cistrans.h

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/**********************************************************************
  cistrans.h - Class for handling and storing cis/trans stereochemistry.

  Copyright (C) 2009-2010 by Tim Vandermeersch

  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; either version 2 of the License, or
  (at your option) any later version.

  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.

  You should have received a copy of the GNU General Public License
  along with this program; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
  02110-1301, USA.
 **********************************************************************/
#ifndef OB_CISTRANS_H
#define OB_CISTRANS_H

#include <openbabel/stereo/tetraplanar.h>
#include <vector>

namespace OpenBabel {


class OBAPI OBCisTransStereo : public OBTetraPlanarStereo
{
  public:
#ifndef SWIG
    struct OBAPI Config
    {
      Config() : begin(OBStereo::NoRef), end(OBStereo::NoRef), shape(OBStereo::ShapeU),
          specified(true)
      {  }
      Config(unsigned long _begin, unsigned long _end, const OBStereo::Refs &_refs,
          OBStereo::Shape _shape = OBStereo::ShapeU) : begin(_begin), end(_end),
          refs(_refs), shape(_shape), specified(true)
      {  }
      bool operator==(const Config &other) const;
      bool operator!=(const Config &other) const
      {
        return !(*this == other);
      }

      unsigned long begin, end; //<! The double bond begin and end ids.
      OBStereo::Refs refs; 
      OBStereo::Shape shape; 
      bool specified; 


    };
#endif

    OBCisTransStereo(OBMol *mol);
    virtual ~OBCisTransStereo();


    OBStereo::Type GetType() const { return OBStereo::CisTrans; }
    bool IsValid() const;

#ifndef SWIG
    void SetConfig(const Config &config);
    Config GetConfig(OBStereo::Shape shape = OBStereo::ShapeU) const;
    Config GetConfig(unsigned long start,
        OBStereo::Shape shape = OBStereo::ShapeU) const;
#endif

    bool operator==(const OBCisTransStereo &other) const;
    bool operator!=(const OBCisTransStereo &other) const
    {
      return !(*this == other);
    }

    /*
     * Implement OBGenericData::Clone().
     */
    OBGenericData* Clone(OBBase *mol) const;




    bool IsOnSameAtom(unsigned long id1, unsigned long id2) const;
    bool IsTrans(unsigned long id1, unsigned long id2) const;
    bool IsCis(unsigned long id1, unsigned long id2) const;
    unsigned long GetTransRef(unsigned long id) const;
    unsigned long GetCisRef(unsigned long id) const;

  private:
    Config m_cfg; 
    // The following function sits behind GetCisRef and GetTransRef
    unsigned long GetCisOrTransRef(unsigned long id, bool getcisref) const;
};

} // namespace OpenBabel

#ifndef SWIG
namespace std {


OBAPI ostream& operator<<(ostream &out, const OpenBabel::OBCisTransStereo &ct);
OBAPI ostream& operator<<(ostream &out, const OpenBabel::OBCisTransStereo::Config &cfg);


} // namespace std
#endif // Not SWIG

#endif