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

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/elements.h>

#include <openbabel/generic.h>

using namespace std;

namespace OpenBabel

{

  class CSSRFormat : public OBMoleculeFormat

  {

  public:

    //Register this format type ID

    CSSRFormat()

    {

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

    }

    const char* Description() override  // required

    {

      return

        "CSD CSSR 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 NOTREADABLE;

    }

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

    /// The "API" interface functions

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

  };

  //Make an instance of the format class

  CSSRFormat theCSSRFormat;

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

  bool CSSRFormat::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];

    if (!mol.HasData(OBGenericDataType::UnitCell))

      {

        snprintf(buffer, BUFF_SIZE,

                 " REFERENCE STRUCTURE = 00000   A,B,C =%8.3f%8.3f%8.3f",

                 1.0,1.0,1.0);

        ofs << buffer << endl;

        snprintf(buffer, BUFF_SIZE,

                 "   ALPHA,BETA,GAMMA =%8.3f%8.3f%8.3f    SPGR =    P1"

                 , 90.0f, 90.0f, 90.0f);

        ofs << buffer << endl;

      }

    else

      {

        OBUnitCell *uc = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);

        snprintf(buffer, BUFF_SIZE,

                 " REFERENCE STRUCTURE = 00000   A,B,C =%8.3f%8.3f%8.3f",

                 uc->GetA(), uc->GetB(), uc->GetC());

        ofs << buffer << endl;

        snprintf(buffer, BUFF_SIZE,

                 "   ALPHA,BETA,GAMMA =%8.3f%8.3f%8.3f    SPGR =    P1",

                 uc->GetAlpha() , uc->GetBeta(), uc->GetGamma());

        ofs << buffer << endl;

      }

    snprintf(buffer, BUFF_SIZE, "%4d   1 %s\n",mol.NumAtoms(), mol.GetTitle());

    ofs << buffer << endl << endl;

    OBAtom *atom,*nbr;

    vector<OBAtom*>::iterator i;

    vector<OBBond*>::iterator j;

    vector<int> vtmp(119,0);

    int bonds;

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

      {

        //assign_pdb_number(pdb_types,atom->GetIdx());

        unsigned int atomicNum = atom->GetAtomicNum();

        if (atomicNum >= vtmp.size())

          atomicNum = 0;

        vtmp[atomicNum]++;

        snprintf(buffer, BUFF_SIZE, "%4d%2s%-3d  %9.5f %9.5f %9.5f ",

                 atom->GetIdx(),

                 OBElements::GetSymbol(atomicNum),

                 vtmp[atomicNum],

                 atom->x(),

                 atom->y(),

                 atom->z());

        ofs << buffer;

        bonds = 0;

        for (nbr = atom->BeginNbrAtom(j); nbr; nbr = atom->NextNbrAtom(j))

          {

            if (bonds > 8) break;

            snprintf(buffer, BUFF_SIZE, "%4d",nbr->GetIdx());

            ofs << buffer;

            bonds++;

          }

        for (; bonds < 8; bonds ++)

          {

            snprintf(buffer, BUFF_SIZE, "%4d",0);

            ofs << buffer;

          }

        snprintf(buffer, BUFF_SIZE, " %7.3f%4d", atom->GetPartialCharge(), 1);

        ofs << buffer << endl;

      }

    return(true);

  }

} //namespace OpenBabel