openbabel-sys 0.5.4+openbabel-3.1.1

/**********************************************************************
Copyright (C) 2002-2006 by Geoffrey Hutchison
Based on code Copyright (C) 1999 Joerg-Ruediger Hill
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 ViewMolFormat : public OBMoleculeFormat
{
public:
  //Register this format type ID
  ViewMolFormat()
  {
    OBConversion::RegisterFormat("vmol",this);
  }

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

  virtual const char* SpecificationURL() //optional
  { return "http://viewmol.sourceforge.net/"; };

    //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
ViewMolFormat theViewMolFormat;

/////////////////////////////////////////////////////////////////
bool ViewMolFormat::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];
    OBAtom *atom;
    double x,y,z, border;
    double factor = 1.0;
    int bgn, end, order;
    vector<string> vs;
    bool foundTitle = false;
    bool foundBonds = false;

    mol.Clear();
    mol.BeginModify();

    ifs.getline(buffer,BUFF_SIZE);
    while (ifs.peek() != EOF && ifs.good())
    {
        if (strstr(buffer, "$title") != nullptr)
        {
            if (!ifs.getline(buffer,BUFF_SIZE))
                return (false);
            mol.SetTitle(buffer);
            foundTitle = true;
	    ifs.getline(buffer,BUFF_SIZE);
        }
        else if (strstr(buffer, "$coord") != nullptr)
        {
            tokenize(vs,buffer);
            if (vs.size() == 2)
                factor = atof((char*)vs[1].c_str()); // conversion to angstrom
            while (ifs.getline(buffer,BUFF_SIZE))
            {

                if (buffer[0] == '$')
                    break;
                tokenize(vs,buffer);
                if (vs.size() != 4)
		  break;
                atom = mol.NewAtom();
                x = atof((char*)vs[0].c_str()) * factor;
                y = atof((char*)vs[1].c_str()) * factor;
                z = atof((char*)vs[2].c_str()) * factor;
                atom->SetVector(x,y,z); //set coordinates
                atom->SetAtomicNum(OBElements::GetAtomicNum(vs[3].c_str()));
            }
        }
        else if (strstr(buffer, "$bonds") != nullptr)
        {
            foundBonds = true;
            while (ifs.getline(buffer,BUFF_SIZE))
            {
                if (buffer[0] == '$')
                    break;
                sscanf(buffer,"%d %d %lf",&bgn,&end, &border);
                if (border > 1.0)
                    order = int(border);
                else
                    order = 1;
                mol.AddBond(bgn+1,end+1,order);
            }
        }
        else if (strstr(buffer, "$end") != nullptr)
	  break;
	else // something else (i.e., garbage, blank lines, etc.)
	  ifs.getline(buffer,BUFF_SIZE);
    } // while

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

    mol.EndModify();

    if (!foundTitle)
        mol.SetTitle(title);
    return(true);
}

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

bool ViewMolFormat::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;

    unsigned int i;
    char buffer[BUFF_SIZE];

    if (strlen(mol.GetTitle()) > 0)
        ofs << "$title" << endl << mol.GetTitle() << endl;

    ofs << "$coord 1.0" << endl;

    OBAtom *atom;
    for(i = 1;i <= mol.NumAtoms(); i++)
    {
        atom = mol.GetAtom(i);
        snprintf(buffer, BUFF_SIZE, "%22.14f%22.14f%22.14f %s",
                atom->GetX(),
                atom->GetY(),
                atom->GetZ(),
                OBElements::GetSymbol(atom->GetAtomicNum()));
        ofs << buffer << endl;
    }

    ofs << "$end" << endl;

    return(true);
}

} //namespace OpenBabel