openbabel-sys 0.5.4+openbabel-3.1.1

/**********************************************************************
Copyright (C) 2010 by Geoffrey R. Hutchison

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/obiter.h>
#include <openbabel/elements.h>
#include <openbabel/generic.h>

#include <cstdlib>


using namespace std;
namespace OpenBabel
{

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

  virtual const char* Description() //required
  {
    return
      "FHIaims XYZ format\n"
      "Read Options e.g. -as\n"
      " s  Output single bonds only\n"
      " b  Disable bonding entirely\n\n";
  };

  virtual const char* SpecificationURL()
  {return "http://www.fhi-berlin.mpg.de/th/aims/";}; //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
FHIaimsFormat theFHIaimsFormat;

/////////////////////////////////////////////////////////////////
bool FHIaimsFormat::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();

    char buffer[BUFF_SIZE];
    string str;
    double x,y,z;
    OBAtom *atom;
    vector<string> vs;
    vector<vector3> lattice;

    mol.BeginModify();

    while (ifs.getline(buffer,BUFF_SIZE)) {
      if (buffer[0] == '#')
        continue; // comment line

      if (strstr(buffer, "atom") != nullptr) {
        // atom X Y Z element (in real-space Angstroms)
        tokenize(vs,buffer);
        if (vs.size() < 5)
          continue; // invalid line
        atom = mol.NewAtom();
        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); //set coordinates

        //set atomic number
        int atomicNum = OBElements::GetAtomicNum(vs[4].c_str());
        atom->SetAtomicNum(atomicNum);

      } else if (strstr(buffer, "lattice_vector") != nullptr) {
        // lattice_vector X Y Z (in real-space Angstroms)
        tokenize(vs,buffer);
        if (vs.size() < 4)
          continue;

        x = atof((char*)vs[1].c_str());
        y = atof((char*)vs[2].c_str());
        z = atof((char*)vs[3].c_str());
        lattice.push_back(vector3(x, y, z));
      }
    }

    if (!pConv->IsOption("b",OBConversion::INOPTIONS))
      mol.ConnectTheDots();
    if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS))
      mol.PerceiveBondOrders();

    // clean out remaining blank lines
    std::streampos ipos;
    do
    {
      ipos = ifs.tellg();
      ifs.getline(buffer,BUFF_SIZE);
    }
    while(strlen(buffer) == 0 && !ifs.eof() );
    ifs.seekg(ipos);

    mol.EndModify();
    // Check if there are lattice vectors and add them
    if (lattice.size() == 3) {
      OBUnitCell *uc = new OBUnitCell;
      uc->SetOrigin(fileformatInput);
      uc->SetData(lattice[0], lattice[1], lattice[2]);
      mol.SetData(uc);
    }
    mol.SetTitle(title);
    return(true);
}

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

bool FHIaimsFormat::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;

    char buffer[BUFF_SIZE];

    ofs << "#\n";
    ofs << "# " << mol.GetTitle() << '\n';
    ofs << "# Generated by Open Babel " << BABEL_VERSION << '\n';
    ofs << "#\n";

    FOR_ATOMS_OF_MOL(atom, mol) {
      snprintf(buffer, BUFF_SIZE,
               "atom           %15.5f%15.5f%15.5f  %s",
               atom->GetX(),
               atom->GetY(),
               atom->GetZ(),
               OBElements::GetSymbol(atom->GetAtomicNum()));
        ofs << buffer << '\n';
    }

    if (mol.HasData(OBGenericDataType::UnitCell)) {
        OBUnitCell *uc = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
        ofs << "#\n";
        ofs << "# unit cell\n";
        ofs << "#\n";

        vector<vector3> v = uc->GetCellVectors();

        for (unsigned int i = 0; i < v.size(); ++i) {
          snprintf(buffer, BUFF_SIZE,
                   "lattice_vector %15.5f%15.5f%15.5f\n", v[i].x(), v[i].y(), v[i].z());
          ofs << buffer;
        }
    }

    return(true);
}

} //namespace OpenBabel