relax_main.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 relax_protocols
/// @brief protocols that are specific to relax
/// @detailed
/// @author Mike Tyka, Monica Berrondo
/// @author Roland A. Pache


#include <protocols/relax/RelaxProtocolBase.hh>

#include <core/pose/Pose.hh>
// AUTO-REMOVED #include <core/io/pdb/pose_io.hh>

// AUTO-REMOVED #include <basic/datacache/BasicDataCache.hh> //pba
// AUTO-REMOVED #include <core/pose/datacache/CacheableDataType.hh> //pba

// AUTO-REMOVED #include <core/scoring/ScoreFunction.hh>
// AUTO-REMOVED #include <core/scoring/ScoreFunctionFactory.hh>

#include <core/scoring/constraints/util.hh>
// AUTO-REMOVED #include <core/scoring/electron_density/util.hh>
#include <protocols/simple_moves/symmetry/SetupForSymmetryMover.hh>
#include <protocols/simple_moves/SuperimposeMover.hh>
#include <protocols/simple_moves/ConstraintSetMover.hh>


#include <basic/options/option.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>

#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/util.hh>

#include <protocols/moves/MoverContainer.hh>
// AUTO-REMOVED #include <protocols/electron_density/util.hh>

// ObjexxFCL Headers
#include <ObjexxFCL/string.functions.hh>

#include <basic/Tracer.hh>

#include <core/import_pose/import_pose.hh>
#include <protocols/electron_density/SetupForDensityScoringMover.hh>
#include <protocols/relax/util.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>

using basic::T;
using basic::Error;
using basic::Warning;

static basic::Tracer tr("protocols.relax");

using namespace core;
////////////////////////////////////////////////////////////////////////////////////////////////////

namespace protocols {
namespace relax {
////////////////////////////////////////////////////////////////////////////////////////////////////

int
Relax_main( bool ) {
  using namespace protocols::jobdist;
  using namespace basic::options;
  using namespace basic::options::OptionKeys;

  protocols::moves::MoverOP protocol = generate_relax_from_cmd();
  protocols::jd2::set_native_in_mover( *protocol );

  // add constraints from cmd line
  if ( option[ OptionKeys::constraints::cst_fa_file ].user() || option[ OptionKeys::constraints::cst_file ].user()) {
      protocols::moves::SequenceMoverOP seqmov = new protocols::moves::SequenceMover;
      protocols::simple_moves::ConstraintSetMoverOP loadCsts( new protocols::simple_moves::ConstraintSetMover );
            if (option[ OptionKeys::constraints::cst_fa_file ].user()) {
                loadCsts->constraint_file( core::scoring::constraints::get_cst_fa_file_option() );
            } else {
                loadCsts->constraint_file( core::scoring::constraints::get_cst_file_option() );
            }
            seqmov->add_mover( loadCsts );
      seqmov->add_mover( protocol );
      protocol = seqmov;
  }

  // set pose for density scoring if a map was input
  // (potentially) dock map into density
  if ( option[ OptionKeys::edensity::mapfile ].user() ) {
    protocols::moves::SequenceMoverOP seqmov = new protocols::moves::SequenceMover;
    seqmov->add_mover( new protocols::electron_density::SetupForDensityScoringMover );
    seqmov->add_mover( protocol );
    protocol = seqmov;
  }

  // setup symmetry mover ... this should happen _before_ SetupForDensityScoringMover
  //   to avoid adding extra VRTs
  if ( option[ OptionKeys::symmetry::symmetry_definition ].user() )  {
      protocols::moves::SequenceMoverOP seqmov = new protocols::moves::SequenceMover;
      seqmov->add_mover( new protocols::simple_moves::symmetry::SetupForSymmetryMover );
      seqmov->add_mover( protocol );
      protocol = seqmov;
  }

  // superimpose input model to the native structure or to a supplied PDB file
  if ( option[ OptionKeys::relax::superimpose_to_file ].user() ||
       option[ OptionKeys::relax::superimpose_to_native ].user()
   ) {
      core::pose::Pose ref_pose;
      std::string ref_filename;
      if(  option[ OptionKeys::relax::superimpose_to_file ].user() ) ref_filename = option[ basic::options::OptionKeys::relax::superimpose_to_file ]();
      if(  option[ OptionKeys::relax::superimpose_to_native ].user() ) ref_filename =  option[ basic::options::OptionKeys::in::file::native ]();
      core::import_pose::pose_from_pdb( ref_pose, ref_filename );
      protocols::moves::SequenceMoverOP seqmov = new protocols::moves::SequenceMover;
      protocols::simple_moves::SuperimposeMoverOP sm  =  new protocols::simple_moves::SuperimposeMover;
      sm->set_reference_pose( ref_pose );
      seqmov->add_mover( sm );
      seqmov->add_mover( protocol );
      protocol = seqmov;
  }

  protocols::jd2::JobDistributor::get_instance()->go( protocol );

  return 0;
}



}
}