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

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

Some portions Copyright (C) 2013 by Schrodinger Inc.

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 <openbabel/generic.h>

#include <cstdlib>

using namespace std;

namespace OpenBabel

{

  class CARFormat : public OBMoleculeFormat

  {

  public:

    //Register this format type ID

    CARFormat()

    {

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

      OBConversion::RegisterFormat("arc",this, "chemical/x-msi-car");

    }

    const char* Description() override  // required

    {

      return

        "Accelrys/MSI Biosym/Insight II CAR 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://www.centrcn.umontreal.ca/accelrys/life/insight2000.1/formats980/Files980TOC.doc.html"; // XXX dead

    }

    const char* GetMIMEType() override

    { return "chemical/x-msi-car"; }

    unsigned int Flags() override

    {

      return NOTWRITABLE;

    }

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

    /// The "API" interface functions

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

  };

  //Make an instance of the format class

  CARFormat theCARFormat;

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

  bool CARFormat::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();

    bool hasPartialCharges = false;

    char buffer[BUFF_SIZE];

    string str;

    double x,y,z;

    OBAtom *atom;

    vector<string> vs;

    mol.BeginModify();

    while (ifs.getline(buffer,BUFF_SIZE))

      {

        if(strstr(buffer, "end") != nullptr)

          {

            if (mol.NumAtoms() > 0) // we've already read in a molecule, so exit

              break;

            // else, we hit the end of the previous molecular system

            // (in a multimolecule file)

            ifs.getline(buffer,BUFF_SIZE); // title

            ifs.getline(buffer,BUFF_SIZE); // DATE

          }

        if (strncmp(buffer, "!BIOSYM", 7) == 0)

          {

            continue;

          }

        if (strstr(buffer, "PBC") != nullptr)

          {

            if (strstr(buffer, "ON") != nullptr)

              {

                ifs.getline(buffer,BUFF_SIZE); // title

                ifs.getline(buffer,BUFF_SIZE); // DATE

                ifs.getline(buffer,BUFF_SIZE); // PBC a b c alpha beta gamma SG

                string str = buffer;

                // parse cell parameters

                tokenize(vs,str," \t\r\n", 7);

                if (vs.size() >= 7)

                  {

                    //parse cell values

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

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

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

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

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

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

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

                    OBUnitCell *uc = new OBUnitCell;

                    uc->SetOrigin(fileformatInput);

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

                    if(vs.size() > 7) 

                      {

                        string& space_group = vs[7];

                        // Remove parentheses enclosing the space

                        // group and remove white space from front

                        // and back of string.

                        Trim(space_group);

                        if(space_group[0] == '(')

                          {

                            space_group.erase(0, 1);

                            space_group.erase(space_group.size()-1); 

                          }

                        Trim(space_group);

                        uc->SetSpaceGroup(space_group);

                      }

                    mol.SetData(uc);

                  }

              }

            else // PBC=OFF

              {

                ifs.getline(buffer,BUFF_SIZE); // title

                ifs.getline(buffer,BUFF_SIZE); // !DATE

              }

            continue;

          } // PBC

        // reading real data!

        tokenize(vs,buffer);

        if (vs.size() < 8) {

          break;

        }

        atom = mol.NewAtom();

        atom->SetAtomicNum(OBElements::GetAtomicNum(vs[7].c_str()));

        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);

        // vs[0] contains atom label

        // vs[4] contains "type of residue containing atom"

        // vs[5] contains "residue sequence name"

        // vs[6] contains "potential type of atom"

        if (vs.size() == 9)

          {

            atom->SetPartialCharge(atof((char*)vs[8].c_str()));

            hasPartialCharges = true;

          }

      }

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

      mol.ConnectTheDots();

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

      mol.PerceiveBondOrders();

    mol.EndModify();

    if (hasPartialCharges)

      mol.SetPartialChargesPerceived();

    mol.SetTitle(title);

    return(true);

  }

} //namespace OpenBabel