MoleculeComponent.hh

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#ifndef GGL_CHEM_MOLECULECOMPONENT_HH_
#define GGL_CHEM_MOLECULECOMPONENT_HH_

#include <string>
#include <vector>
#include <vector>

#include "sgm/Pattern.hh"
#include "ggl/Graph.hh"

namespace ggl {
namespace chem {

    /*! @brief Molecule component definition
     *
     * Describes a molecule component that e.g. is used by
     * ggl::chem::MoleculeDecomposition
     * to assess thermodynamic properties of a molecule. It describes the
     * molecule component pattern to be matched and the according
     * properties.
     *
     * @author Martin Mann - 2010 - http://www.bioinf.uni-freiburg.de/~mmann/
     */
    class MoleculeComponent {

    public:

          //! type of the pattern graph
        typedef ggl::Graph PatternGraph;

          //! type of a node ID set
        typedef std::set<size_t> NodeSet;

          //! type of a Match_Constraint vector
        typedef sgm::Pattern_Interface::ConstraintVec ConstraintVec;

          //! type of a ring fragment definition, i.e. a list of nodes
        typedef std::vector< size_t > RingFragmentList;

          //! different types of ring fragments to consider
        enum RingFragmentType {
            RF_aromaticHydrocarbon = 0
            , RF_heteroaromatic = 1
            , RF_nonaromatic = 2
            , RF_undefined = 3
        };

          //! a ring fragment description
        class RingFragment {
        public:
              //! the type of the ring fragment
            RingFragmentType type;
              //! the definition of the ring fragment node list
            RingFragmentList fragment;

              //! construction
              //! @param type the type to set
              //! @param fragment the fragment definition to set
            RingFragment( const RingFragmentType& type
                        , const RingFragmentList& fragment);
        };

          //! container for ring fragments
        typedef std::vector< RingFragment > RingFragVec;

    public:
          //! description of the component to be matched
        std::string description;
          //! the priority of this component
          //! (used in ggl::chem::MoleculeDecomposition for an ordering)
        size_t priority;
          //! the free energy contribution of the component
          //! (used in ggl::chem::MoleculeDecomposition for energy calculations)
        double freeEnergy;
          //! the pattern to be matched for this component
        PatternGraph pattern;
          //! the set of node IDs from the pattern that are described by this
          //! component
        NodeSet compIDs;
          //! additional matching constraints
        ConstraintVec constraints;
          //! additional ring fragments information that has to be matched
        RingFragVec ringFragments;

    public:
          //! default construction
        MoleculeComponent();

          //! copy construction
          //! @param toCopy the object to make this a copy of
        MoleculeComponent( const MoleculeComponent& toCopy );

          //! destruction
        ~MoleculeComponent();

          //! assignment operator
          //! @param toCopy the object to make this a copy of
          //! @return access to the changed *this object
        MoleculeComponent&
        operator = (const MoleculeComponent& toCopy );

    };

}  // namespace chem
} // namespace ggl

#endif /* GGL_CHEM_MOLECULECOMPONENT_HH_ */