DisulfideDistance.hh

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// vi: set ts=2 noet:
//
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/// @file   protocols/frag_picker/scores/MidPhiOut.hh
/// @brief  Scores fragments by disulfide-linke Calpha distances
/// @author Robert Vernon

#ifndef INCLUDED_protocols_frag_picker_scores_DisulfideDistance_hh
#define INCLUDED_protocols_frag_picker_scores_DisulfideDistance_hh

// package headers
#include <protocols/frag_picker/FragmentCandidate.fwd.hh>
// AUTO-REMOVED #include <protocols/frag_picker/PhiPsiTalosIO.hh>

#include <protocols/frag_picker/scores/CachingScoringMethod.hh>
#include <protocols/frag_picker/scores/FragmentScoreMap.fwd.hh>

// mini
#include <core/types.hh>

// AUTO-REMOVED #include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {
namespace scores {

/// @brief  scores a fragment by the root mean square deviation of Phi and Psi angles.
class DisulfideDistance: public CachingScoringMethod {
public:

  /// @brief  creates a Calpha distance based scoring function.
  /// @detailed Scores distance matches for short range disulfides (ie: within fragment)
  DisulfideDistance(Size priority, Real lowest_acceptable_value, bool use_lowest,
                    utility::vector1< Size > disulfide_data, Size largest_fragment);

  void do_caching(VallChunkOP);
  void clean_up();
  bool score(FragmentCandidateOP, FragmentScoreMapOP);
  bool cached_score(FragmentCandidateOP, FragmentScoreMapOP);

private:
  Size n_res_;
  std::string cached_scores_id_;

  ObjexxFCL::FArray2D_double chunk_ca_distances_;

  utility::vector1< Size > disulfide_data_;
  Size largest_fragment_;
};

/// @brief  Matker class that produces a new DisulfideDistance object
class MakeDisulfideDistance: public MakeFragmentScoringMethod {
public:

  MakeDisulfideDistance() :
    MakeFragmentScoringMethod("DisulfideDistance") {
  }

  FragmentScoringMethodOP make(Size, Real, bool, FragmentPickerOP, std::string);
};

} // scores
} // frag_picker
} // protocols

#endif // INCLUDED_protocols_frag_picker_scores_DisulfideDistance_HH