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

Copyright (C) 1998-2003 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/math/matrix3x3.h>

#include <openbabel/obmolecformat.h>

#include <openbabel/mol.h>

#include <openbabel/atom.h>

#include <openbabel/elements.h>

#include <openbabel/generic.h>

#include <cstdlib>

using namespace std;

namespace OpenBabel

{

  class ShelXFormat : public OBMoleculeFormat

  {

  public:

    //Register this format type ID

    ShelXFormat()

    {

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

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

    }

    const char* Description() override  // required

    {

      return

        "ShelX 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 "http://shelx.uni-ac.gwdg.de/SHELX/"; }  // optional

    const char* GetMIMEType() override

    { return "chemical/x-shelx"; }

    //Flags() can return be any the following combined by | or be omitted if none apply

    // NOTREADABLE  READONEONLY  NOTWRITABLE  WRITEONEONLY

    unsigned int Flags() override

    {

      return NOTWRITABLE;

    }

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

    /// The "API" interface functions

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

  };

  //Make an instance of the format class

  ShelXFormat theShelXFormat;

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

  bool ShelXFormat::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 natoms; CM

    double A,B,C,Alpha,Beta,Gamma;

    matrix3x3 m;

    ifs.getline(buffer,BUFF_SIZE);

    mol.SetTitle(buffer);

    while (ifs.getline(buffer,BUFF_SIZE) &&!EQn(buffer,"CELL",4))

      ;

    if (!EQn(buffer,"CELL",4))

      return(false);

    vector<string> vs;

    tokenize(vs,buffer," \n\t,");

    if (vs.size() != 8)

      return(false);

    //parse cell values

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

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

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

    Alpha = atof((char*)vs[5].c_str());

    Beta  = atof((char*)vs[6].c_str());

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

    OBUnitCell *uc = new OBUnitCell;

    uc->SetOrigin(fileformatInput);

    uc->SetData(A, B, C, Alpha, Beta, Gamma);

    mol.SetData(uc);

    //  int i; CM

    double x,y,z;

    char type[16], *j;

    OBAtom *atom;

    vector3 v;

    //skip until FVAR found

    while (ifs.getline(buffer,BUFF_SIZE) &&!EQn(buffer,"FVAR",4))

      ;

    mol.BeginModify();

    //read atom records

    while (ifs.getline(buffer,BUFF_SIZE) &&!EQn(buffer,"HKLF",4))

      {

        tokenize(vs,buffer," \n\t,");

        //skip AFIX and PART instructions

        if (vs.size() < 7)

          continue;

        atom = mol.NewAtom();

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

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

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

        v.Set(x,y,z);

        v = uc->FractionalToCartesian(v);

        strncpy(type,vs[0].c_str(), sizeof(type));

        type[sizeof(type) - 1] = '\0';

        j = strpbrk(type, "0123456789");

        j[0] = '\0';

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

        atom->SetVector(v);

        //skip next line if anisotropic atoms.

        if (vs.size() == 9)

          ifs.getline(buffer,BUFF_SIZE);

      } //while

    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);

  }

} //namespace OpenBabel