LoopBuild.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.

/// @brief demo program for implementing loop relax + FA relax
/// @author Srivatsan Raman
/// @author James Thompson
/// @author Mike Tyka
/// @author Daniel J. Mandell

//unit headers
#include <protocols/loop_build/LoopBuild.hh>
#include <protocols/loop_build/LoopBuildMover.hh>

// basic headers
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>

#include <basic/Tracer.hh>


#include <core/chemical/ChemicalManager.hh>
#include <core/fragment/FragSet.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/types.hh>
#include <core/kinematics/Jump.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/electron_density/util.hh>
#include <core/scoring/ScoreFunction.hh>

#include <protocols/comparative_modeling/LoopRelaxMover.hh>
#include <protocols/electron_density/SetupForDensityScoringMover.hh>
#include <protocols/evaluation/EvaluatorFactory.hh>
#include <protocols/evaluation/PoseEvaluator.hh>
#include <protocols/evaluation/util.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/util.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/LoopsFileIO.hh>
#include <protocols/moves/MoverStatus.hh>
#include <protocols/simple_filters/RmsdEvaluator.hh>

#include <core/io/silent/silent.fwd.hh>
#include <core/io/silent/SilentStructFactory.hh>

#include <utility/vector1.hh>
#include <utility/exit.hh>

#include <numeric/random/random.hh>

#if defined(WIN32) || defined(__CYGWIN__)
  #include <ctime>
#endif

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

namespace protocols {
namespace loop_build {

int
LoopBuild_main( bool  ) {
  basic::Tracer TR("protocols.loop_build.LoopBuild");

  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  using namespace core::scoring;
  using namespace core::scoring::constraints;
  using namespace core::chemical;
  using namespace core::id;
  using namespace jobdist;
  
  //using namespace basic::resource_manager;

  std::string remodel            ( option[ OptionKeys::loops::remodel ]() );
  std::string const intermedrelax( option[ OptionKeys::loops::intermedrelax ]() );
  std::string const refine       ( option[ OptionKeys::loops::refine ]() );
  std::string const relax        ( option[ OptionKeys::loops::relax ]() );
  //bool const keep_time      ( option[ OptionKeys::loops::timer ]() );

  TR << "==== Loop protocol: ================================================="
    << std::endl;
  TR << " remodel        " << remodel        << std::endl;
  TR << " intermedrelax  " << intermedrelax  << std::endl;
  TR << " refine         " << refine         << std::endl;
  TR << " relax          " << relax          << std::endl;


  // fragment initialization
  // is there any way to clean this up? This logic is very convoluted.
  utility::vector1< core::fragment::FragSetOP > frag_libs;
  if ( remodel == "perturb_ccd" || remodel == "quick_ccd" ||
      remodel == "quick_ccd_moves" || remodel == "old_loop_relax" ||
      remodel == "sdwindow" ||
      option[ OptionKeys::loops::build_initial ].value() ||
      ( option[ OptionKeys::loops::frag_files ].user()
          && (refine == "refine_ccd" || intermedrelax != "no" || relax != "no")
      )
  ) {
    // these protocols optionally take a fragment set .. only load if
    // specified
    loops::read_loop_fragments( frag_libs );
  }

  //setup of looprelax_mover
  comparative_modeling::LoopRelaxMover looprelax_mover;
  looprelax_mover.frag_libs( frag_libs );
  looprelax_mover.relax( relax );
  looprelax_mover.refine( refine );
  looprelax_mover.remodel( remodel );
  looprelax_mover.intermedrelax( intermedrelax );

  LoopBuildMoverOP loopbuild_mover = new protocols::loop_build::LoopBuildMover(looprelax_mover);


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

  return 0;
} // Looprelax_main

} // namespace loop_build
} // namespace protocols