openbabel-sys 0.5.4+openbabel-3.1.1

/**********************************************************************
Copyright (C) 2005 by Chris Morley

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>
#ifdef WIN32
#pragma warning (disable : 4786)
#pragma warning (disable : 4251) //
#endif
#include <string>
#include <iomanip>
#include <openbabel/obmolecformat.h>
#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/elements.h>

#include <openbabel/kinetics.h>
#include <cstdlib>

using namespace std;
namespace OpenBabel
{
class ThermoFormat : public OBMoleculeFormat
{
public:
  ThermoFormat()
  {
      OBConversion::RegisterFormat("therm",this);
      OBConversion::RegisterFormat("tdd",this);
  }

  virtual const char* Description()
  {
    return
      "Thermo format\n"
      "Reads and writes old-style NASA polynomials in original fixed format\n"
      "Read Options e.g. -ae\n"
      " e Terminate on \"END\"\n\n";
  }

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

////////////////////////////////////////////
//Make an instance of the format class
ThermoFormat theThermoFormat;
////////////////////////////////////////////

bool ThermoFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
  OBMol* pmol = pOb->CastAndClear<OBMol>();
  if(!pmol)
    return false;
  bool stopOnEnd = pConv->IsOption("e", OBConversion::INOPTIONS) != nullptr;
  pmol->SetDimension(0);
  OBNasaThermoData* pND = new OBNasaThermoData; //to store rate constant data
  pND->SetOrigin(fileformatInput);
  pmol->SetData(pND);

  istream &ifs = *pConv->GetInStream();

  double DefaultMidT = 1500;
  char ln[BUFF_SIZE];
  unsigned int i;

  //find line with 1 in col 80
  do
  {
    if (!ifs.getline(ln,BUFF_SIZE) || (stopOnEnd && !strncasecmp(ln,"END",3)))
      return false;
  }while(ln[79]!='1');

  char phase, nam[25], dum[7], elname[3];
  elname[2]=0;
  int elnum;
  double Coeff[14];

  sscanf(ln,"%18s%6s",nam,dum);
  pmol->SetTitle(nam);
  char* p=ln+24;
  if(ln[80]=='&')
  {
    //Reaction Design extension
    p+=20;
    string line;
    if(!getline(ifs,line))return false;
    vector<string> toks;
    tokenize(toks,line," \t\n\r");
    for(i=0;i<toks.size();i+=2)
    {
      OBAtom atom;
      atom.SetAtomicNum(OBElements::GetAtomicNum(toks[i].c_str()));
      elnum = atoi(toks[i+1].c_str());
      for(;elnum>0;--elnum)
        pmol->AddAtom(atom);
    }
  }
  else
  {
    for(i=0;i<4;i++,p+=5)
    {
      char snum[4]={0,0,0,0};//Was problem with F   10   0 reading as ten
      sscanf(p,"%c%c%c%c%c",elname,elname+1,snum,snum+1,snum+2);
      elnum=atoi(snum);
      if(elname[0]!=' ' && elname[0]!='0')
      {
        if(elname[1]==' ')
          elname[1]=0;
        OBAtom atom;
        atom.SetAtomicNum(OBElements::GetAtomicNum(elname));
        for(;elnum>0;--elnum)
          pmol->AddAtom(atom);
      }
    }
  }
  double LoT, HiT, MidT=0;
  /* int nc = */sscanf(p,"%c%10lf%10lf10%lf",&phase, &LoT, &HiT, &MidT);
  pND->SetPhase(phase);
  pND->SetLoT(LoT);
  pND->SetHiT(HiT);
  if(MidT>HiT || MidT<LoT)
    MidT=DefaultMidT;
  pND->SetMidT(MidT);
  if (!ifs.getline(ln, BUFF_SIZE)) return false;
  p=ln;
  for(i=0;i<5;i++,p+=15)
    sscanf(p,"%15lf",&Coeff[i]);
  if (!ifs.getline(ln, BUFF_SIZE)) return false;
  p=ln;
  for(i=5;i<10;i++,p+=15)
    sscanf(p,"%15lf",&Coeff[i]);
  if (!ifs.getline(ln, BUFF_SIZE)) return false;
  p=ln;
  for(i=10;i<14;i++,p+=15)
    sscanf(p,"%15lf",&Coeff[i]);

  for(i=0;i<14;++i)
    pND->SetCoeff(i, Coeff[i]);

  pmol->AssignSpinMultiplicity();
  return true;
}

////////////////////////////////////////
bool ThermoFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
  OBMol* pmol = dynamic_cast<OBMol*>(pOb);
  string title(pmol->GetTitle());
  OBNasaThermoData* pND = static_cast<OBNasaThermoData*>(pmol->GetData(ThermoData));
  if(!pND)
  {
    obErrorLog.ThrowError(__FUNCTION__,"No thermo data in " + title, obWarning);
    return false;
  }
  ostream &ofs = *pConv->GetOutStream();
  unsigned int i;
#if defined(_MSC_VER) && (_MSC_VER < 1900)
  unsigned oldf = _set_output_format(_TWO_DIGIT_EXPONENT);
#endif
  string formula = pmol->GetSpacedFormula();
  vector<string> toks;
  tokenize(toks,formula);

  ofs << left << setw(24) << title.substr(0,24);
  //Check that atom numbers are less than 999
  bool toobig=toks.size()>8;
  for(i=0;i<toks.size() && !toobig ;i+=2)
    if(atoi(toks[i+1].c_str())>999)
      toobig =true;
  if(toobig)
    //Reaction Design extension
    ofs << string(20,' ');
  else
  {
    toks.resize(8);
    for(i=0;i<8;i+=2)
    ofs << left << setw(2) << toks[i] << right << setw(3) << toks[i+1];
  }
  ofs << right << pND->GetPhase() << fixed << setprecision(3) << setw(10) << pND->GetLoT();
  ofs << setw(10) << pND->GetHiT() << setw(9) << pND->GetMidT() << "    01";

  if(toobig)
    ofs << "&\n" << formula << '\n';
  else
    ofs << '\n';

  ofs << scientific << setprecision(7);
  for(i=0;i<5;++i)
    ofs << setw(15) << pND->GetCoeff(i);
  ofs << "    2\n";
  for(i=5;i<10;++i)
    ofs << setw(15) << pND->GetCoeff(i);
  ofs << "    3\n";
  for(i=10;i<14;++i)
    ofs << setw(15) << pND->GetCoeff(i);
  ofs << "                   4\n";

#ifdef _MSC_VER
#if _MSC_VER < 1900
  _set_output_format(oldf);
#endif
#endif

  return true;
}

}//OpenBabel namespace