ProfileScoreBlosum62.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/ProfileScore.cc
/// @brief  scores a fragment by an amino acid sequence identity
/// @author Dominik Gront (dgront@chem.uw.edu.pl)


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

#include <protocols/frag_picker/scores/ProfileScoreBlosum62.hh>

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

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

#include <utility/file/FileName.hh>

// option key includes
#include <basic/options/keys/OptionKeys.hh>

// utils
#include <basic/prof.hh>
#include <basic/Tracer.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {
namespace scores {

using namespace basic::options;
using namespace basic::options::OptionKeys;
  using namespace core::chemical;

static basic::Tracer trProfScoreBlosum62(
    "protocols.frag_picker.scores.ProfileScoreBlosum62");

ProfileScoreBlosum62::~ProfileScoreBlosum62() {}

ProfileScoreBlosum62::ProfileScoreBlosum62(Size priority, Real lowest_acceptable_value, bool use_lowest,
      sequence::SequenceProfileOP query_profile, Size longest_vall_chunk) :
    CachingScoringMethod(priority, lowest_acceptable_value, use_lowest,
        "ProfileScoreBlosum62")
{
  query_profile_ = query_profile;

  for (Size i = 1; i <= query_profile->length(); ++i) {
    utility::vector1<Real> row(longest_vall_chunk);
    scores_.push_back(row);
  }

  sequence::MatrixScoringScheme blosum_reader;

  utility::file::FileName const fn("/work/rvernon/yangshen/adjust_tables/BLOSUM62");

  blosum_reader.read_from_file(fn);

  blosum_matrix_ = blosum_reader.scoring_matrix();

}


void ProfileScoreBlosum62::do_caching(VallChunkOP chunk) {

  std::string & tmp = chunk->chunk_key();
  if (tmp.compare(cached_scores_id_) == 0)
    return;
  cached_scores_id_ = tmp;
  Size size_q = query_profile_->length();

  trProfScoreBlosum62.Debug << "caching profile score for " << chunk->get_pdb_id()
      << " of size " << chunk->size() << std::endl;
  PROF_START( basic::FRAGMENTPICKING_PROFILE_CAHING );
  for (Size i = 1; i <= size_q; ++i) {
    utility::vector1<Real> query_prof_row = query_profile_->prof_row(i);

    for (Size j = 1; j <= chunk->size(); ++j) {

      //AA aa = aa_from_oneletter_code( chunk->at(j)->aa() );

      utility::vector1<Real> tmplt_prof_row = chunk->at(j)->profile();
      Real score = 0.0;
      for (Size k1 = 1; k1 <= 20; k1++) {
        //score -= query_prof_row[k]*blosum_matrix_[k][aa];//*tmplt_prof_row[k];
        for (Size k2 = 1; k2 <= 20; k2++) {

          Real diff = query_prof_row[k1]*sqrt(tmplt_prof_row[k2]);

          Real sign(0.0);

          if ( blosum_matrix_[k1][k2] < 0 ) {
            sign = -1.0;
          } else {
            sign = 1.0;
          }

          Real blosum( pow(abs(blosum_matrix_[k1][k2]), 1/4) );

          score -= sign/(1+exp((-10*diff*blosum)+5));

          //score -= query_prof_row[k1]*tmplt_prof_row[k2]*blosum_matrix_[k1][k2];//*tmplt_prof_row[k];;
        }
      }
      scores_[i][j] = score;
    }


    //for (Size j = 1; j <= chunk->size(); ++j) {
    //  utility::vector1<Real> tmplt_prof_row = chunk->at(j)->profile();
    //  Real score = 0.0;
    //  for (Size k = 1; k <= 20; k++){
    //    score += std::abs(tmplt_prof_row[k] - query_prof_row[k]);
    //  }
    //  scores_[i][j] = score;
    //}
  }

  PROF_STOP( basic::FRAGMENTPICKING_PROFILE_CAHING );
  trProfScoreBlosum62.Debug << "precomputed matrix of scores " << scores_.size()
      << "x" << chunk->size() << std::endl;
}

bool ProfileScoreBlosum62::cached_score(FragmentCandidateOP f, FragmentScoreMapOP empty_map) {

  std::string & tmp = f->get_chunk()->chunk_key();

  if (tmp.compare(cached_scores_id_) != 0)
    do_caching(f->get_chunk());

  Real totalScore = 0.0;
  for (Size i = 1; i <= f->get_length(); i++) {
    assert(f->get_first_index_in_query() + i - 1 <= scores_.size());
    assert(f->get_first_index_in_vall()
        + i - 1<= scores_[1].size());
    totalScore
        += scores_[f->get_first_index_in_query() + i - 1][f->get_first_index_in_vall()
            + i - 1];
  }
  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 ProfileScoreBlosum62::score(FragmentCandidateOP f, FragmentScoreMapOP empty_map) {

  return cached_score( f, empty_map);

//  PROF_START( basic::FRAGMENTPICKING_PROFILE_SCORE );

//  Real totalScore = 0.0;
//  for (Size i = 1; i <= f->get_length(); i++) {
//    utility::vector1<Real> query_prof_row = query_profile_->prof_row(f->get_first_index_in_query() + i - 1);
//    VallChunkOP chunk = f->get_chunk();
//    utility::vector1<Real> tmplt_prof_row = chunk->at(f->get_first_index_in_vall() + i - 1)->profile();
//    for (Size k = 1; k <= 20; k++){
//        totalScore += std::abs(tmplt_prof_row[k] - query_prof_row[k]);
//    }
//  }
//  totalScore /= (Real) f->get_length();
//  empty_map->set_score_component(totalScore, id_);
//  PROF_STOP( basic::FRAGMENTPICKING_PROFILE_SCORE );
//  if ((totalScore > lowest_acceptable_value_) && (use_lowest_ == true))
//    return false;
//  return true;
}


FragmentScoringMethodOP MakeProfileScoreBlosum62::make(Size priority,
    Real lowest_acceptable_value, bool use_lowest, FragmentPickerOP picker, std::string) {

  Size len = picker->get_vall()->get_largest_chunk_size();
  trProfScoreBlosum62 << "Profile scoring method is: Blosum62" << std::endl;
  return (FragmentScoringMethodOP) new ProfileScoreBlosum62(priority,
      lowest_acceptable_value, use_lowest, picker->get_query_seq(), len);
}

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