SMILESwriterOB.hh

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#ifndef GGL_CHEM_SMILESWRITEROB_HH_
#define GGL_CHEM_SMILESWRITEROB_HH_


#include <sstream>
#include <iostream>
#include <memory>

#include "ggl/chem/Molecule.hh"
#include "ggl/chem/MoleculeUtil.hh"

#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>



namespace ggl {
 namespace chem {

     /*! @brief Molecule to SMILES writer via OpenBabel
      *
      * Utility class to generate a canonical SMILES string from a molecule
      * graph representation. It expects atom (node) and edge (bond) label
      * following the Daylight's SMILES description. See 
      * ggl::chem::SMILES_grammar for further details.
      * 
      * It utilizes the OpenBabel library (http://openbabel.org) for the 
      * conversion.
      * 
      * @author Martin Mann (c) 2009 http://www.bioinf.uni-freiburg.de/~mmann/
      * 
      */
    class SMILESwriterOB
    {
    
    protected:

          //! the OpenBabel conversion object used
        static std::auto_ptr<OpenBabel::OBConversion> converter;
    
    public:
        SMILESwriterOB();
        
          /*! Generates a canonical SMILES string of the given graph 
           * representation of a molecule.
           * 
           * NOTE: THE FUNCTIONALITY IS INCOMPLETE, i.e. only a few atom and
           * bond types are possible! See class description!
           * 
           * @param mol the molecule graph to parse
           * @return a canonical SMILES string representing the given molecule
           */
        static
        std::string
        getSMILES( const Molecule& mol)
        {
              // setup converter if not done yet
            if (converter.get() == 0) {
                  // create converter
                converter.reset( new OpenBabel::OBConversion(NULL,NULL));
                  // setup conversion scheme
                converter->SetInAndOutFormats("CML","CAN");
            }

              // get CML representation of the molecule
            std::stringstream molCML, outSMILES;
            MoleculeUtil::convertCML( mol, molCML );

              // convert from CML to canonical SMILES
            converter->Convert( &molCML, &outSMILES );

              // trim whitespaces
            std::string out = outSMILES.str();
            size_t from = out.find_first_not_of(" \t\n");
                assert(from != out.npos);
            size_t to = out.find_last_not_of(" \t\n");
                assert(to != out.npos);
              // return conversion result
            return out.substr(from, to-from+1);
        }
        
        
    };
    
      // create member
    std::auto_ptr<OpenBabel::OBConversion>
    SMILESwriterOB::converter = std::auto_ptr<OpenBabel::OBConversion>();

 } // namespace chem
} // namespace ggl


#endif /*GGL_CHEM_SMILESWRITEROB_HH_*/