HydrophobicityProfileSimilarity.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/HydrophobicityProfileSimilarity.cc
/// @brief  a base class for fragment scoring
/// @author David E Kim

#include <protocols/frag_picker/scores/HydrophobicityProfileSimilarity.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>

// mini headers
#include <core/chemical/AA.hh>

namespace protocols {
namespace frag_picker {
namespace scores {

void HydrophobicityProfileSimilarity::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 HydrophobicityProfileSimilarity::cached_score(FragmentCandidateOP fragment,
    FragmentScoreMapOP scores) {

  return score( fragment, scores );

}

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

  static const Real MIN_HYDROPHOBIC_PROBABILITY(0.75);

  Real totalScore = 0;
  VallChunkOP chunk = f->get_chunk();
  for (Size i = 1; i <= f->get_length(); i++) {
    Size qindex = i + f->get_first_index_in_query() - 1;
    if (is_hydrophobic_[query_[qindex - 1]]) {
      utility::vector1<Real> query_prof_row = query_profile_->prof_row(qindex);
      Real query_hydrophobic_sum = query_prof_row[core::chemical::aa_from_oneletter_code( 'F' )] +
          query_prof_row[core::chemical::aa_from_oneletter_code( 'I' )] +
          query_prof_row[core::chemical::aa_from_oneletter_code( 'L' )] +
          query_prof_row[core::chemical::aa_from_oneletter_code( 'M' )] +
          query_prof_row[core::chemical::aa_from_oneletter_code( 'V' )] +
          query_prof_row[core::chemical::aa_from_oneletter_code( 'W' )] +
          query_prof_row[core::chemical::aa_from_oneletter_code( 'Y' )];
      if (query_hydrophobic_sum > MIN_HYDROPHOBIC_PROBABILITY) {
        Size vallindex = f->get_first_index_in_vall() + i - 1;
        utility::vector1<Real> tmplt_prof_row = chunk->at(vallindex)->profile();
        Real tmplt_residue_hydrophobic_sum = tmplt_prof_row[core::chemical::aa_from_oneletter_code( 'F' )] +
            tmplt_prof_row[core::chemical::aa_from_oneletter_code( 'I' )] +
            tmplt_prof_row[core::chemical::aa_from_oneletter_code( 'L' )] +
            tmplt_prof_row[core::chemical::aa_from_oneletter_code( 'M' )] +
            tmplt_prof_row[core::chemical::aa_from_oneletter_code( 'V' )] +
            tmplt_prof_row[core::chemical::aa_from_oneletter_code( 'W' )] +
            tmplt_prof_row[core::chemical::aa_from_oneletter_code( 'Y' )];
        utility::vector1<Real> tmplt_prof_struct_row = chunk->at(vallindex)->profile_struct();
        tmplt_residue_hydrophobic_sum += tmplt_prof_struct_row[core::chemical::aa_from_oneletter_code( 'F' )] +
            tmplt_prof_struct_row[core::chemical::aa_from_oneletter_code( 'I' )] +
            tmplt_prof_struct_row[core::chemical::aa_from_oneletter_code( 'L' )] +
            tmplt_prof_struct_row[core::chemical::aa_from_oneletter_code( 'M' )] +
            tmplt_prof_struct_row[core::chemical::aa_from_oneletter_code( 'V' )] +
            tmplt_prof_struct_row[core::chemical::aa_from_oneletter_code( 'W' )] +
            tmplt_prof_struct_row[core::chemical::aa_from_oneletter_code( 'Y' )];
        tmplt_residue_hydrophobic_sum /= (Real) 2.0;
        if (tmplt_residue_hydrophobic_sum < MIN_HYDROPHOBIC_PROBABILITY - 0.10) { // .1 buffer
          totalScore += 0.5; // penalty if avg sum of hydrophobic residue profile values from vall sequence and structure profiles less than query avg sum
        }
      }
    }
  }
  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> HydrophobicityProfileSimilarity::is_hydrophobic_;

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