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