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

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 <openbabel/data.h>

#include <cstdlib>

using namespace std;

namespace OpenBabel

{

  class AlchemyFormat : public OBMoleculeFormat

  {

  public:

    //Register this format type ID

    AlchemyFormat()

    {

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

    }

    const char* Description() override  // required

    {

      return

        "Alchemy format\n"

        "No comments yet\n";

    }

    const char* SpecificationURL() override

    { return ""; }  // optional

    const char* GetMIMEType() override

    { return "chemical/x-alchemy"; }

    //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

  AlchemyFormat theAlchemyFormat;

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

  bool AlchemyFormat::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();

    int i;

    int natoms = 0, nbonds = 0;

    char buffer[BUFF_SIZE];

    ifs.getline(buffer,BUFF_SIZE);

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

    if (!natoms)

      {

        ifs.getline(buffer,BUFF_SIZE);

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

        if (!natoms)

          return(false);

      }

    mol.ReserveAtoms(natoms);

    mol.BeginModify();

    ttab.SetFromType("ALC");

    string str;

    double x,y,z;

    OBAtom *atom;

    vector<string> vs;

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

      {

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

          return(false);

        tokenize(vs,buffer);

        if (vs.size() < 5)

          return(false);

        atom = mol.NewAtom();

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

        y = atof((char*)vs[3].c_str());

        z = atof((char*)vs[4].c_str());

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

        //set atomic number

        ttab.SetToType("ATN");

        ttab.Translate(str,vs[1]);

        atom->SetAtomicNum(atoi(str.c_str()));

        //set type

        ttab.SetToType("INT");

        ttab.Translate(str,vs[1]);

        atom->SetType(str);

      }

    char bobuf[100];

    string bostr;

    int bgn,end,order;

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

      {

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

          return(false);

        sscanf(buffer," %*d%d%d%99s",&bgn,&end,bobuf);

        bostr = bobuf;

        order = 1;

        if      (bostr == "DOUBLE")

          order = 2;

        else if (bostr == "TRIPLE")

          order = 3;

        else if (bostr == "AROMATIC")

          order = 5;

        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();

    mol.SetTitle(title);

    return(true);

  }

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

  bool AlchemyFormat::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;

    char buffer[BUFF_SIZE];

    char bond_string[10];

    snprintf(buffer, BUFF_SIZE, "%5d ATOMS, %5d BONDS,     0 CHARGES",

             mol.NumAtoms(),

             mol.NumBonds());

    ofs << buffer << endl;

    OBAtom *atom;

    string str,str1;

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

      {

        atom = mol.GetAtom(i);

        str = atom->GetType();

        ttab.SetFromType("INT");

        ttab.SetToType("ALC");

        ttab.Translate(str1,str);

        snprintf(buffer, BUFF_SIZE, "%5d %-6s%8.4f %8.4f %8.4f     0.0000",

                 i,

                 (char*)str1.c_str(),

                 atom->GetX(),

                 atom->GetY(),

                 atom->GetZ());

        ofs << buffer << endl;

      }

    OBBond *bond;

    vector<OBBond*>::iterator j;

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

      {

        switch(bond->GetBondOrder())

          {

          case 1 :

            strcpy(bond_string,"SINGLE");

            break;

          case 2 :

            strcpy(bond_string,"DOUBLE");

            break;

          case 3 :

            strcpy(bond_string,"TRIPLE");

            break;

          case 5 :

            strcpy(bond_string,"AROMATIC");

            break;

          default :

            strcpy(bond_string,"SINGLE");

          }

        snprintf(buffer, BUFF_SIZE, "%5d  %4d  %4d  %s",

                 bond->GetIdx()+1,

                 bond->GetBeginAtomIdx(),

                 bond->GetEndAtomIdx(),

                 bond_string);

        ofs << buffer << endl;

      }

    return(true);

  }

} //namespace OpenBabel