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

Copyright (C) 2000 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/obiter.h>

#include <openbabel/elements.h>

#include <cstdlib>

using namespace std;

namespace OpenBabel

{

  class HINFormat : public OBMoleculeFormat

  {

  public:

    //Register this format type ID

    HINFormat()

    {

      OBConversion::RegisterFormat("hin",this, "chemical/x-hin");

    }

    const char* Description() override  // required

    {

      return "HyperChem HIN format\n"

             "No comments yet\n";

    }

    const char* SpecificationURL() override

    { return ""; }  // optional

    const char* GetMIMEType() override

    { return "chemical/x-hin"; }  // optional

    //*** 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

  HINFormat theHINFormat;

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

  bool HINFormat::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();

    // Right now only read in the first molecule

    int i;

    int max, bo;

    char buffer[BUFF_SIZE];

    string str,str1;

    double x,y,z;

    OBAtom *atom;

    vector<string> vs;

    ifs.getline(buffer, BUFF_SIZE);

    while (ifs.good() && (strstr(buffer, "mol") == nullptr || buffer[0] == ';')) //The "mol" in comment line should be ignored.

      {

        ifs.getline(buffer, BUFF_SIZE);

        if (ifs.peek() == EOF || !ifs.good())

          return false;

      }

    ifs.getline(buffer, BUFF_SIZE);

    if (!ifs.good())

      return false; // ended early

    mol.BeginModify();

    while (ifs.good() && strstr(buffer, "endmol") == nullptr)

      {

  if(buffer[0]==';'){

     ifs.getline(buffer, BUFF_SIZE);

     continue; //The comment Line in HIN should be ignored.

  }

        tokenize(vs,buffer); // Don't really know how long it'll be

        if (vs.size() < 11)

          {

            ifs.getline(buffer, BUFF_SIZE);

            continue;

          }

        atom = mol.NewAtom();

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

        atom->SetPartialCharge(atof(vs[6].c_str()));

        x = atof((char*)vs[7].c_str());

        y = atof((char*)vs[8].c_str());

        z = atof((char*)vs[9].c_str());

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

        // Bond count comes straight from the file; clamp it to what the

        // line actually holds so a huge or negative value can't overflow

        // "max" or send the loop below reading past the end of vs[].

        int numbonds = atoi((char *)vs[10].c_str());

        if (numbonds < 0)

          numbonds = 0;

        if (numbonds > ((int)vs.size() - 11) / 2)

          numbonds = ((int)vs.size() - 11) / 2;

        max = 11 + 2 * numbonds;

        for (i = 11; i < max; i+=2)

          {

            switch(((char*)vs[i+1].c_str())[0]) // First char in next token

              {

              case 's':

                bo = 1;

                break;

              case 'd':

                bo = 2;

                break;

              case 't':

                bo = 3;

                break;

              case 'a':

                bo = 5;

                break;

              default :

                bo = 1;

                break;

              }

            mol.AddBond(mol.NumAtoms(), atoi((char *)vs[i].c_str()), bo);

          }

        ifs.getline(buffer, BUFF_SIZE);

      }

    // clean out remaining blank lines

    // blank lines cleaning codes rewritten for avoiding peek() and tellg() bugs

    // https://github.com/openbabel/openbabel/issues/1569

    std::streampos ipos;

    do

    {

      ipos = ifs.tellg();

      ifs.getline(buffer,BUFF_SIZE);

    }

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

    ifs.seekg(ipos);

    mol.EndModify();

    mol.SetTitle(title);

    mol.SetPartialChargesPerceived();

    return(true);

  }

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

  bool HINFormat::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;

    unsigned int i, file_num = 1;

    string str,str1;

    char buffer[BUFF_SIZE];

    OBAtom *atom;

    OBBond *bond;

    vector<OBBond*>::iterator j;

    char bond_char;

    // make sure to escape titles in double quotes

    // PR#1501694

    ofs << "mol " << file_num << " \"" << mol.GetTitle() << "\"\n";

    for(i = 1;i <= mol.NumAtoms(); i++)

      {

        atom = mol.GetAtom(i);

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

                i,

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

                atom->GetPartialCharge(),

                atom->GetX(),

                atom->GetY(),

                atom->GetZ(),

                atom->GetExplicitDegree());

        ofs << buffer;

        for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))

          {

            switch(bond->GetBondOrder())

              {

              case 1 :

                bond_char = 's';

                break;

              case 2 :

                bond_char = 'd';

                break;

              case 3 :

                bond_char = 't';

                break;

              case 5 :

                bond_char = 'a';

                break;

              default:

                bond_char = 's';

                break;

              }

            if (bond->IsAromatic())

              bond_char = 'a';

            snprintf(buffer,BUFF_SIZE, "%d %c ", (bond->GetNbrAtom(atom))->GetIdx(), bond_char);

            ofs << buffer;

          }

        ofs << endl;

      }

    ofs << "endmol " << file_num << endl;

    return(true);

  }

} //namespace OpenBabel