RamaScore.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   protocols/frag_picker/scores/RamaScore.hh
/// @brief  a base class for fragment scoring
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_scores_RamaScore_hh
#define INCLUDED_protocols_frag_picker_scores_RamaScore_hh

// type headers
#include <core/types.hh>

// package headers
#include <protocols/frag_picker/FragmentCandidate.fwd.hh>
#include <protocols/frag_picker/FragmentPicker.hh>

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

#include <core/fragment/SecondaryStructure.fwd.hh>

namespace protocols {
namespace frag_picker {
namespace scores {


class RamaScore;
typedef utility::pointer::owning_ptr< RamaScore > RamaScoreOP;
typedef utility::pointer::owning_ptr< RamaScore const > RamaScoreCOP;

/// @brief  RamaScore score counts identical residues
/// @detailed Resulting score is the number of identical residues
/// on corresponding positions in a vall fragment and a query sequence
class RamaScore: public CachingScoringMethod {
public:

  RamaScore(Size, Real, bool, std::string&,std::string);

  RamaScore(Size, Real, bool, std::string&, core::fragment::SecondaryStructureOP,std::string);

  void SetupRamaTables();

  void do_caching(VallChunkOP);
  void clean_up();

  bool score(FragmentCandidateOP f, FragmentScoreMapOP empty_map);
  bool cached_score(FragmentCandidateOP f, FragmentScoreMapOP empty_map);

  /// @brief prints a detailed explanation how a fragment score has been computed
  /// @detailed besides extensive output, the method should return the same result as score()
  bool describe_score(FragmentCandidateOP f, FragmentScoreMapOP empty_map,
      std::ostream& out);

  std::string & get_prediction_name() { return prediction_name_; }

private:
  Real minScoreAllowed_;
  std::string& query_;
  core::fragment::SecondaryStructureOP query_ss_;
  std::string prediction_name_;

  std::string cached_scores_id_;

  utility::vector1< utility::vector1< Real > > scores_;

  //Sequence Specific Ramachandran Surfaces (keep only one copy of this so we don't have to keep reading it from the database for each instance)
  static utility::vector1< utility::vector1< utility::vector1< Real > > > sequence_rama_tables_;

};

/// @brief  Maker class that produces a new RamaScore object
class MakeRamaScore: public MakeFragmentScoringMethod {
public:

  MakeRamaScore() :
    MakeFragmentScoringMethod("RamaScore") {
  }

  FragmentScoringMethodOP make(Size priority, Real lowest_acceptable_value, bool use_lowest,
      FragmentPickerOP picker, std::string prediction_id ) {

    if ( prediction_id == "" ) {
      core::fragment::SecondaryStructureOP default_ss = new core::fragment::SecondaryStructure;
      Size query_len = picker->get_query_seq_string().size();
      default_ss->extend( query_len );
      for ( Size i = 1; i <= query_len; ++i ) {
        default_ss->set_fractions(i, 0.333, 0.333, 0.334);
      }

      //      std::cout << "CO_PREDICTION_ID " << prediction_id << std::endl;
      std::string default_prediction_name("uniform_default");
      return (FragmentScoringMethodOP) new RamaScore(priority,
        lowest_acceptable_value, use_lowest, picker->get_query_seq_string(), default_ss,default_prediction_name);
    } else {

      //std::cout << "PREDICTION_ID " << prediction_id << std::endl;
      return (FragmentScoringMethodOP) new RamaScore(priority,
        lowest_acceptable_value, use_lowest, picker->get_query_seq_string(), picker->get_query_ss(prediction_id),prediction_id);
    }
  }
};

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


#endif /* INCLUDED_protocols_frag_picker_scores_RamaScore_HH */