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

#include <vector>

namespace BALL
{
  class Residue;
  class Atom;
  class Composite;

  class BALL_EXPORT AddHydrogenProcessor
    : public UnaryProcessor<Composite>
  {

    public:

      AddHydrogenProcessor();

      virtual ~AddHydrogenProcessor();

      virtual bool start();

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

      Size getConnectivity(const Atom& atom) const;

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

      Size getNumberOfAddedHydrogens() const { return nr_hydrogens_;}

    protected:
      Processor::Result placePeptideBondH_(Residue* res);

      Size countBondOrders(const Atom& atom) const;

      void addHydrogen_(Atom& atom, Vector3 position);

      bool isRingAtom_(const Atom& atom) const;

      vector<Atom*> getPartners_(Atom& atom) const;

      Vector3 getNormal_(const Vector3& v) const;

      bool normalize_(Vector3& v) const;

      bool hasMultipleBond_(const Atom& atom) const;

      float getBondLength_(Position element) const;

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

} //namespace BALL

#endif // BALL_STRUCTURE_ADDHYDROGENPROCESSOR_H