AP_NSPDK_Model.hh

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#ifndef GGL_CHEM_AP_NSPDK_MODEL_HH_
#define GGL_CHEM_AP_NSPDK_MODEL_HH_

#include <string>
#include <map>
#include <set>

#include <boost/shared_ptr.hpp>


//  // set spirit closure limit if neccessary
//#if !defined(BOOST_SPIRIT_CLOSURE_LIMIT)
//#define BOOST_SPIRIT_CLOSURE_LIMIT 5
//#elif BOOST_SPIRIT_CLOSURE_LIMIT < 5
//#error "GGL_GRAPH_GML_GRAMMAR : BOOST_SPIRIT_CLOSURE_LIMIT too low, has to be at least 5"
//#endif
//
//  // set phoenix limit if neccessary
//#if !defined(PHOENIX_LIMIT)
//#define PHOENIX_LIMIT 5
//#elif PHOENIX_LIMIT < 5
//#error "GGL_GRAPH_GML_GRAMMAR : PHOENIX_LIMIT too low, has to be at least 5"
//#endif
//
//#include <boost/version.hpp>
//#if BOOST_VERSION >= 103800
//#include <boost/spirit/include/qi.hpp>
//#include <boost/spirit/include/phoenix_core.hpp>
//#include <boost/spirit/include/classic.hpp>
//#include <boost/spirit/include/phoenix1.hpp>
//#include <boost/spirit/include/classic_actor.hpp>
//#define NS_BOOSTSPIRIT boost::spirit::classic
//#else
//#include <boost/spirit.hpp>
//#include <boost/spirit/phoenix.hpp>
//#include <boost/spirit/actor.hpp>
//#define NS_BOOSTSPIRIT boost::spirit
//#endif


#include "sgd/svmmodel.h"

#include "nspdk/SVector.h"


namespace ggl {
namespace chem {

     /*! @brief NSPDK aromaticity model
      *
      * A linear SVM model derived using the NSPDK kernel that defines an
      * aromaticity classifier used by ggl::chem::AP_NSPDK to identify
      * aromatic rings.
      *
      * @author Martin Mann (c) 2011  http://www.bioinf.uni-freiburg.de/~mmann/
      *
      */
    class AP_NSPDK_Model : public sgd::SvmModel {

    public:
          //! construction
        AP_NSPDK_Model();
          //! destruction
        ~AP_NSPDK_Model();

          //! the ID of the model
        std::string modelID;

          //! a description of the model, e.g. its sources etc.
        std::string description;

          //! whether or not the NSPDK features are ring centered or not
        bool ringCentered;

          /*!
           * If ringCentered == true, this parameter defines up to what
           * distance of ring nodes nodes are viewPoints, ie. a value of 0
           * restricts the viewpoints to the ring only.
           */
        size_t nspdk_maxRingDistance;

          //! the NSPDK distance parameter used to generate the model
        size_t nspdk_maxDistance;

          //! the NSPDK radius parameter used to generate the model
        size_t nspdk_maxRadius;

          //! the NSPDK parameter that defines the number of bits that
          //! define the feature space size used to generate the model
        size_t nspdk_featureBitSize;

          //! the maximal ring size considered when the model was created
        size_t maxRingSize;

          //! the prefix added to all node label within all rings,
          //! used to minimize the uncertain information for prediction
          //! NOTE: the node label has to be set non-aromatic as well!
        std::string ringNodeLabelPrefix;

          //! the edge label used within all rings,
          //! used to minimize the uncertain information for prediction
        std::string ringEdgeLabel;

          //! the label prefix that is added in front of each node and edge
          //! label participating in the ring currently under consideration
        std::string ringViewLabelPrefix;

          //! the weights for each feature
        using sgd::SvmModel::w;

          //! the weight scale for better precision
        using sgd::SvmModel::wscale;

          //! the bias that marks the treshold to reach to be classified as a
          //! positive instance
        using sgd::SvmModel::bias;


    protected : // static members

        typedef boost::shared_ptr<AP_NSPDK_Model> AP_NSPDK_Model_Pointer;
          //! container of all available predefined models
        static std::map < std::string, AP_NSPDK_Model_Pointer > availableModels;
          //! list of all available IDs of predefined models
        static std::set < std::string > availableModelIDs;

    public: // static functions

          /*!
           * Access to the predefined instances via their identifier.
           *
           * @param modelID the identifier of the model of interest
           * @return the model or NULL if no model is available for the given
           *         identifier
           */
        static
        const AP_NSPDK_Model * const
        getInstance( const std::string & modelID );

          /*!
           * Enables the access to all registered predefined model IDs that are
           * handled via getInstance(modelID).
           * @return the set of all available model IDs
           */
        static
        const std::set < std::string > &
        getAvailableModels( void );

    protected:  // static model data

          //! the number of entries covered by the model "OpenBabel:2013"
        static int OpenBabel_2013_wdatasize;
          //! the feature weight entries of the model "OpenBabel:2013"
        static sgd::SVector::Pair OpenBabel_2013_wdata[];

          //! the number of entries covered by the model "Marvin:general:2013"
        static int Marvin_general_2013_wdatasize;
          //! the feature weight entries of the model "Marvin:general:2013"
        static sgd::SVector::Pair Marvin_general_2013_wdata[];


    };


}} // namespace

#endif /* GGL_CHEM_AP_NSPDK_MODEL_HH_ */