/**********************************************************************
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/elements.h>
#include <cstdlib>


using namespace std;
namespace OpenBabel
{

class CCCFormat : public OBMoleculeFormat
{
public:
    //Register this format type ID
    CCCFormat()
    {
        OBConversion::RegisterFormat("ccc",this);
    }

    virtual const char* Description() //required
    {
        return
          "CCC format\n"
          "No comments yet\n";
    };

  virtual const char* SpecificationURL()
  {return "";}; //optional

    //Flags() can return be any the following combined by | or be omitted if none apply
    // NOTREADABLE  READONEONLY  NOTWRITABLE  WRITEONEONLY
    virtual unsigned int Flags()
    {
        return NOTWRITABLE;
    };

    ////////////////////////////////////////////////////
    /// The "API" interface functions
    virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv);

 };

//Make an instance of the format class
CCCFormat theCCCFormat;

/////////////////////////////////////////////////////////////////
bool CCCFormat::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];
    ifs.getline(buffer,BUFF_SIZE);

    if (strlen(buffer) > 5)
        mol.SetTitle(&buffer[5]);
    mol.SetEnergy(0.0);

    int natoms;
    ifs.getline(buffer,BUFF_SIZE);
    sscanf(buffer,"%*s%d",&natoms);
    mol.ReserveAtoms(natoms);
    mol.BeginModify();

    int end,order;
    double x,y,z;
    OBAtom atom;
    vector3 v;
    vector<string> vs;
    char element[3];
    element[2] = '\0';

    for (int i = 1;i <= natoms;i++)
    {
        if (!ifs.getline(buffer,BUFF_SIZE))
            return(false);
        atom.Clear();
        element[0] = buffer[0];
        element[1] = (buffer[1] != ' ') ? buffer[1]:'\0';
        atom.SetAtomicNum(OBElements::GetAtomicNum(element));
        sscanf(&buffer[15],"%lf%lf%lf",&x,&y,&z);
        v.Set(x,y,z);
        atom.SetVector(v);

        if (!mol.AddAtom(atom))
            return(false);
        tokenize(vs,&buffer[60]);
        vector<string>::iterator j;

        for (j = vs.begin();j != vs.end();++j)
            if (!j->empty())
            {
                //get the bond order
                switch((char)(*j)[j->size()-1])
                {
                case 'S':
                    order = 1;
                    break;
                case 'D':
                    order = 2;
                    break;
                case 'T':
                    order = 3;
                    break;
                default:
                    order = 1;
                }
                (*j)[j->size()-1] = ' ';
                end = atoi(j->c_str());
                if (i>end)
                    mol.AddBond(i,end,order);
            }
    }

    mol.EndModify();
    return(true);
}

} //namespace OpenBabel
