SequenceIdentity.cc

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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 && 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/SequenceIdentity.cc
/// @brief  a base class for fragment scoring
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#include <protocols/frag_picker/scores/SequenceIdentity.hh>

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

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

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {
namespace scores {

bool SequenceIdentity::score(FragmentCandidateOP f,
    FragmentScoreMapOP empty_map) {

  // describe_score(f, empty_map, std::cerr);

  Real totalScore = 0;
  for (Size i = 1; i <= f->get_length(); i++) {
    VallResidueOP r = f->get_residue(i);
    if (r->aa() == query_[i + f->get_first_index_in_query() - 2])
      totalScore += REWARD;
    else
      totalScore += PENALTY;
  }
  totalScore /= (Real) f->get_length();
  empty_map->set_score_component(totalScore, id_);
  if ((totalScore > lowest_acceptable_value_) && (use_lowest_ == true))
    return false;
  return true;
}

bool SequenceIdentity::describe_score(FragmentCandidateOP f,
    FragmentScoreMapOP empty_map, std::ostream& out) {

  Real totalScore = 0;

  out << f->get_chunk()->get_pdb_id() << "  " << I(5,
      f->get_first_index_in_vall()) << " ";
  for (Size i = 1; i <= f->get_length(); i++)
    out << f->get_residue(i)->aa();
  out << std::endl << "            ";
  for (Size i = 1; i <= f->get_length(); i++) {
    VallResidueOP r = f->get_residue(i);
    if (r->aa() == query_[i + f->get_first_index_in_query() - 2]) {
      totalScore += REWARD;
      out << "+";
    } else {
      totalScore += PENALTY;
      out << "-";
    }
  }
  out << "\nquery " << I(5, f->get_first_index_in_query()) << " ";
  for (Size i = 1; i <= f->get_length(); i++)
    out << query_[i + f->get_first_index_in_query() - 2];
  if ((totalScore > lowest_acceptable_value_) && (use_lowest_ == true))
    out << "\nTotal score " << F(5, 3, totalScore) << " ACCEPTED"
        << std::endl;
  else
    out << "\nTotal score " << F(5, 3, totalScore) << " REJECTED"
        << std::endl;

  totalScore /= (Real) f->get_length();
  empty_map->set_score_component(totalScore, id_);
  if ((totalScore > lowest_acceptable_value_) && (use_lowest_ == true))
    return false;
  return true;
}

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