openbabel-sys 0.5.4+openbabel-3.1.1

/**********************************************************************
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/bond.h>
#include <openbabel/elements.h>
#include <openbabel/data.h>
#include <openbabel/generic.h>
#include <cstdlib>


using namespace std;
namespace OpenBabel
{

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

    virtual const char* Description() //required
    {
      return
        "MSI BGF 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 READONEONLY | WRITEONEONLY;
    };

    //*** This section identical for most OBMol conversions ***
    ////////////////////////////////////////////////////
    /// The "API" interface functions
    virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv);
    virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv);
  };
  //***

  //Make an instance of the format class
  BGFFormat theBGFFormat;

  /////////////////////////////////////////////////////////////////
  bool BGFFormat::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
    mol.BeginModify();

    char buffer[BUFF_SIZE];
    char tmp[16],tmptyp[16];
    vector<string> vs;

    while (ifs.getline(buffer,BUFF_SIZE)) {
      if (EQn(buffer,"CRYSTX",6)) {
        // Parse unit cell
        tokenize(vs,buffer," \n\t,");
        if (vs.size() != 7)
          continue; // something strange

        double A, B, C, Alpha, Beta, Gamma;
        A = atof(vs[1].c_str());
        B = atof(vs[2].c_str());
        C = atof(vs[3].c_str());
        Alpha = atof(vs[4].c_str());
        Beta  = atof(vs[5].c_str());
        Gamma = atof(vs[6].c_str());
        OBUnitCell *uc = new OBUnitCell;
        uc->SetOrigin(fileformatInput);
        uc->SetData(A, B, C, Alpha, Beta, Gamma);
        mol.SetData(uc);
      } else if (EQn(buffer,"FORMAT",6))
        break;
    }

    ttab.SetFromType("DRE");
    ttab.SetToType("INT");
    OBAtom *atom;
    double x,y,z,chrg;
    for (;;)
      {
        if (!ifs.getline(buffer,BUFF_SIZE))
          break;
        if (EQn(buffer,"FORMAT",6))
          break;

        sscanf(buffer,"%*s %*s %*s %*s %*s %*s %lf %lf %lf %15s %*s %*s %lf",
               &x,&y,&z,
               tmptyp,
               &chrg);
        atom = mol.NewAtom();

        ttab.Translate(tmp,tmptyp);
        atom->SetType(tmp);

        CleanAtomType(tmptyp);
        atom->SetAtomicNum(OBElements::GetAtomicNum(tmptyp));

        atom->SetVector(x,y,z);
      }
    unsigned int i;
    vector<int> vtmp;
    vector<vector<int> > vcon;
    vector<vector<int> > vord;

    for (i = 0; i < mol.NumAtoms();i++)
      {
        vcon.push_back(vtmp);
        vord.push_back(vtmp);
      }

    unsigned int bgn;
    for (;;)
      {
        if (!ifs.getline(buffer,BUFF_SIZE) || EQn(buffer,"END",3))
          break;

        tokenize(vs,buffer);
        if (vs.empty() || vs.size() < 3 || vs.size() > 10)
          continue;

        if (EQn(buffer,"CONECT",6))
          {
            bgn = atoi((char*)vs[1].c_str()) - 1;
            if (bgn < 1 || bgn > mol.NumAtoms())
              continue;
            for (i = 2;i < vs.size();i++)
              {
                vcon[bgn].push_back(atoi((char*)vs[i].c_str()));
                vord[bgn].push_back(1);
              }
          }
        else
          if (EQn(buffer,"ORDER",5))
            {
              bgn = atoi((char*)vs[1].c_str()) - 1;
              if (bgn < 1 || bgn > mol.NumAtoms())
                continue;
              if (vs.size() > vord[bgn].size()+2)
                continue;
              for (i = 2;i < vs.size();i++)
                vord[bgn][i-2] = atoi((char*)vs[i].c_str());
            }
      }

    unsigned int j;
    for (i = 1;i <= mol.NumAtoms();i++)
      if (!vcon[i - 1].empty())
        for (j = 0;j < vcon[i - 1].size();j++)
          {
            mol.AddBond(i,vcon[i - 1][j],vord[i - 1][j]);
          }

    //load up the next line after the END marker
    ifs.getline(buffer,BUFF_SIZE);

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

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

  bool BGFFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
  {
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if (pmol == nullptr)
      return false;

    //Define some references so we can use the old parameter names
    ostream &ofs = *pConv->GetOutStream();
    OBMol &mol = *pmol;

    vector<OBAtom*>::iterator i;
    int max_val;
    OBAtom *atom;
    char buffer[BUFF_SIZE];
    char elmnt_typ[8], dreid_typ[8], atm_sym[16], max_val_str[8];

    ofs << "BIOGRF 200\n";
    snprintf(buffer, BUFF_SIZE, "DESCRP %s\n",mol.GetTitle());
    ofs << buffer;
    snprintf(buffer, BUFF_SIZE, "REMARK BGF file created by Open Babel %s\n",BABEL_VERSION);
    ofs << "FORCEFIELD DREIDING  \n";

    // write unit cell if available
    if (mol.HasData(OBGenericDataType::UnitCell))
      {
        OBUnitCell *uc = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
        // e.g. CRYSTX    49.30287   49.23010   25.45631   90.00008   89.99995   57.10041
        snprintf(buffer, BUFF_SIZE,
                 "CRYSTX%12.5f%12.5f%12.5f%12.5f%12.5f%12.5f",
                 uc->GetA(), uc->GetB(), uc->GetC(),
                 uc->GetAlpha() , uc->GetBeta(), uc->GetGamma());
        ofs << buffer << "\n";
      }

    ofs << "FORMAT ATOM   (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5)\n";

    ttab.SetFromType("INT");

    for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
      {
        strncpy(elmnt_typ,OBElements::GetSymbol(atom->GetAtomicNum()), 7); // make sure to null-terminate
        elmnt_typ[sizeof(elmnt_typ) - 1] = '0';
        ToUpper(elmnt_typ);

        ttab.SetToType("DRE");
        ttab.Translate(dreid_typ,atom->GetType());
        ttab.SetToType("HAD");
        ttab.Translate(max_val_str,atom->GetType());
        max_val = atoi(max_val_str);
        if (max_val == 0)
          max_val = 1;
        snprintf(atm_sym,16,"%s%d",elmnt_typ,atom->GetIdx());
        snprintf(buffer,BUFF_SIZE,"%6s %5d %-5s %3s %1s %5s%10.5f%10.5f%10.5f %-5s%3d%2d %8.5f\n",
                "HETATM",
                atom->GetIdx(),
                atm_sym,
                "RES",
                "A",
                "444",
                atom->GetX(),
                atom->GetY(),
                atom->GetZ(),
                dreid_typ,
                max_val,
                0,
                atom->GetPartialCharge());
        ofs << buffer;
      }
    ofs<< "FORMAT CONECT (a6,12i6)\n\n";

    OBAtom *nbr;
    vector<OBBond*>::iterator j;
    for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
      if (atom->GetExplicitDegree())
        {
          snprintf(buffer,BUFF_SIZE,"CONECT%6d",atom->GetIdx());
          ofs << buffer;
          for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
            {
              snprintf(buffer,BUFF_SIZE,"%6d",nbr->GetIdx());
              ofs << buffer;
            }
          ofs << endl;

          snprintf(buffer,BUFF_SIZE,"ORDER %6d",atom->GetIdx());
          ofs << buffer;
          for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
            {
              snprintf(buffer,BUFF_SIZE,"%6d",(*j)->GetBondOrder());
              ofs << buffer;
            }
          ofs << endl;
        }

    ofs << "END" << endl;
    return(true);
  }

} //namespace OpenBabel