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.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_MOLECULEFORMAT_H
#define OB_MOLECULEFORMAT_H

#ifdef _WIN32
  #include <hash_map>
#endif

#include <openbabel/mol.h>
#include <openbabel/obconversion.h>

namespace OpenBabel {

// 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
{
private:
  static std::map<std::string, OBMol*> IMols;
  static OBMol* _jmol; 
  static std::vector<OBMol> MolArray; 
  static bool StoredMolsReady; 

public:

  OBMoleculeFormat()
  {
    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, 0,OBConversion::GENOPTIONS); 
    OBConversion::RegisterOptionParam("t", NULL, 0,OBConversion::GENOPTIONS);
    OBConversion::RegisterOptionParam("k", NULL, 0,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   DeferMolOutput(OBMol* pmol, OBConversion* pConv, OBFormat* pF);
  static bool   OutputDeferredMols(OBConversion* pConv);
  static bool   DeleteDeferredMols();
  static OBMol* MakeCombinedMolecule(OBMol* pFirst, OBMol* pSecond);

#ifdef _WIN32
  typedef stdext::hash_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*);
  }

};

}
#endif //OB_MOLECULEFORMAT_H

---

This file is part of the documentation for Open Babel, version 2.1.0.

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