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

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.

Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison

Some portions Copyright (C) 2004 by Chris Morley

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 <openbabel/obmolecformat.h>

#include <openbabel/mol.h>

#include <openbabel/atom.h>

#include <openbabel/bond.h>

#include <openbabel/elements.h>

#include <cstdlib>

using namespace std;

namespace OpenBabel

{

  class ChemDrawFormat : public OBMoleculeFormat

  {

  public:

    //Register this format type ID

    ChemDrawFormat()

    {

      OBConversion::RegisterFormat("ct",this);

    }

    const char* Description() override  // required

    {

      return

        "ChemDraw Connection Table format\n"

        "No comments yet\n";

    }

    const char* SpecificationURL() override

    { return ""; }  // optional

    //Flags() can return be any the following combined by | or be omitted if none apply

    // NOTREADABLE  READONEONLY  NOTWRITABLE  WRITEONEONLY

    unsigned int Flags() override

    {

      return READONEONLY | WRITEONEONLY;

    }

    //*** This section identical for most OBMol conversions ***

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

    /// The "API" interface functions

    bool ReadMolecule(OBBase* pOb, OBConversion* pConv) override;

    bool WriteMolecule(OBBase* pOb, OBConversion* pConv) override;

  };

  //***

  //Make an instance of the format class

  ChemDrawFormat theChemDrawFormat;

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

  bool ChemDrawFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)

  {

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

    if (pmol == nullptr)

      return false;

    //Define some references so we can use the old parameter names

    ostream &ofs = *pConv->GetOutStream();

    OBMol &mol = *pmol;

    char buffer[BUFF_SIZE];

    ofs << mol.GetTitle() << endl;

    ofs << " " << mol.NumAtoms() << " " << mol.NumBonds() << endl;

    OBAtom *atom;

    vector<OBAtom*>::iterator i;

    for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))

      {

        snprintf(buffer, BUFF_SIZE, " %9.4f %9.4f    0.0000 %-1s",

                 atom->x(),

                 atom->y(),

                 OBElements::GetSymbol(atom->GetAtomicNum()));

        ofs << buffer << endl;

      }

    OBBond *bond;

    vector<OBBond*>::iterator j;

    for(bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))

      {

        snprintf(buffer, BUFF_SIZE, "%3d%3d%3d%3d",

                 bond->GetBeginAtomIdx(),

                 bond->GetEndAtomIdx(),

                 bond->GetBondOrder(), bond->GetBondOrder());

        ofs << buffer << endl;

      }

    return(true);

  }

  bool ChemDrawFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)

  {

    OBMol* pmol = pOb->CastAndClear<OBMol>();

    if (pmol == nullptr)

      return false;

    //Define some references so we can use the old parameter names

    istream &ifs = *pConv->GetInStream();

    OBMol &mol = *pmol;

    const char* title = pConv->GetTitle();

    char buffer[BUFF_SIZE];

    unsigned int natoms, nbonds;

    unsigned int bgn, end, order;

    vector<string> vs;

    OBAtom *atom;

    double x, y, z;

    mol.SetDimension(2);

    mol.BeginModify();

    ifs.getline(buffer,BUFF_SIZE);

    if (strlen(buffer) == 0)

      mol.SetTitle(buffer);

    else

      mol.SetTitle(title);

    ifs.getline(buffer,BUFF_SIZE);

    sscanf(buffer," %d %d", &natoms, &nbonds);

    for (unsigned int i = 1; i <= natoms; i ++)

      {

        if (!ifs.getline(buffer,BUFF_SIZE)) return(false);

        tokenize(vs,buffer);

        if (vs.size() != 4) return(false);

        atom = mol.NewAtom();

        x = atof((char*)vs[0].c_str());

        y = atof((char*)vs[1].c_str());

        z = atof((char*)vs[2].c_str());

        atom->SetVector(x,y,z); //set coordinates

        atom->SetAtomicNum(OBElements::GetAtomicNum(vs[3].c_str()));

      }

    if (nbonds != 0)

      for (unsigned int i = 0; i < nbonds; i++)

        {

          if (!ifs.getline(buffer,BUFF_SIZE)) return(false);

          tokenize(vs,buffer);

          if (vs.size() != 4) return(false);

          if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false);

          mol.AddBond(bgn,end,order);

        }

    // clean out remaining blank lines

    std::streampos ipos;

    do

    {

      ipos = ifs.tellg();

      ifs.getline(buffer,BUFF_SIZE);

    }

    while(strlen(buffer) == 0 && !ifs.eof() );

    ifs.seekg(ipos);

    mol.EndModify();

    return(true);

  }

} //namespace OpenBabel