/**********************************************************************

gen2d.cpp - A OBOp for generation of 2D coordinates

Copyright (C) 2007,2008 by Sergei V. Trepalin sergey_trepalin@chemical-block.com

Copyright (C) 2007,2008 by Andrei Gakh andrei.gakh@nnsa.doe.gov

          (C) 2007 by 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.

***********************************************************************/

#include <openbabel/babelconfig.h>

#include <iostream>

#include<openbabel/op.h>

#include<openbabel/mol.h>

#include <openbabel/mcdlutil.h>

#include <openbabel/stereo/stereo.h>

namespace OpenBabel

{

class OpGen2D : public OBOp

{

public:

  OpGen2D(const char* ID) : OBOp(ID, false){};

  const char* Description() override { return

    "Generate 2D coordinates\n"

    "Trepalin, S. V.; Yarkov, A. V.; Pletnev, I. V.; Gakh, A.A."

    "A Java Chemical Structure Editor Supporting the"

    "Modular Chemical Descriptor Language (MCDL)."

    "Molecules, 2006, 11, 219-231"; }

  bool WorksWith(OBBase* pOb) const override { return dynamic_cast<OBMol*>(pOb) != nullptr; }

  bool Do(OBBase* pOb, const char* OptionText=nullptr, OpMap* pOptions=nullptr,

      OBConversion* pConv=nullptr) override;

};

/////////////////////////////////////////////////////////////////

OpGen2D theOpGen2D("gen2D"); //Global instance

/////////////////////////////////////////////////////////////////

bool OpGen2D::Do(OBBase* pOb, const char* OptionText, OpMap* pOptions, OBConversion* pConv)

{

  OBMol* pmol = dynamic_cast<OBMol*>(pOb);

  if(!pmol)

    return false;

  // If we are coming from a 0D structure, then we need to perceive the cis/trans

  // bonds *now*, before adding the coordinates, to mark unspecified cis/trans

  // as such. Otherwise, when writing a MOL file it will be missing the '3', or

  // similarly when depicting it would be presented as specified.

  // Really, all we need to do is handle the cis/trans bond cases.

  // However, the current API requires us to also reperceive the tet stereo,

  // and to remove any stereo that is not real.

  if (pmol->GetDimension() == 0) {

    pmol->UnsetFlag(OB_CHIRALITY_MOL);

    StereoFrom0D(pmol);

  }

  generateDiagram(pmol);

  pmol->SetDimension(2);

  return true;

}

}//namespace