SymPackRotamersMover.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:
//
// This file is part of the Rosetta software suite and is made available under license.
// The Rosetta software is developed by the contributing members of the Rosetta Commons consortium.
// (C) 199x-2009 Rosetta Commons participating institutions and developers.
// For more information, see http://www.rosettacommons.org/.

/// @file
/// @brief
/// @author Ingemar Andre

// Unit headers
#include <protocols/simple_moves/symmetry/SymPackRotamersMover.hh>
#include <protocols/simple_moves/symmetry/SymPackRotamersMoverCreator.hh>

// Project headers
#include <core/pack/interaction_graph/InteractionGraphBase.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_set/RotamerSets.hh>
#include <core/pack/rotamer_set/symmetry/SymmetricRotamerSets.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/SymmetryInfo.fwd.hh>

#include <core/pose/symmetry/util.hh>
// AUTO-REMOVED #include <core/conformation/symmetry/util.hh>

// AUTO-REMOVED #include <protocols/moves/DataMap.hh>
// AUTO-REMOVED #include <protocols/rosetta_scripts/util.hh>
#include <utility/tag/Tag.hh>

#include <basic/Tracer.hh>
using basic::T;
using basic::Error;
using basic::Warning;

static basic::Tracer TR("protocols.simple_moves.symmetry.SymPackRotamersMover");

// Utility Headers
#include <utility/exit.hh>
#include <utility/vector0.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace simple_moves {
namespace symmetry {

using core::conformation::symmetry::SymmetricConformation;
using core::conformation::symmetry::SymmetryInfoCOP;

using namespace core;
  using namespace pack;
    using namespace task;
      using namespace operation;
  using namespace scoring;

// creator
std::string
SymPackRotamersMoverCreator::keyname() const {
  return SymPackRotamersMoverCreator::mover_name();
}

protocols::moves::MoverOP
SymPackRotamersMoverCreator::create_mover() const {
  return new SymPackRotamersMover;
}

std::string
SymPackRotamersMoverCreator::mover_name() {
  return "SymPackRotamersMover";
}

//////////////////////////
/// PackRotamersMover

SymPackRotamersMover::SymPackRotamersMover()
  : protocols::simple_moves::PackRotamersMover(),
    sym_rotamer_sets_( new rotamer_set::symmetry::SymmetricRotamerSets() ),
    symmetric_ig_(0)
{}

  // constructors with arguments
SymPackRotamersMover::SymPackRotamersMover(
  ScoreFunctionCOP scorefxn,
  task::PackerTaskCOP task,
  Size nloop
) : protocols::simple_moves::PackRotamersMover( scorefxn, task, nloop ),
    sym_rotamer_sets_( new rotamer_set::symmetry::SymmetricRotamerSets() ),
    symmetric_ig_(0)
{}

SymPackRotamersMover::~SymPackRotamersMover(){}

SymPackRotamersMover::SymPackRotamersMover( PackRotamersMover const & other )
  : protocols::simple_moves::PackRotamersMover( other )
{
  sym_rotamer_sets_ = new rotamer_set::symmetry::SymmetricRotamerSets();

}

/*void
SymPackRotamersMover::apply( pose::Pose & pose )
{
  // jec update_residue_neighbors() required to update EnergyGraph (ensures graph_state == GOOD) when calling Interface.cc
  pose.update_residue_neighbors();
  // guarantee of valid ScoreFunction and PackerTask postponed until now

//  else assert( task_is_valid( pose ) );

  // get rotamers, energies
  this->setup( pose );

  this->run( pose );

}*/

std::string
SymPackRotamersMover::get_name() const {
  return "SymPackRotamersMover";
}

void SymPackRotamersMover::setup( pose::Pose & pose )
{

  // jec update_residue_neighbors() required to update EnergyGraph (ensures graph_state == GOOD) when calling Interface.cc
  pose.update_residue_neighbors();
  // guarantee of valid ScoreFunction and PackerTask postponed until now
  if ( score_function() == 0 ) {
    Warning() << "undefined ScoreFunction -- creating a default one" << std::endl;
    ScoreFunctionCOP scfx ( ScoreFunctionFactory::create_score_function( STANDARD_WTS ) );
    score_function( scfx );
  }

   // if present, task_factory_ always overrides/regenerates task_
    if ( task() != 0 ) {
      symmetric_task_ = (task())->clone();
    }
    if ( task_factory() != 0 ) {
      symmetric_task_ = task_factory()->create_task_and_apply_taskoperations( pose );
    } else if ( task() == 0 ) {
    Warning() << "undefined PackerTask -- creating a default one" << std::endl;
    symmetric_task_ = core::pack::task::TaskFactory::create_packer_task( pose );
  }
  // in case PackerTask was not generated locally, verify compatibility with pose
  //else runtime_assert( task_is_valid( pose ) );
  make_symmetric_task( pose, symmetric_task_ );

  symmetric_pack_rotamers_setup( pose, *( score_function() ), symmetric_task_, sym_rotamer_sets_, symmetric_ig_ );

  setup_IG_res_res_weights( pose, symmetric_task_, sym_rotamer_sets_, symmetric_ig_ );
}

core::PackerEnergy SymPackRotamersMover::run( pose::Pose & pose, utility::vector0< int > rot_to_pack ) const
{
  return symmetric_pack_rotamers_run( pose, symmetric_task_, sym_rotamer_sets_, symmetric_ig_, rot_to_pack );
}

void
SymPackRotamersMover::make_symmetric_task(
  pose::Pose & pose,
  task::PackerTaskOP task
)
{
  assert( pose::symmetry::is_symmetric( pose ) );
  if( task->symmetrize_by_union() || task->symmetrize_by_intersection() ) return; // new machinery

  SymmetricConformation & SymmConf (
    dynamic_cast<SymmetricConformation &> ( pose.conformation()) );
  core::conformation::symmetry::SymmetryInfoCOP symm_info( SymmConf.Symmetry_Info() );

  utility::vector1<bool> allow_repacked( pose.total_residue(), false );
  for (Size res=1; res <= pose.total_residue(); ++res ) {
    if ( pose.residue(res).aa() != core::chemical::aa_vrt && symm_info->fa_is_independent(res) ) {
      allow_repacked.at(res) = true;
    }
  }
  task->restrict_to_residues( allow_repacked );
}

protocols::moves::MoverOP SymPackRotamersMover::clone() const { return new  SymPackRotamersMover( *this ); }
protocols::moves::MoverOP SymPackRotamersMover::fresh_instance() const { return new  SymPackRotamersMover; }

///@brief parse XML (specifically in the context of the parser/scripting scheme)
void
SymPackRotamersMover::parse_my_tag(
  TagPtr const tag,
  protocols::moves::DataMap & data,
  Filters_map const &fm,
  protocols::moves::Movers_map const &mm,
  Pose const &pose ) 
{
  PackRotamersMover::parse_my_tag( tag,data,fm,mm,pose );
}

void SymPackRotamersMover::parse_def( utility::lua::LuaObject const & def,
    utility::lua::LuaObject const & score_fxns,
    utility::lua::LuaObject const & tasks,
    protocols::moves::MoverCacheSP cache ){
  PackRotamersMover::parse_def( def, score_fxns, tasks, cache);
}

}
} // moves
} // protocols