connectivityBase.h

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// -*- Mode: C++; tab-width: 2: -*-
// vi: set ts=2:
//
//

#ifndef BALL_QSAR_CONNECTIVITYBASE_H
#define BALL_QSAR_CONNECTIVITYBASE_H

#ifndef BALL_COMMON_GLOBAL_H
  #include <BALL/COMMON/global.h>
#endif 

#ifndef BALL_QSAR_DESCRIPTOR_H
  #include <BALL/QSAR/descriptor.h>
#endif

namespace BALL
{
  // forward declarations
  template <typename Key, typename Value> class HashMap;

  class BALL_EXPORT ConnectivityBase
    : public Descriptor
  {
    public:
        
    ConnectivityBase();

    ConnectivityBase(const ConnectivityBase& cb);

    ConnectivityBase(const String& name);

    ConnectivityBase(const String& name, const String& unit);

    virtual ~ConnectivityBase();

    virtual ConnectivityBase& operator = (const ConnectivityBase& cb);
    
    void computeAllDescriptors(AtomContainer& ac);
    
    protected:

    bool isValid_(AtomContainer& ac);
    
    void calculate_(AtomContainer& ac);
    
    


    private:

    /*_ @name Accessors
    */
    /*_ Dijkstra recursion. Performs a single source shortest path approach
        @param distances to the other nodes are stored in referenced vector<double>
        @param Atom which acts as source atom
        @param indices map, which maps for each atom a index for the dist vector
    */
    void recursion_(std::vector<double>& dists, const Atom* source, HashMap<const Atom*, Size>& index_map);

  };

} // namespace BALL

#endif