SequenceCoupling1BDConstraint.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/constraints/SequenceCoupling1BDConstraint.cc
/// @brief  This is a constraint that refers to a core::sequence::SequenceProfile? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design). A note about the SequenceProfile::read_from_checkpoint function that is used to read in scores for amino acid types: the first line of the file will be ignored.
/// @author ashworth

#include <protocols/constraints_additional/SequenceCoupling1BDConstraint.hh>

#include <core/conformation/Residue.hh>
#include <core/sequence/SequenceProfile.hh>
#include <core/pose/Pose.hh>

#include <core/scoring/ScoreType.hh>

#include <basic/Tracer.hh>

#include <utility/file/file_sys_util.hh> // file_exists, create_directory

// AUTO-REMOVED #include <basic/options/option.hh>
// option key includes
// AUTO-REMOVED #include <basic/options/keys/in.OptionKeys.gen.hh>

//Auto Headers
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/constraints/XYZ_Func.hh>
#include <core/sequence/SequenceCoupling.hh>
#include <utility/vector1.hh>
#include <basic/options/keys/OptionKeys.hh>


namespace protocols {
namespace constraints_additional {

using namespace core;
using namespace chemical;
using namespace conformation;
using namespace basic::options;
using namespace scoring;
using namespace constraints;
using namespace sequence;

using basic::t_warning;
using basic::t_info;
using basic::t_debug;
using basic::t_trace;
static basic::Tracer TR("protocols.constraints_additional.SequenceCoupling1BDConstraint");

  SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint()
  :core::scoring::constraints::SequenceProfileConstraint( )
{}

  SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint(
    Pose const & pose,
    core::Size numpos,
    SequenceProfileCOP profile
    ):core::scoring::constraints::SequenceProfileConstraint(pose, numpos,profile)
{}

  SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint(
    core::Size numpos,
    SequenceProfileCOP profile
    ):core::scoring::constraints::SequenceProfileConstraint(numpos, profile)
{}
SequenceCoupling1BDConstraint::~SequenceCoupling1BDConstraint() {}

ConstraintOP
SequenceCoupling1BDConstraint::clone() const {
  return new SequenceCoupling1BDConstraint( *this );
}

///@details one line definition "SequenceProfile resindex profilefilename" (profilefilename can also be set to "none" in the constraints file, and specified by -in::file::pssm)
void
SequenceCoupling1BDConstraint::read_def(
  std::istream & is,
  Pose const & pose,
  FuncFactory const &
)
{
  Size residue_index(0);
  std::string profile_filename;

//  note: is >> "SequenceProfile" has already occured
  is >> residue_index >> profile_filename;

  TR(t_debug) << "reading: " << residue_index << " " << profile_filename << std::endl;
  if ( residue_index < 1 || residue_index > pose.total_residue() ) {
    std::cerr << "no such residue index " << residue_index << " in pose!)" << std::endl;
    utility_exit();
  }

  seqpos(residue_index);

  // figure out sequence profile filename
  using namespace utility::file;
  // if specified, verify file exists
  if ( profile_filename != "none" ) {
    if ( ! file_exists( profile_filename ) ) {
      utility_exit_with_message( "no such file " + profile_filename );
    }
  // if filename not specified, load from commandline option -pssm only if sequence_profile_ is NULL
  } else {
      utility_exit_with_message("\"none\" is not a valid value for -pssm in this context!");
  }

  // if filename is not "none" by this point, read it even if sequence_profile_ is not currently NULL
  if ( profile_filename != "none" ) {
    SequenceCouplingOP c = new SequenceCoupling;
    c->read_from_file( FileName(profile_filename) );
    set_sequence_profile(c);
  }

  // if sequence_profile_ is still NULL by this point, it is assumed that the user intended so

} // read_def

void
SequenceCoupling1BDConstraint::show( std::ostream & os ) const {
  os << "SequenceCoupling1BD Constraint at seqpos " << seqpos() << ": ";
  if ( ! sequence_profile() ) os << "(uninitialized sequence profile)";
  os << '\n';
}

// Calculates a score for this constraint using XYZ_Func, and puts the UNWEIGHTED score into
// emap. Although the current set of weights currently is provided, Constraint objects
// should put unweighted scores into emap.
void
SequenceCoupling1BDConstraint::score(
  XYZ_Func const & xyz_func,
  EnergyMap const & weights,
  EnergyMap & emap
) const
{
  if ( weights[ this->score_type() ] == 0 ) return; // what's the point?
  runtime_assert( sequence_profile() );

  chemical::AA aa( xyz_func.residue( seqpos()).type().aa() );
  utility::vector1< utility::vector1< Real > > const & profile( sequence_profile()->profile() );

  if ( seqpos() > profile.size() ) return; // safety/relevance check
  utility::vector1< Real > const & position_profile( profile[ seqpos() ] );
  if ( size_t(aa) > position_profile.size() ) return; // safety/relevance check
  Real const score( profile[seqpos()][aa] );
  TR(t_trace) << "seqpos " << seqpos() << " aa " << aa << " " << score << std::endl;
  emap[ this->score_type() ] += score;
}

void
SequenceCoupling1BDConstraint::fill_f1_f2(
  AtomID const & ,//atom,
  XYZ_Func const & ,//conformation,
  Vector & ,//f1,
  Vector & ,//f2,
  EnergyMap const & //weights
) const
{
  // Do nothing, as the value of this function doesn't change with respect to
  // the torsions.
}

} // namespace constraints_additional
} // namespace protocols