ChemicalShiftScoringScheme.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 and 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 ChemicalShiftScoringScheme.cc
/// @brief method implementations for ChemicalShiftScoringScheme class.
/// @author James Thompson

#include <core/types.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/ChemicalShiftSequence.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/sequence/ChemicalShiftScoringScheme.hh>

#include <utility/exit.hh>
// AUTO-REMOVED #include <iostream>
#include <string>

#include <complex>

#include <utility/vector1.hh>



namespace core {
namespace sequence {

Real ChemicalShiftScoringScheme::score(
  SequenceOP seq1,
  SequenceOP seq2,
  core::Size pos1,
  core::Size pos2
) {

  using core::Size;
  using core::Real;

  ChemicalShiftSequenceOP prof1 = ChemicalShiftSequenceOP(
    dynamic_cast< ChemicalShiftSequence * > ( seq1() )
  );
  ChemicalShiftSequenceOP prof2 = ChemicalShiftSequenceOP(
    dynamic_cast< ChemicalShiftSequence * > ( seq2() )
  );

  runtime_assert( pos1 <= prof1->length() );
  runtime_assert( pos2 <= prof2->length() );
  runtime_assert( prof1->prof_row(pos1).size() == prof2->prof_row(pos2).size() );

  //CA.q.dat.dev 0.828795509906
  //CB.q.dat.dev 0.969003290496
  //C.q.dat.dev  0.948093982461
  //HA.q.dat.dev 0.231641960268
  //HN.q.dat.dev 0.725943902221
  //N.q.dat.dev  2.78164308475

  Real const a(2), b(4); // constants for sigmoid smoothing trick

  Size n_aa( prof1->prof_row(pos1).size() );
  Size count( 0 );
  Real score( 0.0 );
  for ( Size i = 1; i <= n_aa; ++i ) {
    Real const & q_shift( prof1->prof_row(pos1)[i] );
    Real const & v_shift( prof2->prof_row(pos2)[i] );
    Real const & v_sigma( prof2->sigma(pos2,i) );

    if ( is_good( q_shift ) && is_good( v_shift ) ) {
      Real sig_diff(std::abs((q_shift - v_shift) / v_sigma ));
      Real sigmoid_diff( 1 / ( 1 + exp((a*sig_diff)-b) ) );

      //for ( Size jj = 1; jj < i; ++jj ) std::cout << " ";
      //std::cout << "comparing " << q_shift << " and " << v_shift <<
      //  " (sig_diff = " << sig_diff << ")" << std::endl <<
      //  " (v_sigma = " << v_sigma << ")" << std::endl;
      //for ( Size jj = 1; jj < i; ++jj ) std::cout << " ";
      //std::cout << "sigmoid_diff = " << sigmoid_diff  << std::endl;

      ++count;
      score += sigmoid_diff;
    }
  }

  if ( count != 0 ) {
    score = ( score / count ) * n_aa;
  }

  //score *= 3;
  //std::cout << "score(" << pos1 << "," << pos2 << ") = " << score
  //  << std::endl << std::endl;

  return score;
} // score

} // sequence
} // core