on the heap or the stack.
92			virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv)
93			{ std::cerr << "Not a valid input format"; return false;}
94
95			/// @brief The "Convert" interface Read function.
96
97			/// Possibly reads multiple new objects on the heap and subjects them
98			/// to its DoTransformations() function, which may delete them again.
99			/// Sends result to pConv->AddChemObject()
100			virtual bool ReadChemObject(OBConversion* pConv)
101			{ std::cerr << "Not a valid input format"; return false;}
102
103			/// @brief The "API" interface Write function.
104
105			/// Writes a single object
106			/// Does not delete the object;
107			/// can be used with a pointer to an chem object on the heap or the stack.
108			/// Returns false on error.
109			virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv)
110			{ std::cerr << "Not a valid output format"; return false;}
111
112			/// @brief The "Convert" interface Write function.
113
114			/// Writes a single object
115			/// Deletes the object after writing
116			/// Returns false on error
117			virtual bool WriteChemObject(OBConversion* pConv)
118			{ std::cerr << "Not a valid output format"; return false;}
119
120			/// @brief Information on this format. Printed out in response to -Hxxx option where xxx id the id of the format.
121
122			/// Must be provided by each format class.
123			/// Can include a list of command line Options. These may be used to construction
124			/// check boxes, radio buttons etc for GUI interface.
125			virtual const char* Description()=0;
126
127			/// @brief A decription of the chemical object converted by this format.
128
129			/// If not provided, the object type used by the default format is used (usually OBMol).
130			virtual const char* TargetClassDescription();
131
132			/// @brief Returns the type of chemical object used by the format.
133
134			/// Defaults to that used by the default format. Useful for checking
135			/// that a format can handle a particular object.
136			virtual const std::type_info& GetType();
137
138			/// @brief Web address where the format is defined.
139			virtual const char* SpecificationURL() { return ""; }
140
141			/// @brief Chemical MIME type associated with this file type (if any)
142			virtual const char* GetMIMEType() { return ""; }
143
144			/// @brief Decribes the capabilities of the format (Read only etc.)
145
146			/// Currently, can be a bitwise OR of any of the following
147			/// NOTREADABLE READONEONLY NOTWRITABLE WRITEONEONLY DEFAULTFORMAT
148			/// READBINARY WRITEBINARY
149			virtual unsigned int Flags() { return 0;};
150
151			/// @brief Skip past first n objects in input stream (or current one with n=0)
152
153			/// Returns 1 on success, -1 on error and 0 if not implemented
154			virtual int SkipObjects(int n, OBConversion* pConv)
155			{
156			return 0; //shows not implemented in the format class
157			};
158
159			/// @brief Returns a pointer to a new instance of the format, or NULL if fails.
160
161			/// Normally a single global instance is used but this may cause problems
162			/// if there are member variables and the format is used in more than one place
163			/// in the program.
164			virtual OBFormat* MakeNewInstance()
165			{
166			return NULL; //shows not implemented in the format class
167			}
168
169			/// @brief Format classes do not have a destructor
170			virtual ~OBFormat(){};
171			};
172
173			//*************************************************
174			/// @brief Case insensitive string comparison for FormatsMap key.
175			struct CharPtrLess : public std::binary_function<const char,const char, bool>
176			{
177			bool operator()(const char* p1,const char* p2) const
178			{ return strcasecmp(p1,p2)<0; }
179			};
180
181			typedef std::map<const char,OBFormat,CharPtrLess > FMapType;
182			typedef FMapType::iterator Formatpos;
183
184			//*************************************************
185
186			/// Class to convert from one format to another.
187			class OBCONV OBConversion
188			{
189			/// @nosubgrouping
190			public:
191			/// @name Construction
192			//@{
193			OBConversion(std::istream* is=NULL, std::ostream* os=NULL);
194			/// @brief Copy constructor
195			OBConversion(const OBConversion& o);
196			virtual ~OBConversion();
197			//@}
198			/// @name Collection of formats
199			//@{
200			/// @brief Called once by each format class
201			static int RegisterFormat(const char* ID, OBFormat* pFormat, const char* MIME = NULL);
202			/// @brief Searches registered formats
203			static OBFormat* FindFormat(const char* ID);
204			/// @brief Searches registered formats for an ID the same as the file extension
205			static OBFormat* FormatFromExt(const char* filename);
206			/// @brief Searches registered formats for a MIME the same as the chemical MIME type passed
207			static OBFormat* FormatFromMIME(const char* MIME);
208
209			///Repeatedly called to recover available Formats
210			static bool GetNextFormat(Formatpos& itr, const char& str,OBFormat& pFormat);
211			//@}
212
213			/// @name Information
214			//@{
215			static const char* Description(); //generic conversion options
216			//@}
217
218			/// @name Parameter get and set
219			//@{
220			std::istream* GetInStream() const {return pInStream;};
221			std::ostream* GetOutStream() const {return pOutStream;};
222			void SetInStream(std::istream* pIn){pInStream=pIn;};
223			void SetOutStream(std::ostream* pOut){pOutStream=pOut;};
224			bool SetInAndOutFormats(const char* inID, const char* outID);///< Sets the formats from their ids, e g CML
225			bool SetInAndOutFormats(OBFormat* pIn, OBFormat* pOut);
226			bool SetInFormat(const char* inID);
227			bool SetInFormat(OBFormat* pIn);
228			bool SetOutFormat(const char* outID);
229			bool SetOutFormat(OBFormat* pOut);
230
231			OBFormat* GetInFormat() const{return pInFormat;};
232			OBFormat* GetOutFormat() const{return pOutFormat;};
233			std::string GetInFilename() const{return InFilename;};
234
235			///Get the position in the input stream of the object being read
236			std::streampos GetInPos()const{return wInpos;};
237
238			///Get the length in the input stream of the object being read
239			size_t GetInLen()const{return wInlen;};
240
241			///@brief Returns a default title which is the filename
242			const char* GetTitle() const;
243
244			///@brief Extension method: deleted in ~OBConversion()
245			OBConversion* GetAuxConv() const {return pAuxConv;};
246			void SetAuxConv(OBConversion* pConv) {pAuxConv=pConv;};
247			//@}
248			/// @name Option handling
249			//@{
250			///@brief Three types of options set on the the command line by -a? , -x? , or -?
251			enum Option_type { INOPTIONS, OUTOPTIONS, GENOPTIONS };
252
253			///@brief Determine whether an option is set. Returns NULL if option not and a pointer to the associated text if it is
254			const char* IsOption(const char* opt,Option_type opttyp=OUTOPTIONS);
255
256			///@brief Access the map with option name as key and any associated text as value
257			const std::map<std::string,std::string>* GetOptions(Option_type opttyp)
258			{ return &OptionsArray[opttyp];};
259
260			///@brief Set an option of specified type, with optional text
261			void AddOption(const char* opt, Option_type opttyp, const char* txt=NULL);
262
263			bool RemoveOption(const char* opt, Option_type optype);
264
265			///@brief Set several single character options of specified type from string like ab"btext"c"ctext"
266			void SetOptions(const char* options, Option_type opttyp);
267
268			///@brief For example -h takes 0 parameters; -f takes 1. Call in a format constructor.
269			static void RegisterOptionParam(std::string name, OBFormat* pFormat,
270			int numberParams=0, Option_type typ=OUTOPTIONS);
271
272			///@brief Returns the number of parameters registered for the option, or 0 if not found
273			static int GetOptionParams(std::string name, Option_type typ);
274			//@}
275
276			/// @name Conversion
277			//@{
278			/// @brief Conversion for single input and output stream
279			int Convert(std::istream* is, std::ostream* os);
280
281			/// @brief Conversion with existing streams
282			int Convert();
283
284			/// @brief Conversion with multiple input/output files:
285			/// makes input and output streams, and carries out normal, batch, aggregation, and splitting conversion.
286			int FullConvert(std::vector<std::string>& FileList,
287			std::string& OutputFileName, std::vector<std::string>& OutputFileList);
288			//@}
289
290			/// @name Conversion loop control
291			//@{
292			int AddChemObject(OBBase* pOb);///< @brief Adds to internal array during input
293			OBBase* GetChemObject(); ///< @brief Retrieve from internal array during output
294			bool IsLast();///< @brief True if no more objects to be output
295			bool IsFirstInput();///< @brief True if the first input object is being processed
296			int GetOutputIndex() const ;///< @brief Retrieves number of ChemObjects that have been actually output
297			void SetOutputIndex(int indx);///< @brief Sets ouput index (maybe to control whether seen as first object)
298			void SetMoreFilesToCome();///<@brief Used with multiple input files. Off by default.
299			void SetOneObjectOnly();///<@brief Used with multiple input files. Off by default.
300			//@}
301			/// @name Convenience functions
302			//@{
303			///The default format is set in a single OBFormat class (generally it is OBMol)
304			static OBFormat* GetDefaultFormat(){return pDefaultFormat;};
305
306			/// @brief Outputs an object of a class derived from OBBase.
307
308			/// Part of "API" interface.
309			/// The output stream can be specified and the change is retained in the OBConversion instance
310			bool Write(OBBase* pOb, std::ostream* pout=NULL);
311
312			/// @brief Outputs an object of a class derived from OBBase as a string
313
314			/// Part of "API" interface.
315			/// The output stream is temporarily changed to the string and then restored
316			/// This method is primarily intended for scripting languages without "stream" classes
317			std::string WriteString(OBBase* pOb);
318
319			/// @brief Outputs an object of a class derived from OBBase as a file (with the supplied path)
320
321			/// Part of "API" interface.
322			/// The output stream is changed to the supplied file and the change is retained in the
323			/// OBConversion instance.
324			/// This method is primarily intended for scripting languages without "stream" classes
325			bool WriteFile(OBBase* pOb, std::string filePath);
326
327			/// @brief Reads an object of a class derived from OBBase into pOb.
328
329			/// Part of "API" interface.
330			/// The input stream can be specified and the change is retained in the OBConversion instance
331			/// Returns false and pOb=NULL on error
332			bool Read(OBBase* pOb, std::istream* pin=NULL);
333
334			/// @brief Reads an object of a class derived from OBBase into pOb from the supplied string
335
336			/// Part of "API" interface.
337			/// Returns false and pOb=NULL on error
338			/// This method is primarily intended for scripting languages without "stream" classes
339			bool ReadString(OBBase* pOb, std::string input);
340
341			/// @brief Reads an object of a class derived from OBBase into pOb from the file specified
342
343			/// Part of "API" interface.
344			/// The output stream is changed to the supplied file and the change is retained in the
345			/// OBConversion instance.
346			/// Returns false and pOb=NULL on error
347			/// This method is primarily intended for scripting languages without "stream" classes
348			bool ReadFile(OBBase* pOb, std::string filePath);
349
350
351			///Replaces * in BaseName by InFile without extension and path
352			static std::string BatchFileName(std::string& BaseName, std::string& InFile);
353			///Replaces * in BaseName by Count
354			static std::string IncrementedFileName(std::string& BaseName, const int Count);
355			//@}
356
357			protected:
358			bool SetStartAndEnd();
359			static FMapType& FormatsMap();///<contains ID and pointer to all OBFormat classes
360			static FMapType& FormatsMIMEMap();///<contains MIME and pointer to all OBFormat classes
361			typedef std::map<std::string,int> OPAMapType;
362			static OPAMapType& OptionParamArray(Option_type typ);
363			static int LoadFormatFiles();
364			bool OpenAndSetFormat(bool SetFormat, std::ifstream* is);
365
366			std::string InFilename;
367			std::istream* pInStream;
368			std::ostream* pOutStream;
369			static OBFormat* pDefaultFormat;
370			OBFormat* pInFormat;
371			OBFormat* pOutFormat;
372
373			std::map<std::string,std::string> OptionsArray[3];
374
375			int Index;
376			unsigned int StartNumber;
377			unsigned int EndNumber;
378			int Count;
379			bool m_IsLast;
380			bool MoreFilesToCome;
381			bool OneObjectOnly;
382			bool ReadyToInput;
383			static int FormatFilesLoaded;
384			OBBase* pOb1;
385			std::streampos wInpos; ///<position in the input stream of the object being written
386			std::streampos rInpos; ///<position in the input stream of the object being read
387			size_t wInlen; ///<length in the input stream of the object being written
388			size_t rInlen; ///<length in the input stream of the object being read
389
390			OBConversion* pAuxConv;///<Way to extend OBConversion
391			};
392
393			///For OBFormat::Flags()
394			#define NOTREADABLE 0x01
395			#define READONEONLY 0x02
396			#define READBINARY 0x04
397			#define NOTWRITABLE 0x10
398			#define WRITEONEONLY 0x20
399			#define WRITEBINARY 0x40
400			#define DEFAULTFORMAT 0x4000
401
402			} //namespace OpenBabel
403			#endif //OB_CONV_H
404
405			//! \file
406			//! \brief Handle file conversions. Declaration of OBFormat, OBConversion.
407
408