obmolecformat.h

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/**********************************************************************
obmolecformat.h - Subclass of OBFormat for conversion of OBMol.

Copyright (C) 2005 Chris Morley

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

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_MOLECULEFORMAT_H
#define OB_MOLECULEFORMAT_H

#ifdef _MSC_VER
 #include <unordered_map>
#endif

#include <ciso646> // detect std::lib
#ifdef _LIBCPP_VERSION
 #include <unordered_map>
#elif __GNUC__ == 4 && __GNUC_MINOR__ >= 1
 #include <tr1/unordered_map>
#elif defined(USE_BOOST)
 #include <boost/tr1/unordered_map.hpp>
#endif

#include <openbabel/babelconfig.h>
#include <openbabel/obconversion.h>
#include <typeinfo>
#include <cstdlib>

namespace OpenBabel {

 class OBMol;
 class OBDescriptor;
#ifdef HAVE_SHARED_POINTER
 class OBReaction;
#endif

// This macro is used in DLL builds. If it has not
// been set in babelconfig.h, define it as nothing.
#ifndef OBCOMMON
 #define OBCOMMON
#endif


class OBCOMMON OBMoleculeFormat : public OBFormat
{
public:

 OBMoleculeFormat()
 {
 if(!OptionsRegistered)
 {
 OptionsRegistered=true;
 OBConversion::RegisterOptionParam("b", this, 0, OBConversion::INOPTIONS);
 OBConversion::RegisterOptionParam("s", this, 0, OBConversion::INOPTIONS);
 OBConversion::RegisterOptionParam("title", this, 1, OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("addtotitle",this, 1, OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("property", this, 2, OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("C", this, 0, OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("j", this, 0, OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("join", this, 0, OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("separate", this, 0, OBConversion::GENOPTIONS);

 //The follow are OBMol options, which should not be in OBConversion.
 //But here isn't entirely appropriate either, since one could have
 //OBMol formats loaded but which don't derived from this class.
 //However, this possibility is remote.
 OBConversion::RegisterOptionParam("s", NULL, 1,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("v", NULL, 1,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("h", NULL, 0,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("d", NULL, 0,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("b", NULL, 0,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("c", NULL, 0,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("p", NULL, 1,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("t", NULL, 0,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("k", NULL, 0,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("filter", NULL, 1,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("add", NULL, 1,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("delete", NULL, 1,OBConversion::GENOPTIONS);
 OBConversion::RegisterOptionParam("append", NULL, 1,OBConversion::GENOPTIONS);
 }
 }

 static bool ReadChemObjectImpl(OBConversion* pConv, OBFormat*);
 static bool WriteChemObjectImpl(OBConversion* pConv, OBFormat*);

 virtual bool ReadChemObject(OBConversion* pConv)
 { return ReadChemObjectImpl(pConv, this);}

 virtual bool WriteChemObject(OBConversion* pConv)
 { return WriteChemObjectImpl(pConv, this);}

 static bool DoOutputOptions(OBBase* pOb, OBConversion* pConv);


 static bool DeferMolOutput(OBMol* pmol, OBConversion* pConv, OBFormat* pF);
 static bool OutputDeferredMols(OBConversion* pConv);
 static bool DeleteDeferredMols();
 static OBMol* MakeCombinedMolecule(OBMol* pFirst, OBMol* pSecond);

#ifdef HAVE_SHARED_POINTER
 static bool OutputMolsFromReaction
 (OBReaction* pReact, OBConversion* pConv, OBFormat* pFormat);
#endif

#ifdef _MSC_VER
 typedef std::tr1::unordered_map<std::string, unsigned> NameIndexType;
#elif defined(_LIBCPP_VERSION)
 typedef std::unordered_map<std::string, unsigned> NameIndexType;
#elif (__GNUC__ == 4 && __GNUC_MINOR__ >= 1 && !defined(__APPLE_CC__)) || defined (USE_BOOST)
 typedef std::tr1::unordered_map<std::string, unsigned> NameIndexType;
#else
 typedef std::map<std::string, unsigned> NameIndexType;
#endif

 // documentation in obmolecformat.cpp
 static bool ReadNameIndex(NameIndexType& index, const std::string& datafilename,
 OBFormat* pInFormat);

 const std::type_info& GetType()
 {
 return typeid(OBMol*);
 }

private:

 static bool OptionsRegistered;
 static std::map<std::string, OBMol*> IMols;
 static OBMol* _jmol; 
 static std::vector<OBMol> MolArray; 
 static bool StoredMolsReady; 
 static OBDescriptor* _pDesc;

};

}
#endif //OB_MOLECULEFORMAT_H