/**********************************************************************
Copyright (C) 2006 by Geoff Hutchison
Portions Copyright (C) 2010 by Joerg Kurt Wegner
Portions Copyright (C) 2012 by NextMove Software

This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>

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/xml.h>
#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/bond.h>
#include <openbabel/obiter.h>
#include <openbabel/elements.h>
#include <openbabel/obfunctions.h>
#include <algorithm>
#include <vector>

#ifdef WIN32
#pragma warning (disable : 4800)
#endif

using namespace std;
namespace OpenBabel
{

struct Boundary
{
  double xMin;
  double xMax;
  double yMin;
  double yMax;
};

struct Coord2D
{
  double x;
  double y;
};

class ChemDrawXMLFormat : public XMLMoleculeFormat
{
public:
	ChemDrawXMLFormat(): Order (-1)
	{
		OBConversion::RegisterFormat("cdxml", this, "chemical/x-cdxml");
		XMLConversion::RegisterXMLFormat(this, false, "http://www.camsoft.com/xml/cdxml.dtd");
		XMLConversion::RegisterXMLFormat(this);
	}
	const char* NamespaceURI() const override { return "http://www.cambridgesoft.com/xml/cdxml.dtd"; }
  const char* Description() override
  {
    return
      "ChemDraw CDXML format\n"
      "Minimal support of chemical structure information only.\n\n";
  }

  const char* GetMIMEType() override
  { return "chemical/x-cdxml"; };

  const char* SpecificationURL() override
  {return "http://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/";}


  unsigned int Flags() override
  {
      return READXML;
  };

    bool WriteMolecule(OBBase* pOb, OBConversion* pConv) override;
    bool DoElement(const string& name) override;
    bool EndElement(const string& name) override;

	// EndTag is used so that the stream buffer is is filled with the XML from
	// complete objects, as far as possible.
	const char* EndTag() override { return "/fragment>"; }

    //atoms and bonds might have no content, so EndElement is not always called
    // that's why we need to ensure that atoms and bonds are really added.
    void EnsureEndElement(void);

private:
  Boundary CalculateMoleculeBoundary(OBMol* pMol);
  void CalculateCdxmlShift(OBMol* pMol);
  Coord2D TransformCdxmlCoord(OBAtom* pAtom);

private:
  OBAtom _tempAtom; //!< A temporary atom as the atom tag is read
  int Begin, End, Order, Flag; // Data for current bond
  map <int, int> atoms; // maps chemdraw atom id to openbabel idx.
  int _offset; // used to ensure that atoms have different ids.
  double _scale; // current scale
  double xCdxmlShift, yCdxmlShift;
  std::vector<unsigned int> _handleImplicitHydrogens; //list of atoms w/o hydrogen count
};

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

ChemDrawXMLFormat theChemDrawXMLFormat;

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

bool ChemDrawXMLFormat::DoElement(const string& name)
{
  string buf;
  if(name=="fragment")
  {
    //This is the start of the molecule we are extracting and it will
    //be put into the OBMol* _pmol declared in the parent class.
    //initialise everything
    _tempAtom.Clear();
    atoms.clear();
    _handleImplicitHydrogens.clear();

    _pmol->SetDimension(2);
    _pmol->BeginModify();

    buf = _pxmlConv->GetAttribute("id");
    if (buf.length())
    {
      _pmol->SetTitle(buf);
    }
  }
  else if(name=="n")
  {
    EnsureEndElement();
    buf = _pxmlConv->GetAttribute("Type");
    if (buf.length())
    {
      if (buf != "Unspecified" && buf != "Element")
      {
        cerr << "CDXML Format: Node type \"" << buf <<
                  "\" is not currently supported." << endl;
        return false; // FIXME: use as many types as possible
	  }
    }
    _tempAtom.SetAtomicNum(6); // default is carbon
    buf = _pxmlConv->GetAttribute("id");
    if (buf.length())
      _tempAtom.SetIdx(atoi(buf.c_str()));
    buf = _pxmlConv->GetAttribute("Element");
    if (buf.length())
      _tempAtom.SetAtomicNum(atoi(buf.c_str()));

    buf = _pxmlConv->GetAttribute("p"); // coords
    if (buf.length())
    {
      double x = 0., y = 0.;
      sscanf(buf.c_str(), "%lf %lf", &x, &y);
      _tempAtom.SetVector(x, y, 0.);
    }
    buf = _pxmlConv->GetAttribute("Charge");
    if (buf.length())
      _tempAtom.SetFormalCharge(atoi(buf.c_str()));
    buf = _pxmlConv->GetAttribute("Isotope");
    if (buf.length())
      _tempAtom.SetIsotope(atoi(buf.c_str()));
    buf = _pxmlConv->GetAttribute("NumHydrogens");
    if (buf.length())
    {
      _tempAtom.SetImplicitHCount(atoi(buf.c_str()));
    }
    else
      _handleImplicitHydrogens.push_back(_tempAtom.GetIdx());
  }
  else if(name=="b")
  {
    EnsureEndElement();
	  bool invert_ends = false;
	  Begin = End = Flag = 0;
    buf = _pxmlConv->GetAttribute("Order");
    if (buf.length())
      Order = atoi(buf.c_str());
    else
      Order = 1; //default value
    buf = _pxmlConv->GetAttribute("Display");
    if (buf.length())
    {
      if (buf == "WedgeEnd")
      {
        invert_ends = true;
        Flag = OB_HASH_BOND;
      }
      else if (buf == "WedgeBegin")
      {
        Flag = OB_HASH_BOND;
      }
      else if (buf == "Hash" ||buf == "WedgedHashBegin")
      {
        Flag = OB_WEDGE_BOND;
      }
      else if (buf == "WedgedHashEnd")
      {
        invert_ends = true;
        Flag = OB_WEDGE_BOND;
      }
    }
    buf = _pxmlConv->GetAttribute("B");
    if (buf.length())
    {
      if (invert_ends)
        End = atoms[atoi(buf.c_str())];
      else
        Begin = atoms[atoi(buf.c_str())];
    }
    buf = _pxmlConv->GetAttribute("E");
    if (buf.length())
    {
      if (invert_ends)
        Begin = atoms[atoi(buf.c_str())];
      else
        End = atoms[atoi(buf.c_str())];
    }
  }
  /*
  // Forget that, the fragment, aka molecule, is in another XML hierachy tree than the data.
  // Parsing has already stopped before ever getting to this point
  else if(name=="tags")
  {
  	buf = _pxmlConv->GetAttribute("ID");
    if (buf.length())
    {
    }
  }
  else if(name=="tableCell")
  {
  	buf = _pxmlConv->GetAttribute("value");
    if (buf.length())
    {
    }
  }
  */
  return true;
}

bool ChemDrawXMLFormat::EndElement(const string& name)
{
  //unsigned int i;
  if(name=="n")
  {
    _pmol->AddAtom(_tempAtom);
    atoms[_tempAtom.GetIdx()] = _pmol->NumAtoms();
    _tempAtom.Clear();
  }
  else if(name=="b")
  {
    _pmol->AddBond(Begin, End, Order, Flag);
	Order = -1;
  }
  else if(name=="fragment") //this is the end of the molecule we are extracting
  {
    EnsureEndElement();
    
    // Add implicit hydrogens on atoms without "hydrogens" property
    for (vector<unsigned int>::iterator vit = _handleImplicitHydrogens.begin();
         vit != _handleImplicitHydrogens.end(); ++vit)
           OBAtomAssignTypicalImplicitHydrogens(_pmol->GetAtom(atoms[*vit]));

    _pmol->EndModify();

    // This alone will already store the "Formula" property in the molecule property block
    // The "Formula" is required for older ChemDraw generations allowing to match molecules to reaction properties
    string MolFormula=_pmol->GetFormula();

    // additional adding of "Formula" property is not required, as described above
    //OBPairData *dp = new OBPairData;
    //dp->SetAttribute("MolecularFormula");
    //dp->SetValue(MolFormula);
    //dp->SetOrigin(fileformatInput);
    //_pmol->SetData(dp);

    // alternative is using the molecular title, but a test is needed for preventing overwriting given titles, aka molecule ID
    //_pmol->SetTitle(MolFormula);

    atoms.clear();
    return false;//means stop parsing
  }
  /*
  // Forget that, the fragment, aka molecule, is in another XML hierachy tree than the data.
  // Parsing has already stopped before ever getting to this point
  else if(name=="tags")
  {
  }
  else if(name=="tableCell")
  {
    //OBPairData *dp = new OBPairData;
    //dp->SetAttribute(attr);
    //dp->SetValue(buff);
    //dp->SetOrigin(fileformatInput);
    //mol.SetData(dp);
  }*/

  return true;
}

void ChemDrawXMLFormat::EnsureEndElement(void)
{
  if (_tempAtom.GetAtomicNum() != 0)
  {
    _pmol->AddAtom(_tempAtom);
    atoms[_tempAtom.GetIdx()] = _pmol->NumAtoms();
    _tempAtom.Clear();
  }
  else if (Order >= 0)
  {
    _pmol->AddBond(Begin, End, Order, Flag);
	Order = -1;
  }
}

// Calculate boundary coordintates xMin, xMax, yMin, yMax of the molecule.
Boundary ChemDrawXMLFormat::CalculateMoleculeBoundary(OBMol* pMol)
{
  OBAtom *patom;
  vector<OBAtom *>::iterator i;
  vector<double> atomXs;
  vector<double> atomYs;

  for (patom = pMol->BeginAtom(i); patom; patom = pMol->NextAtom(i))
  {
    atomXs.push_back(patom->GetX());
    atomYs.push_back(patom->GetY());
  }

  Boundary bd = {
    *min_element(atomXs.begin(), atomXs.end()),
    *max_element(atomXs.begin(), atomXs.end()),
    *min_element(atomYs.begin(), atomYs.end()),
    *max_element(atomYs.begin(), atomYs.end()),
  };

  return bd;
}

// [1] Calculate necessary shifts when converting to CDXML,
//      since ChemDraw will not auto-center the molecule.
// [2] Reverse coordinate on Y direction.
void ChemDrawXMLFormat::CalculateCdxmlShift(OBMol* pMol)
{
  const double xDelta = 3.0;
  const double yDelta = 3.0;

  Boundary molBd = CalculateMoleculeBoundary(pMol);
  this->xCdxmlShift = xDelta - molBd.xMin;
  this->yCdxmlShift = yDelta + molBd.yMax;
}

// Given atom coordinates, and transform them to CDXML coordinates.
// Transformation includes centering & y-inverse.
Coord2D ChemDrawXMLFormat::TransformCdxmlCoord(OBAtom* pAtom)
{
  const double xTransform = (this->xCdxmlShift + pAtom->GetX()) * this->_scale;
  const double yTransfrom = (this->yCdxmlShift - pAtom->GetY()) * this->_scale;
  Coord2D cd = {
    xTransform,
    yTransfrom,
  };

  return cd;
}

bool ChemDrawXMLFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
  static const xmlChar C_MOLECULE[]         = "fragment";
  static const xmlChar C_CDXML[]            = "CDXML";
  static const xmlChar C_BONDLENGTH[]       = "BondLength";
  static const xmlChar C_PAGE[]             = "page";
  static const xmlChar C_ATOM[]             = "n";
  static const xmlChar C_BOND[]             = "b";
  static const xmlChar C_ID[]               = "id";

  static const xmlChar C_CHARGE[]           = "Charge";
  static const xmlChar C_COORDS[]           = "p";
  static const xmlChar C_ELEMENT[]          = "Element";
  static const xmlChar C_ISOTOPE[]          = "Isotope";
  static const xmlChar C_ORDER[]            = "Order";
  static const xmlChar C_BEGIN[]            = "B";
  static const xmlChar C_END[]              = "E";
  static const xmlChar C_DISPLAY[]          = "Display";

  _pxmlConv = XMLConversion::GetDerived(pConv,false);
  if(!_pxmlConv)
    return false;

  OBMol* pmol = dynamic_cast<OBMol*>(pOb);
  if (pmol == nullptr)
	return false;
  OBMol &mol = *pmol;

  OBBond *pbond;
  vector<OBBond*>::iterator j;
  if(_pxmlConv->GetOutputIndex() == 1)
  {
    xmlTextWriterStartDocument(writer(), nullptr, nullptr, nullptr);
    xmlTextWriterWriteDTD(writer(), BAD_CAST "CDXML", nullptr, BAD_CAST "http://www.camsoft.com/xml/cdxml.dtd", nullptr);
    xmlTextWriterStartElement(writer(), C_CDXML);
    xmlTextWriterWriteFormatAttribute(writer(), C_BONDLENGTH , "30");
    xmlTextWriterStartElement(writer(), C_PAGE); // put everything on one page
    // now guess the average bond size for the first molecule and scale to 30.
    _scale = 0.;
    if (mol.NumBonds())
    {
      for (pbond = mol.BeginBond(j);pbond;pbond = mol.NextBond(j))
        _scale += pbond->GetLength();
      _scale /= mol.NumBonds();
	}
    else
      _scale = 1.; // FIXME: what happens if the molecule has no bond?
    _scale = 30. / _scale;
    _offset = 0;
  }

  CalculateCdxmlShift(pmol);
  xmlTextWriterStartElement(writer(), C_MOLECULE);

  OBAtom *patom;
  vector<OBAtom*>::iterator i;
  int n;

  for (patom = mol.BeginAtom(i);patom;patom = mol.NextAtom(i))
  {
    xmlTextWriterStartElement(writer(), C_ATOM);
    xmlTextWriterWriteFormatAttribute(writer(), C_ID , "%d", patom->GetIdx() + _offset);

    Coord2D transformCd = TransformCdxmlCoord(patom);
    xmlTextWriterWriteFormatAttribute(
      writer(), C_COORDS , "%f %f", transformCd.x, transformCd.y
    );

    n = patom->GetAtomicNum();
    if (n != 6)
    {
      xmlTextWriterWriteFormatAttribute(writer(), C_ELEMENT , "%d", n);
    }
    n = patom->GetFormalCharge();
    if (n != 0)
    {
      xmlTextWriterWriteFormatAttribute(writer(), C_CHARGE , "%d", n);
    }
    n = patom->GetIsotope();
    if (n != 0)
    {
      xmlTextWriterWriteFormatAttribute(writer(), C_ISOTOPE , "%d", n);
    }
    xmlTextWriterEndElement(writer());
  }

  for (pbond = mol.BeginBond(j);pbond;pbond = mol.NextBond(j))
  {
    xmlTextWriterStartElement(writer(), C_BOND);
	patom = pbond->GetBeginAtom();
    xmlTextWriterWriteFormatAttribute(writer(), C_BEGIN , "%d", patom->GetIdx() + _offset);
	patom = pbond->GetEndAtom();
    xmlTextWriterWriteFormatAttribute(writer(), C_END , "%d", patom->GetIdx() + _offset);
	n = pbond->GetBondOrder();
    if (n != 1)
    {
      xmlTextWriterWriteFormatAttribute(writer(), C_ORDER , "%d", n);
    }
    if (pbond->IsHash())
      xmlTextWriterWriteFormatAttribute(writer(), C_DISPLAY , "WedgedHashBegin");
    else if (pbond->IsWedge())
      xmlTextWriterWriteFormatAttribute(writer(), C_DISPLAY , "WedgeBegin");
    xmlTextWriterEndElement(writer());
  }
  _offset += mol.NumAtoms ();

  xmlTextWriterEndElement(writer());//molecule

  //TODO: Writing property block

  if(_pxmlConv->IsLast())
  {
    xmlTextWriterEndDocument(writer()); // page
    xmlTextWriterEndDocument(writer()); //document
    OutputToStream();
  }
  return true;
}

}//namespace
