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