MembraneEnvEnergy.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/EnvPairEnergy.cc
/// @brief  Statistically derived rotamer pair potential class implementation
/// @author Phil Bradley
/// @author Andrew Leaver-Fay


// Unit headers
// AUTO-REMOVED #include <core/scoring/methods/util.hh>
#include <core/scoring/methods/MembraneEnvEnergy.hh>
#include <core/scoring/methods/MembraneEnvEnergyCreator.hh>
// AUTO-REMOVED #include <basic/MetricValue.hh>
// Package headers
#include <core/scoring/MembranePotential.hh>
#include <core/scoring/MembraneTopology.hh>
#include <core/scoring/ScoringManager.hh>
// AUTO-REMOVED #include <core/scoring/EnergyGraph.hh>

// Project headers
#include <core/pose/Pose.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <core/conformation/Residue.hh>

#include <core/scoring/EnergyMap.hh>
#include <utility/vector1.hh>


// Utility headers

// C++

namespace core {
namespace scoring {
namespace methods {


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

ScoreTypes
MembraneEnvEnergyCreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( Menv );
  return sts;
}


/// c-tor
MembraneEnvEnergy::MembraneEnvEnergy() :
  parent( new MembraneEnvEnergyCreator ),
  potential_( ScoringManager::get_instance()->get_MembranePotential() )
{}


/// clone
EnergyMethodOP
MembraneEnvEnergy::clone() const
{
  return new MembraneEnvEnergy;
}


/////////////////////////////////////////////////////////////////////////////
// scoring
/////////////////////////////////////////////////////////////////////////////


///
void
MembraneEnvEnergy::setup_for_scoring( pose::Pose & pose, ScoreFunction const & ) const
{
  // compute interpolated number of neighbors at various distance cutoffs
  pose.update_residue_neighbors();
  potential_.compute_centroid_environment( pose );
  potential_.compute_membrane_embedding( pose );

}

void
MembraneEnvEnergy::setup_for_derivatives( pose::Pose & pose, ScoreFunction const & sf) const
{
  setup_for_scoring(pose,sf);
}


///////////////////////////////////////
//
// ENV SCORE
void
MembraneEnvEnergy::residue_energy(
  conformation::Residue const & rsd,
  pose::Pose const & pose,
  EnergyMap & emap
) const
{
  Real env_score( 0.0 ); // cb_score( 0.0 ); //, cb_score12( 0.0 ), cb_score( 0.0 );
//  basic::MetricValue<core::Vector> depth_vector;
//  pose.metric("MCN","depth",depth_vector);
//  Size pos=rsd.seqpos();
//  Real depth=depth_vector[ rsd.seqpos() ];
//  Real depth=30;
//  std::cout << rsd.seqpos() << "\n "; << depth << "\n";
  //std::cout << pos << "\n";
  if ( rsd.aa() == core::chemical::aa_vrt ) return;
  if(MembraneTopology_from_pose( pose ).allow_scoring(rsd.seqpos()))
  {
    potential_.evaluate_env( pose, rsd, env_score);
  //potential_.evaluate_cbeta( pose, rsd,cb_score);
  }
//  env_score *= 0.5;2.019;
  //cb_score = 2.667 * ( cb_score ) * 0.3;
//bw is this something we like?
  //core::Real rsd_wt = get_residue_weight_by_ss( pose.conformation().secstruct( rsd.seqpos() ) );

    emap[ Menv ] += env_score;// * rsd_wt;
  //emap[ Mcbeta ] = cb_score;// * rsd_wt;

} // residue_energy

void
MembraneEnvEnergy::finalize_total_energy(
  pose::Pose & pose,
  ScoreFunction const &,
  EnergyMap &
) const
{
  /*
  std::cout << "BEFORE emap[ Menv ] " << emap[ Menv ] << std::endl;
  if(potential_.Menv_penalties()) //bw quick hack before putting them as individual scoring terms....
  {
    Real tm_projection(0);
    Real hbond_pen(0);
    Real termini_pen(0);
    potential_.tm_projection_penalty(pose,tm_projection);
    potential_.hbond_penalty(pose,hbond_pen);
    potential_.termini_penalty(pose,termini_pen);
    emap[ Menv ]+=(tm_projection+hbond_pen+termini_pen+10);

    std::cout << "Menv_penalties (tm_projection+hbond_pen+termini_pen+10) " << tm_projection << " " << hbond_pen << " " << termini_pen << std::endl;
  }
  std::cout << "AFTER emap[ Menv ] " << emap[ Menv ] << std::endl;
   */
  potential_.finalize( pose );
  //std::cout << "AFTER2 emap[ Menv ] " << emap[ Menv ] << std::endl;
}
MembraneTopology const &
MembraneEnvEnergy::MembraneTopology_from_pose( pose::Pose const & pose ) const
{
  //using core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY;
  return *( static_cast< MembraneTopology const * >( pose.data().get_const_ptr( core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY )() ));
}
core::Size
MembraneEnvEnergy::version() const
{
  return 1; // Initial versioning
}

}
}
}