HydrophobicitySimilarity.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.
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// (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
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/// @file   protocols/frag_picker/scores/HydrophobicitySimilarity.cc
/// @brief  a base class for fragment scoring
/// @author David E Kim

#include <protocols/frag_picker/scores/HydrophobicitySimilarity.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 {

void HydrophobicitySimilarity::do_caching(VallChunkOP current_chunk) {
  std::string ctmp = current_chunk()->chunk_key();
  if (ctmp.compare("change to 'cached_scores_id_' when ready") != 0) {
    return; // CACHING NOT BUILT IN YET
  }
}

bool HydrophobicitySimilarity::cached_score(FragmentCandidateOP fragment,
    FragmentScoreMapOP scores) {

  return score( fragment, scores );

}

bool HydrophobicitySimilarity::score(FragmentCandidateOP f,
    FragmentScoreMapOP empty_map) {
  Real totalScore = 0;
  for (Size i = 1; i <= f->get_length(); i++) {
    VallResidueOP r = f->get_residue(i);
    // scoring based on SEGMER hydrophobicity energy term
    if (is_hydrophobic_[r->aa()] && is_hydrophobic_[query_[i + f->get_first_index_in_query() - 2]])
      continue; // no penalty if both query and vall residue are hydrophobic
    else if (r->aa() == query_[i + f->get_first_index_in_query() - 2]) {
      if (r->aa() == 'G' || r->aa() == 'g' || r->aa() == 'P' || r->aa() == 'p')
        continue; // no penalty for identical G or P
      else
        totalScore += 0.3; // small penalty if residues are equal
    } else
      totalScore += 1.0; // penalty if different and not hydrophobic
  }
  totalScore /= (Real) f->get_length();
  empty_map->set_score_component(totalScore, id_);
  if ((totalScore > lowest_acceptable_value_) && (use_lowest_ == true))
    return false;
  return true;
}

std::map<char,bool> HydrophobicitySimilarity::is_hydrophobic_;

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