ReportPSSMDifference.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 devel/protein_interface_design/ReportPSSMDifference.cc
/// @brief calculation of the difference in PSSM score between mutated and native pose
/// @author Hermann Zellner (hermann1.zellner@biologie.uni-regensburg.de)


#include <core/pose/Pose.hh>
#include <core/chemical/AA.hh>
#include <core/types.hh>
// AUTO-REMOVED #include <core/conformation/Conformation.hh>

#include <basic/Tracer.hh>


// Utility Headers
#include <utility/vector1.hh>

// Unit Headers
// C++ headers
#include <map>
#include <fstream>
#include <protocols/protein_interface_design/ReportPSSMDifference.hh>

#include <core/pack/task/PackerTask.hh>

//Auto Headers
#include <core/conformation/Residue.hh>

static basic::Tracer TR( "protocols.protein_interface_design.movers.InterfaceRecapitulationMover" );

bool
protocols::protein_interface_design::ReportPSSMDifferences::load_pssm_data(
  std::string const & native_filename
)
{
    std::string native_substr = native_filename.substr( 0, native_filename.size() - 4 );
    std::string pssm_file_name = native_substr + ".fasta";
    std::cerr << "Openning PSSM File " << pssm_file_name << " " << std::endl;
    std::ifstream pssm_file( pssm_file_name.c_str() );

    utility::vector1< Real > pssm_prob_dist( core::chemical::num_canonical_aas, 0.0 );
    Size linenum( 0 );
    pssm_data_.clear();
    while ( pssm_file ) {
      ++linenum;
      char line_aa;
      pssm_file >> line_aa;
      core::chemical::AA aa( core::chemical::aa_from_oneletter_code( line_aa ));
      Real sum( 0.0 );
      for ( Size ii = 1; ii <= core::chemical::num_canonical_aas; ++ii ) {
        pssm_file >> pssm_prob_dist[ ii ];
        sum += pssm_prob_dist[ ii ];
      }
      if ( std::abs( sum - 1 ) > 0.001 ) {
        TR << "Warning: pssm probability distribution does not sum to 1.0: " << sum << std::endl;
        TR << "Problem on line " << linenum << " of " << pssm_file_name << std::endl;
      }
      pssm_data_.push_back( std::make_pair( aa, pssm_prob_dist ));
    }

    if ( pssm_data_.size() == 0 ) { std::cerr << "Did not read file -- possibly not found" << std::endl; return false; }

    return true;
}


core::Real
protocols::protein_interface_design::ReportPSSMDifferences::calculate(
    core::pose::Pose const & pose1_in, core::pose::Pose const & pose2_in, core::pack::task::PackerTaskCOP const & task
)
{
  using namespace core::scoring;

  core::pose::Pose pose1( pose1_in );
  core::pose::Pose pose2( pose2_in );
  core::Real pssm = 0.;

  for( core::Size i = 1; i <= pose1.total_residue(); ++i ) {
    if( !pose1.residue(i).is_protein() ) continue;
    core::chemical::AA const restype( pose2.residue(i).aa() );

    if (task->being_designed( i ))
    {
      if ( pssm_data_[i].first == restype )
      {
        pssm += pssm_data_[i].second[ restype ];
      }
      else
      {
        TR << "Warning: No pssm data found. Falling back on Sequence comparison." << std::endl;
        if ( pose1.residue(i).aa() ==  pose2.residue(i).aa() )
        {
          pssm += 1.;
        }
      }
    }
  }

  return pssm;
}