HBondProcessor.h

// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: HBondProcessor.h,v 1.7.18.1 2007/03/25 21:25:22 oliver Exp $
//

#ifndef BALL_STRUCTURE_HBONDPROCESSOR_H
#define BALL_STRUCTURE_HBONDPROCESSOR_H

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

#ifndef BALL_KERNEL_RESIDUE_H
#include <BALL/KERNEL/residue.h>
#endif

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

#include <vector>

namespace BALL
{

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

    // constants 
    // 5.2 Angstrom is the maximum distance between N and O in a hydrogen bond.
    // 4.2 Angstrom is an upper bound for the distance between N and O in the same
    // residue. Therefore, if two residues are farther apart than MAX_LENGTH, N and O
    // are farther apart than 5.2 Angstroms and there will be no hydrogen bond.
    const float MAX_LENGTH;
    const float BOND_LENGTH_N_H;
    const float BOND_LENGTH_C_O;

    struct BALL_EXPORT ResidueData
    {
      Vector3 pos_C;
      Vector3 pos_N;
      Vector3 pos_H;
      Vector3 pos_O;
      Size    number;
      Residue*  res; 
      bool is_complete; 
    };
  
    
    
    HBondProcessor();
    
    virtual ~HBondProcessor();
    
    HBondProcessor(const HBondProcessor& hbp);
    

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

    const std::vector< std::vector<Position> >& getHBondPairs() const;

    const std::vector<ResidueData>& getResidueData() const;

    protected:  

    void preComputeBonds_(ResidueIterator& data);

    //_ lower point of the grid
    Vector3 upper_;
    //_ upper point of the grid
    Vector3 lower_;
    
    vector<ResidueData> residue_data_;

    std::vector<std::vector<Position> > h_bond_pairs_;

  }; //class HBondProcessor
} //namesspace BALL


#endif // BALL_STRUCTURE_HBONDPROCESSOR_H

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