ProfileScoreSubMatrix.cc

Go to the documentation of this file.

// -*- 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/ProfileScoreSubMatrix.cc
/// @brief  scores a fragment by substitution matrix (e.g. Blosum62) profile score
/// @author Dan Kulp (dwkulp@gmail.com), based on code from Dominik Gront (dgront@chem.uw.edu.pl)


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

#include <protocols/frag_picker/scores/ProfileScoreSubMatrix.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 trProfScoreSubMatrix(
    "protocols.frag_picker.scores.ProfileScoreSubMatrix");

ProfileScoreSubMatrix::~ProfileScoreSubMatrix() {}

ProfileScoreSubMatrix::ProfileScoreSubMatrix(Size priority, Real lowest_acceptable_value, bool use_lowest,
                                             std::string sequence,Size longest_vall_chunk,std::string subMatrixFile) :
    CachingScoringMethod(priority, lowest_acceptable_value, use_lowest,
        "ProfileScoreSubMatrix")
{
  // Store local copies
  sequence_                = sequence;
  subMatrixFile_           = subMatrixFile;

  // Setup scores to be the proper size, each sequence position has an entry for each chunk position.
  for (Size i = 1; i <= sequence.size(); ++i) {
    utility::vector1<Real> row(longest_vall_chunk);
    scores_.push_back(row);
  }

  // Read in the SubMatrix, should be BLOSUM62 format?
  sequence::MatrixScoringScheme sub_matrix_reader;
  sub_matrix_reader.read_from_file(subMatrixFile_);
  sub_matrix_ = sub_matrix_reader.scoring_matrix();


  // Convert score matrix to probability matrix ?

}


void ProfileScoreSubMatrix::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 = sequence_.size();

  trProfScoreSubMatrix.Debug << "caching profile score for " << chunk->get_pdb_id()
      << " of size " << chunk->size() << std::endl;
  PROF_START( basic::FRAGMENTPICKING_PROFILE_CAHING );

  // For each position in sequence
  for (Size i = 1; i <= size_q; ++i) {

    AA seqAA = aa_from_oneletter_code( sequence_[i-1] );

    // For each position in chunk
    for (Size j = 1; j <= chunk->size(); ++j) {

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

      // For BLOSUM62, a positive score means likely to mutate (F -> Y is 3)
      // Here lower score is better, so invert the substition matrix
      scores_[i][j] = - sub_matrix_[seqAA][chunkAA];
    }
  }

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

bool ProfileScoreSubMatrix::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++) {

    // Check sizes of fragment/chunk and scores
    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 ProfileScoreSubMatrix::score(FragmentCandidateOP f, FragmentScoreMapOP empty_map) {
  return cached_score( f, empty_map);
}

// MISC = Substitution Matrix File Name ... the reader will spit out an error if the file does not exist.
FragmentScoringMethodOP MakeProfileScoreSubMatrix::make(Size priority, Real lowest_acceptable_value, bool use_lowest, FragmentPickerOP picker, std::string misc) {

  Size len = picker->get_vall()->get_largest_chunk_size();

  trProfScoreSubMatrix << "Profile scoring method is: SubMatrix" << std::endl;

  return (FragmentScoringMethodOP) new ProfileScoreSubMatrix(
                                                           priority,
                                                           lowest_acceptable_value,
                                                           use_lowest,
                                                           picker->get_query_seq()->sequence(),
                                                           len,
                                                           misc  // is the substituion matrix file location
                                                             );
}

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