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

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.

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

/* contributed by Walter Scott (wscott@igc.phys.chem.ethz.ch)

   (Actually the routine was copied from write_xyz and and write_pdb and

   then modified...)

   This is a small routine to write a GROMOS96 formatted

   "position coordinate block" (POSITION) or a

   "reduced position coordinate block" (POSITIONRED)

   The former has name information (atom and residue names) while

   the latter only has coordinates.

   This version does not support the writing of binary

   GROMOS files.

   NOTE 1: the actual formats used in writing out the coordinates

   do not matter, as GROMOS96 uses free formatted reads.

   Each line may not be longer than 80 characters.

   (Note, however, in the POSITION block, the first 24 (twenty four)

   character on each line are ignored when the line is read in by GROMOS)

   Comments lines, beginning with hash (#) may occur within a block and are

   used as delimiters for easier reading.

   NOTE 2: Many programs specify the units of the coordinates (e.g. Angstrom).

   GROMOS96 does NOT, as all physical constants, from K_B to EPS are

   NOT hardwired into the code, but specified by the user.

   This allows some (mostly Americans) to use GROMOS96 in KCal and

   Angstrom and the rest of us to use kJoule and nm.

   It also makes it easy to use reduced units.

   We get around this by supplying a routine, wr_sco_gr96, which

   will scale the coordinates by a factor before writing.

   This routine is then called with the factor set to 1.0 in

   write_gr96A, or to 0.1 in write_gr96N depending on the users choice.

   Thus, we always assume that we have read coordinates in Angstrom.

   *** But now handled by a command line option in new framework.

*/

#include <openbabel/babelconfig.h>

#include <openbabel/obmolecformat.h>

#include <openbabel/mol.h>

#include <openbabel/atom.h>

#include <openbabel/elements.h>

using namespace std;

namespace OpenBabel

{

  class GROMOS96Format : public OBMoleculeFormat

  {

  public:

    //Register this format type ID

    GROMOS96Format()

    {

      OBConversion::RegisterFormat("gr96",this);

    }

    const char* Description() override  // required

    {

      return

        "GROMOS96 format\n"

        "Write Options e.g. -xn\n"

        " n output nm (not Angstroms)\n";

    }

    const char* SpecificationURL() override

    {

      return "http://manual.gromacs.org/documentation/current/reference-manual/file-formats.html#g96";

    }

    //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 | WRITEONEONLY;

    }

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

    /// The "API" interface functions

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

  };

  //Make an instance of the format class

  GROMOS96Format theGROMOS96Format;

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

  bool GROMOS96Format::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;

    double fac = pConv->IsOption("n") ? 0.1 : 1.0; //new framework

    char type_name[16];

    char res_name[16];

    char buffer[BUFF_SIZE];

    string res_num;

    snprintf(buffer, BUFF_SIZE, "#GENERATED BY OPEN BABEL %s\n",BABEL_VERSION);

    ofs << buffer;

    /* GROMOS wants a TITLE block, so let's write one*/

    ofs << "TITLE\n" << mol.GetTitle() << "\nEND\n";

    ofs << "POSITION\n";

    OBAtom *atom;

    OBResidue *res;

    vector<OBAtom*>::iterator i;

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

      {

        if ( (res = atom->GetResidue()) )

          {

            // 16 = sizeof(res_name) and sizeof(type_name)

            strncpy(res_name,(char*)res->GetName().c_str(), 16);

            res_name[15] = '\0';

            strncpy(type_name,(char*)res->GetAtomID(atom).c_str(), 16);

            type_name[15] = '\0';

            res_num = res->GetNumString();

          }

        else

          {

            strncpy(type_name,OBElements::GetSymbol(atom->GetAtomicNum()), 16);

            strcpy(res_name,"UNK");

            res_num = "1";

          }

        snprintf(buffer, BUFF_SIZE, "%5s %5s %5s %6d %15.5f %15.5f %15.5f\n",

                res_num.c_str(),res_name,type_name,atom->GetIdx(),

                atom->x()*fac,atom->y()*fac,atom->z()*fac);

        ofs << buffer;

        if (!(atom->GetIdx()%10))

          {

            snprintf(buffer, BUFF_SIZE, "# %d\n",atom->GetIdx());

            ofs << buffer;

          }

      }

    ofs << "END\n";

    return(true);

  }

} //namespace OpenBabel