MoleculeOB.hh

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#ifndef GGL_CHEM_MOLECULEOB_HH_
#define GGL_CHEM_MOLECULEOB_HH_


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


#include <sstream>
#include <iostream>
#include <limits>

#include "ggl/chem/Molecule.hh"


namespace ggl {
namespace chem {


     /*! @brief OpenBabel molecule object port
      *
      * Wrapper class around an OpenBabel molecule object (OBMol).
      *
      * It utilizes the OpenBabel library (http://openbabel.org) for the
      * conversion.
      *
      * @author Martin Mann (c) 2009 http://www.bioinf.uni-freiburg.de/~mmann/
      *
      */
    class MoleculeOB
    {
    protected:

        //! current molecule working on
        OpenBabel::OBMol curMol;

    public:

        /*! Construction
         *
         * NOTE: the protons of the molecule are removed during construction.
         *
         * @param mol the molecule to be represented by this object
         */
        MoleculeOB( const ggl::chem::Molecule & mol );

        /*! Access to the molar mass of the molecule
         *
         * @param implicitH flag whether hydrogens should be added implicitly by openbabel or not
         *
         * @return the standard molar mass given by IUPAC atomic masses (amu)
         */
        double
        getMolWeight( const bool implicitH = true );

        /*! Access to the complete energy of the molecule, calculated via force field methods
         *
         * In error case (e.g. force field not loadable) NaN is returned.
         *
         * @return the complete energy of this molecule (in kJ/mol)
         */
        double
        getMolEnergy();


         /**
          * Converts a Molecule into an OpenBabel molecule instance.
          *
          * NOTE: conversion is done via CML encoding and thus currently
          * inefficient.
          *
          * @param mol the molecule to convert
          * @return the according OBMol instance
          */
        static
        OpenBabel::OBMol
        convert( const Molecule & mol );


         /**
          * Converts an OpenBabel molecule object into a Molecule instance.
          *
          * NOTE: only atom label and formal charge are considered for each
          * atom.
          *
          * @param mol the molecule to convert
          * @return the according Molecule instance
          */
        static
        Molecule
        convert( const OpenBabel::OBMol & mol );

    };

} // namespace chem
} // namespace ggl

 // include function bodies
#include "ggl/chem/MoleculeOB.icc"


#endif /*GGL_CHEM_MOLECULEOB_HH_*/