addHydrogenProcessor.h

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

#ifndef BALL_STRUCTURE_ADDHYDROGENPROCESSOR_H
#define BALL_STRUCTURE_ADDHYDROGENPROCESSOR_H

#ifndef BALL_CONCEPT_PROCESSOR_H
#include <BALL/CONCEPT/processor.h>
#endif

#ifndef BALL_MATHS_VECTOR3_H
#include <BALL/MATHS/vector3.h> 
#endif

#ifndef BALL_KERNEL_ATOM_H
#include <BALL/KERNEL/atom.h>
#endif

#include <vector>

namespace BALL
{

  class BALL_EXPORT AddHydrogenProcessor
    : public UnaryProcessor<Composite>
  {
 
    public:

    AddHydrogenProcessor();
    
    virtual ~AddHydrogenProcessor();
    
    AddHydrogenProcessor(const AddHydrogenProcessor& hbp);

    virtual bool start();
    
    virtual Processor::Result operator() (Composite &composite);

    Size getConnectivity(Atom& atom);

    void setRings(const vector<vector<Atom*> >& rings);

    Size getNumberOfAddedHydrogens() { return nr_hydrogens_;}
    
    protected:

    Size countBondOrders(Atom& atom);
    void addHydrogen_(Atom& atom, Vector3 position);
    inline bool isRingAtom_(Atom& atom);
    vector<Atom*> getPartners_(Atom& atom);
    Vector3 getNormal_(const Vector3& v);
    inline bool normalize_(Vector3& v);
    bool hasMultipleBond_(Atom& atom);
    // get the ideal bond length for the given element with hydrogen atoms
    float getBondLength_(Position element);

    HashSet<Atom*> ring_atoms_;
    Position atom_nr_;
    Atom*    last_atom_;
    Size     nr_hydrogens_;
  }; //class AddHydrogenProcessor

} //namesspace BALL

#endif // BALL_STRUCTURE_ADDHYDROGENPROCESSOR_H