SurfVolEnergy.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/packing/SurfVolEnergy.cc
/// @brief  Packing Score
/// @author Will Sheffler


//Unit headers
#include <core/scoring/packing/SurfVolEnergy.hh>
#include <core/scoring/packing/SurfVolEnergyCreator.hh>

// AUTO-REMOVED #include <core/scoring/packing/PoseBalls.hh>

#include <core/scoring/packing/surf_vol.hh>

//Package headers

//#include <core/scoring/ScoringManager.hh>
// AUTO-REMOVED #include <core/scoring/EnergyGraph.hh>
// AUTO-REMOVED #include <core/scoring/rms_util.hh>
#include <core/pose/Pose.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <core/pose/datacache/CacheableDataType.hh>
// AUTO-REMOVED #include <core/io/pdb/pose_io.hh>
#include <core/id/CacheableAtomID_MapVector.hh>
// AUTO-REMOVED #include <basic/options/option.hh>

// AUTO-REMOVED #include <core/scoring/packing/compute_holes_score_res.hh>

// AUTO-REMOVED #include <basic/prof.hh>

//numeric headers
#include <numeric/numeric.functions.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
// AUTO-REMOVED #include <numeric/xyz.functions.hh>

//utility headers
// AUTO-REMOVED #include <utility/vector1.hh>
#include <utility/exit.hh>

//C++ headers
#include <iostream>

#include <core/chemical/AtomType.hh>
#include <core/pose/util.hh>
#include <core/scoring/EnergyMap.hh>
#include <utility/vector1.hh>

//Auto Headers
#include <core/pose/util.tmpl.hh>

namespace core {
namespace scoring {
namespace packing {


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

ScoreTypes
SurfVolEnergyCreator::score_types_for_method() const {
  ScoreTypes sts;
  // sts.push_back( dab_sasa );
  sts.push_back( dab_sev );
  return sts;
}


//////////////////////////////////////////////////////
//@brief
//////////////////////////////////////////////////////
SurfVolEnergy::SurfVolEnergy() :
  parent( new SurfVolEnergyCreator )
{}


//////////////////////////////////////////////////////
//@brief
//////////////////////////////////////////////////////
void
SurfVolEnergy::finalize_total_energy(
  pose::Pose & pose,
  ScoreFunction const &,
  EnergyMap & totals
) const
{
  SurfVol sv = get_surf_vol(pose,1.4);
  totals[ dab_sasa ] = sv.tot_surf;
  totals[ dab_sev  ] = sv.tot_vol;
}

void
SurfVolEnergy::setup_for_derivatives(
  pose::Pose & pose,
  ScoreFunction const &
) const {
  std::cerr << "SurfVolEnergy::setup_for_derivatives" << std::endl;

  //using namespace core::pose::datacache::CacheableDataType;
  using namespace basic::datacache;
  using namespace id;
  using namespace numeric;

  if( !pose.data().has( core::pose::datacache::CacheableDataType::DAB_SASA_POSE_INFO ) ) {
    pose.data().set( core::pose::datacache::CacheableDataType::DAB_SASA_POSE_INFO, new CacheableAtomID_MapVector );
    pose.data().set(  core::pose::datacache::CacheableDataType::DAB_SEV_POSE_INFO, new CacheableAtomID_MapVector );
  }

  CacheableDataOP dat1( pose.data().get_ptr( core::pose::datacache::CacheableDataType::DAB_SASA_POSE_INFO ) );
  CacheableAtomID_MapVectorOP cachemap1 = static_cast< CacheableAtomID_MapVector * >(dat1());
  AtomID_Map<xyzVector<Real> > & sasa_derivs(cachemap1->map());

  CacheableDataOP dat2( pose.data().get_ptr( core::pose::datacache::CacheableDataType::DAB_SASA_POSE_INFO ) );
  CacheableAtomID_MapVectorOP cachemap2 = static_cast< CacheableAtomID_MapVector * >(dat2());
  AtomID_Map<xyzVector<Real> > & sev_derivs(cachemap2->map());

  SurfVolDeriv svd = get_surf_vol_deriv( pose, 1.4 );

  core::pose::initialize_atomid_map_heavy_only(sasa_derivs,pose);
  core::pose::initialize_atomid_map_heavy_only( sev_derivs,pose);

  for( Size ir = 1; ir <= sasa_derivs.size(); ir++ ) {
    for( Size ia = 1; ia <= sasa_derivs.n_atom(ir); ia++ ) {
      AtomID const i(ia,ir);
      sasa_derivs[i] = svd.dsurf[i];
       sev_derivs[i] = svd. dvol[i];
    }
  }

}


void
SurfVolEnergy::eval_atom_derivative(
  id::AtomID const & aid,
  pose::Pose const & pose,
  kinematics::DomainMap const &,
  ScoreFunction const &,
  EnergyMap const & weights,
  Vector & F1,
  Vector & F2
) const
{
  // std::cerr << "SurfVolEnergy::eval_atom_derivative " << aid << std::endl;
  //using namespace core::pose::datacache::CacheableDataType;
  using namespace basic::datacache;
  using namespace id;
  using namespace numeric;

  // CacheableDataCOP dat( pose.data().get_const_ptr( core::pose::datacache::CacheableDataType::HOLES_POSE_INFO ) );
  // CacheableAtomID_MapVector const *cachemap = (CacheableAtomID_MapVector const *)dat();
  // AtomID_Map<xyzVector<Real> > const & derivs(cachemap->map());

  CacheableDataCOP dat1( pose.data().get_const_ptr( core::pose::datacache::CacheableDataType::DAB_SASA_POSE_INFO ) );
  CacheableAtomID_MapVectorCOP cachemap1 = static_cast< CacheableAtomID_MapVector const * > (dat1());
  AtomID_Map<xyzVector<Real> > const & sasa_derivs(cachemap1->map());

  CacheableDataCOP dat2( pose.data().get_const_ptr( core::pose::datacache::CacheableDataType::DAB_SASA_POSE_INFO ) );
  CacheableAtomID_MapVectorCOP cachemap2 = static_cast< CacheableAtomID_MapVector const * >(dat2());
  AtomID_Map<xyzVector<Real> > const & sev_derivs(cachemap2->map());

  if( aid.rsd() > sasa_derivs.n_residue() || aid.atomno() > sasa_derivs.n_atom(aid.rsd()) ) {
    return;
  }
  // std::cerr << "eval_atom_derivative " << aid << " " << derivs[aid].x() << " " << derivs[aid].y() << " " << derivs[aid].z() << std::endl;
  // F2 += weights * derivs[aid];
  // F1 += weights * derivs[aid].cross(xyzVector<Real>(1,0,0));

  {
      numeric::xyzVector<core::Real> atom_x = pose.xyz(aid);
    numeric::xyzVector<core::Real> const f2( sasa_derivs[aid] );
    numeric::xyzVector<core::Real> const atom_y = atom_x - f2;   // a "fake" atom in the direcion of the gradient
    numeric::xyzVector<core::Real> const f1( atom_x.cross( atom_y ) );
    F1 += weights[ dab_sasa ] * f1;
    F2 += weights[ dab_sasa ] * f2;
  }
  {
      numeric::xyzVector<core::Real> atom_x = pose.xyz(aid);
    numeric::xyzVector<core::Real> const f2( sev_derivs[aid] );
    numeric::xyzVector<core::Real> const atom_y = atom_x - f2;   // a "fake" atom in the direcion of the gradient
    numeric::xyzVector<core::Real> const f1( atom_x.cross( atom_y ) );
    F1 += weights[ dab_sev ] * f1;
    F2 += weights[ dab_sev ] * f2;
  }

}
core::Size
SurfVolEnergy::version() const
{
  return 1; // Initial versioning
}




} // packing
} // scoring
} // core