residueChecker.h

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

#ifndef BALL_STRUCTURE_RESIDUECHECKER_H
#define BALL_STRUCTURE_RESIDUECHECKER_H

#ifndef BALL_MATHS_COMMON_H
# include <BALL/MATHS/common.h>
#endif

#ifndef BALL_COMMON_H
# include <BALL/common.h>
#endif

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

#ifndef BALL_DATATYPE_BITVECTOR_H
# include <BALL/DATATYPE/bitVector.h>
#endif

namespace BALL
{
  class FragmentDB;
  class Residue;

  class BALL_EXPORT ResidueChecker
    : public UnaryProcessor<Residue>
  {
    public:

    BALL_CREATE(ResidueChecker)

    
      
    
    enum TestType
    {
      MISSING_ATOMS = 0,
      EXTRA_ATOMS,
      ELEMENTS, 
      SUSPECT_BOND_LENGTHS,
      NON_INTEGRAL_NET_CHARGE,
      LARGE_CHARGES,
      LARGE_NET_CHARGE,
      NAN_POSITIONS,
      OVERLAPPING_ATOMS,
      STRONGLY_OVERLAPPING_ATOMS,
      DUPLICATE_ATOM_NAMES,
      UNKNOWN_RESIDUES,

      NUMBER_OF_TESTS
    };


    ResidueChecker();

    ResidueChecker(FragmentDB& fragment_db);

    ResidueChecker(const ResidueChecker& residue_checker);

    virtual ~ResidueChecker();


    void enable(TestType t, bool enable = true) ;

    void disable(TestType t) ;

    void enableSelection()  { selection_ = true; }

    void disableSelection()  { selection_ = false; }

    bool isSelectionEnabled()  { return selection_; }

    bool getStatus() const;



    bool isEnabled(TestType t) const ;


    Processor::Result operator () (Residue& residue);

    bool start();

    bool finish();


    bool checkAtomPositions(const Residue& res, const String& res_name)
      ;

    bool checkCharge(const Residue& res, const String& res_name)
      ;

    bool checkCompleteness(const Residue& res, const Residue& reference, const String& res_name)
      ;

    bool checkTemplate(const Residue& res, const Residue& reference, const String& res_name)
      ;
      
      
    protected:
    
    // The fragment database
    FragmentDB* fragment_db_;

    // Bool flag indicating whether any of the tests failed
    bool        status_;

    // A bitvector containing the flags for the tests
    BitVector   tests_;

    // If this flag is set, all atoms/residues having problems will be selected
    bool        selection_;
  }; 
            
} // namespace BALL

#endif // BALL_STRUCTURE_RESIDUE_CHECKER