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/********************************************************************** |
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obconversion.h - Handle file conversions. Declaration of OBFormat, OBConversion |
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|
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Copyright (C) 2004-2005 by Chris Morley |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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#ifndef OB_CONV_H |
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#define OB_CONV_H |
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|
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#include "config.h" |
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|
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#if HAVE_IOSTREAM |
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#include <iostream> |
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#elif HAVE_IOSTREAM_H |
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#include <iostream.h> |
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#endif |
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#if HAVE_FSTREAM |
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#include <fstream> |
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#elif HAVE_FSTREAM_H |
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#include <fstream.h> |
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#endif |
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|
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#if HAVE_SSTREAM |
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#include <sstream> |
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#elif |
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#include <sstream.h> |
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#endif |
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|
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#include <string> |
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#include <vector> |
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#include <map> |
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|
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//#include "dlhandler.h" |
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|
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// These macros are used in DLL builds. If they have not |
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// been set in babelconfig.h, define them as nothing. |
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#ifndef OBCONV |
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#define OBCONV |
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#endif |
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#ifndef OBDLL |
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#define OBDLL |
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#endif |
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|
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//using namespace std; |
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namespace OpenBabel { |
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|
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|
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class OBBase; |
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class OBConversion; |
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//************************************************* |
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|
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/// @brief Base class for file formats. |
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|
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/// Two sets of Read and Write functions are specified for each format |
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/// to handle two different requirements. |
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/// The "Convert" interface is for use in file format conversion applications. The |
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/// user interface, a console, a GUI, or another program is kept unaware of the |
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/// details of the chemistry and does not need to \#include mol.h. It is then |
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/// necessary to manipulate only pointers to OBBase in OBConversion and the user |
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/// interface, with all the construction and deletion of OBMol etc objects being |
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/// done in the Format classes or the OB core. The convention with "Covert" |
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/// interface functions is that chemical objects are made on the heap with new |
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/// in the ReadChemicalObject() functions and and deleted in WriteChemicalObject() |
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/// functions |
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/// |
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/// The "API" interface is for programatic use of the OB routines in application |
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/// programs where mol.h is \#included. There is generally no creation or |
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/// destruction of objects in ReadMolecule() and WriteMolecule() and no restriction |
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/// on whether the pointers are to the heap or the stack. |
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/// |
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class OBCONV OBFormat |
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{ |
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public: |
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/// @brief The "API" interface Read function. |
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|
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/// Reads a single object. |
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/// Does not make a new object on the heap; |
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/// can be used with a pointer to an chem object on the heap or the stack. |
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virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv) |
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{ std::cerr << "Not a valid input format"; return false;} |
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|
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/// @brief The "Convert" interface Read function. |
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|
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/// Possibly reads multiple new objects on the heap and subjects them |
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/// to its DoTransformations() function, which may delete them again. |
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/// Sends result to pConv->AddChemObject() |
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virtual bool ReadChemObject(OBConversion* pConv) |
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{ std::cerr << "Not a valid input format"; return false;} |
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|
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/// @brief The "API" interface Write function. |
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|
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/// Writes a single object |
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/// Does not delete the object; |
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/// can be used with a pointer to an chem object on the heap or the stack. |
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/// Returns false on error. |
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virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv) |
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{ std::cerr << "Not a valid output format"; return false;} |
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|
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/// @brief The "Convert" interface Write function. |
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|
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/// Writes a single object |
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/// Deletes the object after writing |
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/// Returns false on error |
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virtual bool WriteChemObject(OBConversion* pConv) |
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{ std::cerr << "Not a valid output format"; return false;} |
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|
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/// @brief Information on this format. Printed out in response to -Hxxx option where xxx id the id of the format. |
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|
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/// Must be provided by each format class. |
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/// Can include a list of command line Options. These may be used to construction |
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/// check boxes, radio buttons etc for GUI interface. |
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virtual const char* Description()=0; |
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|
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/// @brief A decription of the chemical object converted by this format. |
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|
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/// If not provided, the object type used by the default format is used (usually OBMol). |
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virtual const char* TargetClassDescription(); |
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|
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/// @brief Returns the type of chemical object used by the format. |
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|
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/// Defaults to that used by the default format. Useful for checking |
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/// that a format can handle a particular object. |
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virtual const std::type_info& GetType(); |
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|
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/// @brief Web address where the format is defined. |
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virtual const char* SpecificationURL() { return ""; } |
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|
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/// @brief Chemical MIME type associated with this file type (if any) |
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virtual const char* GetMIMEType() { return ""; } |
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|
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/// @brief Decribes the capabilities of the format (Read only etc.) |
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|
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/// Currently, can be a bitwise OR of any of the following |
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/// NOTREADABLE READONEONLY NOTWRITABLE WRITEONEONLY DEFAULTFORMAT |
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/// READBINARY WRITEBINARY |
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virtual unsigned int Flags() { return 0;}; |
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|
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/// @brief Skip past first n objects in input stream (or current one with n=0) |
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|
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/// Returns 1 on success, -1 on error and 0 if not implemented |
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virtual int SkipObjects(int n, OBConversion* pConv) |
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{ |
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return 0; //shows not implemented in the format class |
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}; |
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|
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/// @brief Returns a pointer to a new instance of the format, or NULL if fails. |
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|
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/// Normally a single global instance is used but this may cause problems |
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/// if there are member variables and the format is used in more than one place |
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/// in the program. |
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virtual OBFormat* MakeNewInstance() |
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{ |
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return NULL; //shows not implemented in the format class |
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} |
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/// @brief Format classes do not have a destructor |
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virtual ~OBFormat(){}; |
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}; |
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|
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//************************************************* |
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/// @brief Case insensitive string comparison for FormatsMap key. |
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struct CharPtrLess : public std::binary_function<const char*,const char*, bool> |
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{ |
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bool operator()(const char* p1,const char* p2) const |
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{ return strcasecmp(p1,p2)<0; } |
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}; |
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|
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typedef std::map<const char*,OBFormat*,CharPtrLess > FMapType; |
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typedef FMapType::iterator Formatpos; |
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|
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//************************************************* |
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|
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/// Class to convert from one format to another. |
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class OBCONV OBConversion |
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{ |
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/// @nosubgrouping |
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public: |
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/// @name Construction |
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//@{ |
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OBConversion(std::istream* is=NULL, std::ostream* os=NULL); |
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/// @brief Copy constructor |
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OBConversion(const OBConversion& o); |
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virtual ~OBConversion(); |
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//@} |
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/// @name Collection of formats |
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//@{ |
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/// @brief Called once by each format class |
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static int RegisterFormat(const char* ID, OBFormat* pFormat, const char* MIME = NULL); |
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/// @brief Searches registered formats |
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static OBFormat* FindFormat(const char* ID); |
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/// @brief Searches registered formats for an ID the same as the file extension |
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static OBFormat* FormatFromExt(const char* filename); |
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/// @brief Searches registered formats for a MIME the same as the chemical MIME type passed |
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static OBFormat* FormatFromMIME(const char* MIME); |
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|
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///Repeatedly called to recover available Formats |
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static bool GetNextFormat(Formatpos& itr, const char*& str,OBFormat*& pFormat); |
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//@} |
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|
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/// @name Information |
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//@{ |
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static const char* Description(); //generic conversion options |
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//@} |
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|
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/// @name Parameter get and set |
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//@{ |
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std::istream* GetInStream() const {return pInStream;}; |
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std::ostream* GetOutStream() const {return pOutStream;}; |
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void SetInStream(std::istream* pIn){pInStream=pIn;}; |
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void SetOutStream(std::ostream* pOut){pOutStream=pOut;}; |
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bool SetInAndOutFormats(const char* inID, const char* outID);///< Sets the formats from their ids, e g CML |
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bool SetInAndOutFormats(OBFormat* pIn, OBFormat* pOut); |
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bool SetInFormat(const char* inID); |
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bool SetInFormat(OBFormat* pIn); |
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bool SetOutFormat(const char* outID); |
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bool SetOutFormat(OBFormat* pOut); |
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|
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OBFormat* GetInFormat() const{return pInFormat;}; |
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OBFormat* GetOutFormat() const{return pOutFormat;}; |
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std::string GetInFilename() const{return InFilename;}; |
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|
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///Get the position in the input stream of the object being read |
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std::streampos GetInPos()const{return wInpos;}; |
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|
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///Get the length in the input stream of the object being read |
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size_t GetInLen()const{return wInlen;}; |
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|
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///@brief Returns a default title which is the filename |
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const char* GetTitle() const; |
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|
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///@brief Extension method: deleted in ~OBConversion() |
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OBConversion* GetAuxConv() const {return pAuxConv;}; |
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void SetAuxConv(OBConversion* pConv) {pAuxConv=pConv;}; |
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//@} |
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/// @name Option handling |
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//@{ |
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///@brief Three types of options set on the the command line by -a? , -x? , or -? |
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enum Option_type { INOPTIONS, OUTOPTIONS, GENOPTIONS }; |
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///@brief Determine whether an option is set. Returns NULL if option not and a pointer to the associated text if it is |
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const char* IsOption(const char* opt,Option_type opttyp=OUTOPTIONS); |
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|
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///@brief Access the map with option name as key and any associated text as value |
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const std::map<std::string,std::string>* GetOptions(Option_type opttyp) |
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{ return &OptionsArray[opttyp];}; |
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|
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///@brief Set an option of specified type, with optional text |
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void AddOption(const char* opt, Option_type opttyp, const char* txt=NULL); |
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|
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bool RemoveOption(const char* opt, Option_type optype); |
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|
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///@brief Set several single character options of specified type from string like ab"btext"c"ctext" |
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void SetOptions(const char* options, Option_type opttyp); |
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|
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///@brief For example -h takes 0 parameters; -f takes 1. Call in a format constructor. |
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static void RegisterOptionParam(std::string name, OBFormat* pFormat, |
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int numberParams=0, Option_type typ=OUTOPTIONS); |
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|
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///@brief Returns the number of parameters registered for the option, or 0 if not found |
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static int GetOptionParams(std::string name, Option_type typ); |
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//@} |
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|
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/// @name Conversion |
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//@{ |
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/// @brief Conversion for single input and output stream |
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int Convert(std::istream* is, std::ostream* os); |
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|
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/// @brief Conversion with existing streams |
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int Convert(); |
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/// @brief Conversion with multiple input/output files: |
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/// makes input and output streams, and carries out normal, batch, aggregation, and splitting conversion. |
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int FullConvert(std::vector<std::string>& FileList, |
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std::string& OutputFileName, std::vector<std::string>& OutputFileList); |
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//@} |
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|
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/// @name Conversion loop control |
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//@{ |
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int AddChemObject(OBBase* pOb);///< @brief Adds to internal array during input |
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OBBase* GetChemObject(); ///< @brief Retrieve from internal array during output |
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bool IsLast();///< @brief True if no more objects to be output |
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bool IsFirstInput();///< @brief True if the first input object is being processed |
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int GetOutputIndex() const ;///< @brief Retrieves number of ChemObjects that have been actually output |
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void SetOutputIndex(int indx);///< @brief Sets ouput index (maybe to control whether seen as first object) |
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void SetMoreFilesToCome();///<@brief Used with multiple input files. Off by default. |
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void SetOneObjectOnly();///<@brief Used with multiple input files. Off by default. |
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//@} |
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/// @name Convenience functions |
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//@{ |
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///The default format is set in a single OBFormat class (generally it is OBMol) |
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static OBFormat* GetDefaultFormat(){return pDefaultFormat;}; |
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|
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/// @brief Outputs an object of a class derived from OBBase. |
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|
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/// Part of "API" interface. |
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/// The output stream can be specified and the change is retained in the OBConversion instance |
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bool Write(OBBase* pOb, std::ostream* pout=NULL); |
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|
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/// @brief Outputs an object of a class derived from OBBase as a string |
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|
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/// Part of "API" interface. |
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/// The output stream is temporarily changed to the string and then restored |
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/// This method is primarily intended for scripting languages without "stream" classes |
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std::string WriteString(OBBase* pOb); |
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|
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/// @brief Outputs an object of a class derived from OBBase as a file (with the supplied path) |
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|
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/// Part of "API" interface. |
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/// The output stream is changed to the supplied file and the change is retained in the |
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/// OBConversion instance. |
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/// This method is primarily intended for scripting languages without "stream" classes |
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bool WriteFile(OBBase* pOb, std::string filePath); |
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|
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/// @brief Reads an object of a class derived from OBBase into pOb. |
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|
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/// Part of "API" interface. |
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/// The input stream can be specified and the change is retained in the OBConversion instance |
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/// Returns false and pOb=NULL on error |
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bool Read(OBBase* pOb, std::istream* pin=NULL); |
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|
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/// @brief Reads an object of a class derived from OBBase into pOb from the supplied string |
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|
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/// Part of "API" interface. |
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/// Returns false and pOb=NULL on error |
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/// This method is primarily intended for scripting languages without "stream" classes |
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bool ReadString(OBBase* pOb, std::string input); |
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|
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/// @brief Reads an object of a class derived from OBBase into pOb from the file specified |
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|
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/// Part of "API" interface. |
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/// The output stream is changed to the supplied file and the change is retained in the |
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/// OBConversion instance. |
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/// Returns false and pOb=NULL on error |
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/// This method is primarily intended for scripting languages without "stream" classes |
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bool ReadFile(OBBase* pOb, std::string filePath); |
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|
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|
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///Replaces * in BaseName by InFile without extension and path |
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static std::string BatchFileName(std::string& BaseName, std::string& InFile); |
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///Replaces * in BaseName by Count |
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static std::string IncrementedFileName(std::string& BaseName, const int Count); |
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//@} |
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|
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protected: |
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bool SetStartAndEnd(); |
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static FMapType& FormatsMap();///<contains ID and pointer to all OBFormat classes |
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static FMapType& FormatsMIMEMap();///<contains MIME and pointer to all OBFormat classes |
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typedef std::map<std::string,int> OPAMapType; |
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static OPAMapType& OptionParamArray(Option_type typ); |
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static int LoadFormatFiles(); |
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bool OpenAndSetFormat(bool SetFormat, std::ifstream* is); |
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|
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std::string InFilename; |
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std::istream* pInStream; |
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std::ostream* pOutStream; |
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static OBFormat* pDefaultFormat; |
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OBFormat* pInFormat; |
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OBFormat* pOutFormat; |
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|
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std::map<std::string,std::string> OptionsArray[3]; |
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|
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int Index; |
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unsigned int StartNumber; |
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unsigned int EndNumber; |
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int Count; |
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bool m_IsLast; |
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bool MoreFilesToCome; |
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bool OneObjectOnly; |
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bool ReadyToInput; |
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static int FormatFilesLoaded; |
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OBBase* pOb1; |
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std::streampos wInpos; ///<position in the input stream of the object being written |
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std::streampos rInpos; ///<position in the input stream of the object being read |
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size_t wInlen; ///<length in the input stream of the object being written |
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size_t rInlen; ///<length in the input stream of the object being read |
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|
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OBConversion* pAuxConv;///<Way to extend OBConversion |
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}; |
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|
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///For OBFormat::Flags() |
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#define NOTREADABLE 0x01 |
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#define READONEONLY 0x02 |
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#define READBINARY 0x04 |
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#define NOTWRITABLE 0x10 |
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#define WRITEONEONLY 0x20 |
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#define WRITEBINARY 0x40 |
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#define DEFAULTFORMAT 0x4000 |
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|
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} //namespace OpenBabel |
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#endif //OB_CONV_H |
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|
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//! \file |
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//! \brief Handle file conversions. Declaration of OBFormat, OBConversion. |
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|
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|
