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

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/elements.h>

#include <cstdlib>

using namespace std;

namespace OpenBabel

{

class UniChemFormat : public OBMoleculeFormat

{

public:

    //Register this format type ID

    UniChemFormat()

    {

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

    }

  const char* Description() override  // required

  {

    return

      "UniChem XYZ 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

UniChemFormat theUniChemFormat;

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

bool UniChemFormat::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;

    char buffer[BUFF_SIZE];

    ifs.getline(buffer,BUFF_SIZE);

    ifs.getline(buffer,BUFF_SIZE);

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

    if (!natoms)

        return(false);

    mol.ReserveAtoms(natoms);

    mol.BeginModify();

    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() != 4)

            return(false);

        atom = mol.NewAtom();

        x = atof((char*)vs[1].c_str());

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

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

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

        //set atomic number

        atom->SetAtomicNum(atoi((char*)vs[0].c_str()));

    }

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

      mol.ConnectTheDots();

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

      mol.PerceiveBondOrders();

    // 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 UniChemFormat::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];

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

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

    OBAtom *atom;

    string str,str1;

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

    {

        atom = mol.GetAtom(i);

        snprintf(buffer, BUFF_SIZE,

    "%3d%15.5f%15.5f%15.5f",

                atom->GetAtomicNum(),

                atom->GetX(),

                atom->GetY(),

                atom->GetZ());

        ofs << buffer << endl;

    }

    return(true);

}

} //namespace OpenBabel