PositionDdGInfo.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
/// @brief
/// @author Liz Kellogg ekellogg@u.washington.edu

// libRosetta headers

#include <core/types.hh>

#include <core/chemical/AA.hh>
// AUTO-REMOVED #include <core/conformation/Residue.hh>
// AUTO-REMOVED #include <core/conformation/ResidueMatcher.hh>
// AUTO-REMOVED #include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>

// AUTO-REMOVED #include <core/scoring/ScoreFunction.hh>
// AUTO-REMOVED #include <core/scoring/ScoreFunctionFactory.hh>
// AUTO-REMOVED #include <protocols/jd2/ScoreMap.hh>

#include <core/pose/Pose.hh>
// AUTO-REMOVED #include <core/io/pdb/pose_io.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>

// AUTO-REMOVED #include <basic/options/util.hh>
// AUTO-REMOVED #include <basic/options/after_opts.hh>
// AUTO-REMOVED #include <basic/options/keys/OptionKeys.hh>


#include <numeric/random/random.hh>

#include <core/io/ddg/PositionDdGInfo.hh>

#include <utility/exit.hh>
#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>
#include <utility/string_util.hh>

// C++ headers
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <string>

#include <utility/vector1.hh>




static numeric::random::RandomGenerator RG(86979347); // <- Magic number, do not change it!!!


namespace core {
namespace io {
namespace PositionDdGInfo{
  

  PositionDdGInfo::PositionDdGInfo(
                   core::Size seqpos,
                   core::chemical::AA wt_aa
                   )
  : seqpos_(seqpos),
  wt_aa_(wt_aa)
  {}
  
  PositionDdGInfo::~PositionDdGInfo(){}
  
  /// @details doesn't check whether something for this mutation already exists,
  /// so previously added stuff will be overwritten
  void
  PositionDdGInfo::add_mutation_ddG(
                    core::chemical::AA aa,
                    core::Real ddG
                    )
  {
    std::map< core::chemical::AA, core::Real >::iterator map_it = mutation_ddGs_.find( aa );
    if( map_it == mutation_ddGs_.end() ){
      mutation_ddGs_.insert( std::pair< core::chemical::AA, core::Real >(aa, ddG) );
    }
    else map_it->second = ddG;
  }
  
  const std::map< core::Size, PositionDdGInfoOP >
  read_ddg_predictions_file( std::string filename )
  {
    
    utility::io::izstream data( filename.c_str() );
    if ( !data ) utility_exit_with_message("File "+filename+"could not be opened.");
    std::map< core::Size, PositionDdGInfoOP > to_return;
    
    while( !data.eof() ) {
      
      std::string line;
      getline(data,line);
      utility::vector1< std::string > tokens; tokens.push_back("");
      tokens = utility::split(line);
      if( tokens.size() < 2 ) continue; //ddg predictions output file has empty lines :(
      std::string mutstring( tokens[2] );
      core::Size mutaaloc( mutstring.length() - 1 );
      std::string wt_res = mutstring.substr(0,1);
      std::string mut_res = mutstring.substr(mutaaloc, 1 );
      std::string string_seqpos( mutstring.substr(1, mutaaloc - 1 ) );
      core::Size mut_seqpos( atoi( string_seqpos.c_str() ));
      core::Real ddG( atof(tokens[3].c_str() ) );
      
      //std::cerr << "Reading ddg out file, at pos " << mut_seqpos << " wt " << wt_res << " turned to " << mut_res << " with ddG of " << ddG << std::endl;
      
      core::chemical::AA wt_aa( core::chemical::aa_from_oneletter_code( wt_res[0] ) );
      core::chemical::AA mut_aa( core::chemical::aa_from_oneletter_code( mut_res[0] ) );
      
      std::map< core::Size, PositionDdGInfoOP >::iterator muts_it( to_return.find( mut_seqpos ));
      if( muts_it == to_return.end() ){
        PositionDdGInfoOP pos_info = new PositionDdGInfo( mut_seqpos, wt_aa );
        to_return.insert( std::pair< core::Size, PositionDdGInfoOP >( mut_seqpos, pos_info ) );
        muts_it = to_return.find( mut_seqpos );
      }
      muts_it->second->add_mutation_ddG( mut_aa, ddG );
    }
    data.close();
    return to_return;
  }
  
} //namespace ddG
} //namespace io
} //namespace core