SequenceDependentRefEnergy.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   core/scoring/methods/SequenceDependentRefEnergy.hh
/// @brief  Reference energy method implementation
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com)

// Unit headers
#include <core/scoring/methods/SequenceDependentRefEnergy.hh>
#include <core/scoring/methods/SequenceDependentRefEnergyCreator.hh>

// Package headers
#include <core/scoring/EnergyMap.hh>
// AUTO-REMOVED #include <core/scoring/methods/EnergyMethodOptions.hh>

// Project headers
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>

// C++ Headers
#include <string>
#include <vector>

// Utility Headers
#include <utility/io/izstream.hh>
#include <utility/string_util.hh>

#include <basic/options/option.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>

#include <utility/vector1.hh>


namespace core {
namespace scoring {
namespace methods {


/// @details This must return a fresh instance of the SequenceDependentRefEnergy class,
/// never an instance already in use
methods::EnergyMethodOP
SequenceDependentRefEnergyCreator::create_energy_method(
  methods::EnergyMethodOptions const &
) const {
  return new SequenceDependentRefEnergy;
}

ScoreTypes
SequenceDependentRefEnergyCreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( seqdep_ref );
  return sts;
}



SequenceDependentRefEnergy::SequenceDependentRefEnergy() :
  parent( new SequenceDependentRefEnergyCreator )
{
  read_energy_weight_table();
}

SequenceDependentRefEnergy::SequenceDependentRefEnergy( utility::vector1< utility::vector1< Real > > const & aa_seq_weights_in ):
  parent( new SequenceDependentRefEnergyCreator )
{
  aa_seq_weights_.clear();
  for ( utility::vector1<utility::vector1< Real > >::const_iterator it = aa_seq_weights_in.begin(); it != aa_seq_weights_in.end(); ++it ) {
      aa_seq_weights_.push_back(*it);
  }
}

SequenceDependentRefEnergy::~SequenceDependentRefEnergy() {}



void SequenceDependentRefEnergy::read_energy_weight_table() {

  using namespace basic::options;

  std::cout << "JL checking for SequenceDependentRefEnergy weights" << std::endl;

  if ( option[ OptionKeys::score::seqdep_refene_fname ].user() ) {
    std::string const in_fname( option[ OptionKeys::score::seqdep_refene_fname ] );
    std::cout << "JL reading SequenceDependentRefEnergy weights from " << in_fname << std::endl;
    utility::io::izstream in_stream( in_fname );
    if (!in_stream.good()) {
      utility_exit_with_message( "[ERROR] Error opening SequenceDependentRefEnergy file" );
    }
    std::string line;
    core::Size seqpos(0);
    while( getline( in_stream, line) ) {
      ++seqpos;
      std::cout << "JL got " << seqpos << " line " << line << std::endl;
      utility::vector1< std::string > const tokens ( utility::split( line ) );
      utility::vector1< Real > energies;
      for ( utility::vector1< std::string >::const_iterator it = tokens.begin(); it != tokens.end(); ++it ) {
        energies.push_back( atof(it->c_str()) );
      }
      aa_seq_weights_.push_back(energies);
    }

    if ( option[ OptionKeys::score::secondary_seqdep_refene_fname ].user() ) {
      std::string const in_fname( option[ OptionKeys::score::secondary_seqdep_refene_fname ] );
      std::cout << "JL reading SECONDARY SequenceDependentRefEnergy weights from " << in_fname << std::endl;
      utility::io::izstream in_stream( in_fname );
      if (!in_stream.good()) {
        utility_exit_with_message( "[ERROR] Error opening SECONDARY SequenceDependentRefEnergy file" );
      }
      std::string line;
      core::Size seqpos(0);
      while( getline( in_stream, line) ) {
        ++seqpos;
        std::cout << "JL got " << seqpos << " line " << line << std::endl;
        utility::vector1< std::string > const tokens ( utility::split( line ) );
        utility::vector1< Real > energies;
        for ( utility::vector1< std::string >::const_iterator it = tokens.begin(); it != tokens.end(); ++it ) {
          energies.push_back( atof(it->c_str()) );
        }
        core::Size aa(0);
        for ( utility::vector1< Real >::const_iterator it = energies.begin(); it != energies.end(); ++it ) {
          ++aa;
          (aa_seq_weights_[seqpos])[ aa ] += *it;
        }
      }
    }

  }

}


EnergyMethodOP
SequenceDependentRefEnergy::clone() const
{
  return new SequenceDependentRefEnergy( aa_seq_weights_ );
}


void
SequenceDependentRefEnergy::residue_energy(
  conformation::Residue const & rsd,
  pose::Pose const &,
  EnergyMap & emap
) const
{
  using namespace chemical;

  if ( aa_seq_weights_.empty() ) return;

  AA const & aa( rsd.aa() );
  Size const & seqpos( rsd.seqpos() );
  if ( seqpos > aa_seq_weights_.size() ) return;

  Real const ene = (aa_seq_weights_[seqpos])[ aa ];
  emap[ seqdep_ref ] += ene;
  //  std::cout << "JL at seqpos " << seqpos << " for aa " << aa << " using seqdep_ref " <<  ene << std::endl;

  return;

}


Real
SequenceDependentRefEnergy::eval_dof_derivative(
  id::DOF_ID const &,
  id::TorsionID const &,
  pose::Pose const &,
  ScoreFunction const &,
  EnergyMap const &
) const
{
  return 0.0;
}

/// @brief SequenceDependentRefEnergy is context independent; indicates that no
/// context graphs are required
void
SequenceDependentRefEnergy::indicate_required_context_graphs( utility::vector1< bool > & ) const
{}
core::Size
SequenceDependentRefEnergy::version() const
{
  return 1; // Initial versioning
}
} // methods
} // scoring
} // core