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

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

namespace protocols {
namespace frag_picker {
namespace scores {

static const core::Real PSI_MIN_CONF = 0.5;

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

  return score( fragment, scores );

}

bool Psi::score(FragmentCandidateOP f,
    FragmentScoreMapOP empty_map) {
  Real totalScore = 0;
  Size conf_positions = 0;
  for (Size i = 1; i <= f->get_length(); i++) {
    // skip low confidence positions
    Size qindex = i + f->get_first_index_in_query() - 1;
    VallResidueOP r = f->get_residue(i);
//    if (query_psi_prediction_conf_[qindex] < PSI_MIN_CONF) continue;
    // skip last residue in query and last residue in vall chunk
    if (qindex >= query_len_ || (i == f->get_length() && qindex >=  f->get_chunk()->size()) ||
        r->dssp_psi() == 360.0 || query_psi_prediction_[qindex] == 360.0) continue;
    // difference / 180
    totalScore += fabs( (query_psi_prediction_[qindex] - r->dssp_psi())/ 180.0 );
    conf_positions++;
  }
  totalScore /= (Real) conf_positions;
  empty_map->set_score_component(totalScore, id_);
  if ((totalScore > lowest_acceptable_value_) && (use_lowest_ == true))
    return false;
  return true;
}


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