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

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/obutil.h>

using namespace std;

namespace OpenBabel

{

  class FEATFormat : public OBMoleculeFormat

  {

  public:

    //Register this format type ID

    FEATFormat()

    {

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

    }

    const char* Description() override  // required

    {

      return

        "Feature format\n"

        "Read Options e.g. -as\n"

        " s  Output single bonds only\n"

        " b  Disable bonding entirely\n\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

  FEATFormat theFEATFormat;

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

  bool FEATFormat::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;

    mol.SetTitle( pConv->GetTitle()); //default title is the filename

    char buffer[BUFF_SIZE];

    int i,natoms;

    ifs.getline(buffer,BUFF_SIZE);

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

    mol.ReserveAtoms(natoms);

    mol.BeginModify();

    if (!ifs.getline(buffer,BUFF_SIZE))

      return(false);

    mol.SetTitle(buffer);

    double x,y,z;

    char type[32];

    OBAtom *atom;

    for (i = 0; i < natoms;i++)

      {

        if (!ifs.getline(buffer,BUFF_SIZE))

          return(false);

        sscanf(buffer,"%30s %lf %lf %lf",

               type,

               &x,

               &y,

               &z);

        CleanAtomType(type);

        atom = mol.NewAtom();

        atom->SetVector(x,y,z);

        atom->SetAtomicNum(OBElements::GetAtomicNum(type));

      }

    // 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);

    if (!pConv->IsOption("b",OBConversion::INOPTIONS))

      mol.ConnectTheDots();

    if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS))

      mol.PerceiveBondOrders();

    mol.EndModify();

    return(true);

  }

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

  bool FEATFormat::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.NumAtoms() << endl;

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

    OBAtom *atom;

    vector<OBAtom*>::iterator i;

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

      {

        snprintf(buffer, BUFF_SIZE, "%-3s %8.5f  %8.5f  %8.5f ",

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

                 atom->x(),

                 atom->y(),

                 atom->z());

        ofs << buffer << endl;

      }

    return(true);

  }

} //namespace OpenBabel