TorsionFeature.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.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
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/// @file protocols/comparative_modeling/TorsionFeature.cc
/// @brief
/// @author James Thompson

#include <core/types.hh>
#include <core/pose/Pose.hh>
// AUTO-REMOVED #include <utility/vector1.hh>

#include <protocols/comparative_modeling/features/ResidueFeature.hh>
#include <protocols/comparative_modeling/features/TorsionFeature.hh>
#include <protocols/comparative_modeling/features/ResidueFeature.fwd.hh>

#include <core/conformation/Residue.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace comparative_modeling {
namespace features {

TorsionFeature::TorsionFeature() :
  torsion_bin_( INVALID )
{}

TorsionFeature::TorsionFeature( TorsionFeature const & other ) :
  ResidueFeature(),
  torsion_bin_( other.torsion_bin() )
{}

TorsionFeature::TorsionFeature( TorsionBin bin ) :
  torsion_bin_( bin )
{}

utility::vector1< ResidueFeatureOP >
TorsionFeature::values_from_pose( core::pose::Pose & pose ) const {
  using core::Real;
  using utility::vector1;
  vector1< TorsionFeatureOP > features;

  for ( Size ii = 1; ii <= pose.total_residue(); ++ii ) {
    vector1< Real > const & torsions( pose.residue(ii).mainchain_torsions() );
    Real phi   = torsions[1];
    Real psi   = torsions[2];
    Real omega = torsions[3];
    features.push_back(
      new TorsionFeature( torsion2big_bin( phi, psi, omega ) )
    );
  }

  return features;
}

std::string TorsionFeature::type() const {
  return "torsion_bin";
}

ResidueFeatureOP TorsionFeature::clone() const {
  TorsionFeatureOP copy( new TorsionFeature( *this ) );
  return copy;
}

TorsionBin TorsionFeature::torsion_bin() const {
  return torsion_bin_;
}

TorsionBin
TorsionFeature::torsion2big_bin(
  core::Real const phi,
  core::Real const psi,
  core::Real const omega
)
{
  if ( std::abs( omega ) < 90.0 ) {
    return O; // cis-omega
  } else if ( phi >= 0.0 ) {
    if ( -100.0 < psi && psi <= 100.0 ) {
      return G; // alpha-L
    } else {
      return E; // E
    }
  } else {
    if ( -125.0 < psi && psi <= 50.0 ) {
      return A; // helical
    } else {
      return B; // extended
    }
  }
  return X;
}

} // features
} // comparative_modeling
} // protocols