CanonicalSamplingApplication.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
/// @brief
/// @author
/// @author

//graphix
#include <protocols/viewer/viewers.hh>

//
#include <protocols/canonical_sampling/CanonicalSamplingApplication.hh>
//#include <devel/Gaussian/BBGaussianMover.hh>
#include <protocols/simple_moves/BBGaussianMover.hh>
#include <protocols/backrub/BackrubMover.hh>
#include <protocols/simple_moves/BBConRotMover.hh>
#include <core/kinematics/MoveMap.hh>

#include <protocols/jd2/NoOutputJobOutputter.hh>
#include <protocols/jd2/JobDistributor.hh>
// AUTO-REMOVED #include <protocols/jd2/MPIFileBufJobDistributor.hh>
#include <protocols/canonical_sampling/CanonicalSamplingMover.hh>
#include <protocols/canonical_sampling/CanonicalSamplingMover.fwd.hh>
#include <protocols/canonical_sampling/mc_convergence_checks/Pool_ConvergenceCheck.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMCMover.hh>

// AUTO-REMOVED #include <protocols/canonical_sampling/mc_convergence_checks/MPIHPool_ConvergenceCheck.hh>

// AUTO-REMOVED #include <core/pack/task/ResfileReader.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>

#include <core/pack/task/TaskFactory.hh>
// AUTO-REMOVED #include <core/pack/task/PackerTask_.hh>
#include <core/pack/task/operation/TaskOperations.hh>

#include <basic/options/option.hh>
// AUTO-REMOVED #include <basic/options/after_opts.hh>
// AUTO-REMOVED #include <basic/options/option_macros.hh>
#include <basic/options/keys/mc.OptionKeys.gen.hh>
// AUTO-REMOVED #include <basic/options/keys/bbg.OptionKeys.gen.hh>
// AUTO-REMOVED #include <basic/options/keys/backrub.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
// AUTO-REMOVED #include <basic/options/keys/cluster.OptionKeys.gen.hh>
#include <basic/options/keys/canonical_sampling.OptionKeys.gen.hh>
// AUTO-REMOVED #include <basic/prof.hh>
#include <basic/Tracer.hh>
#include <core/scoring/mm/MMBondAngleResidueTypeParamSet.hh>

#include <core/chemical/ResidueType.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>




#ifdef USEMPI
#include <mpi.h>
#endif



using namespace basic::options;



namespace protocols {
namespace canonical_sampling {

int
canonical_sampling_main(){

  basic::Tracer tr("src.apps.pilot.liz.test_canonical_mover");

  using namespace protocols::moves;
  using namespace basic;
  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  using namespace core::pack::task;
  
  if( tr.visible() ){
    tr << "resetting clock" << std::endl;
  }
  //basic::prof_reset();

  
  //bool MPI_synchronize_pools = options::option[options::OptionKeys::canonical_sampling::probabilities::MPI_sync_pools];
  bool MPI_bcast = options::option[ options::OptionKeys::canonical_sampling::probabilities::MPI_bcast ];
  bool use_fast_sc_moves = options::option[ options::OptionKeys::canonical_sampling::probabilities::fast_sc_moves ];
  bool no_jd2_output = options::option[options::OptionKeys::canonical_sampling::probabilities::no_jd2_output];
  bool use_hierarchy = options::option[options::OptionKeys::canonical_sampling::probabilities::use_hierarchical_clustering];

  //get rid of unused variable warning
  if( MPI_bcast ) {}
  if( use_hierarchy ) {}

  core::scoring::ScoreFunctionOP sfxn = core::scoring::getScoreFunction();
  //protocols::canonical_sampling::CanonicalSamplingMoverOP csm(new protocols::canonical_sampling::CanonicalSamplingMover(sfxn,pool_ptr,1000));
  protocols::canonical_sampling::CanonicalSamplingMoverOP csm(new CanonicalSamplingMover);
    csm->set_scorefunction(sfxn);

  if( !use_fast_sc_moves ){
    //setup sidechain mover
    protocols::simple_moves::sidechain_moves::SidechainMoverOP scm(new protocols::simple_moves::sidechain_moves::SidechainMover());
    TaskFactoryOP main_task_factory = new TaskFactory;
    operation::RestrictToRepackingOP rtrop = new operation::RestrictToRepacking;
    main_task_factory->push_back( rtrop );
    main_task_factory->push_back( new operation::ReadResfile );
    scm->set_task_factory(main_task_factory);

    if( options::option[ OptionKeys::canonical_sampling::probabilities::sc_prob_uniform ].user() ) {
      scm->set_prob_uniform(options::option[ options::OptionKeys::canonical_sampling::probabilities::sc_prob_uniform ]);
    }
    if( options::option[ options::OptionKeys::canonical_sampling::probabilities::sc_prob_withinrot ].user() ){
      scm->set_prob_withinrot(options::option[ options::OptionKeys::canonical_sampling::probabilities::sc_prob_withinrot ]);
    }
    if( options::option[ options::OptionKeys::canonical_sampling::probabilities::sc_prob_perturbcurrent ].user() ){
      scm->set_prob_random_pert_current(options::option[ options::OptionKeys::canonical_sampling::probabilities::sc_prob_perturbcurrent ]);
    }
    scm->set_preserve_detailed_balance( csm->detailed_balance() );

    csm->add_mover(scm,options::option[options::OptionKeys::canonical_sampling::probabilities::sc]);
  }else{
    //setup sidechain mover
    protocols::simple_moves::sidechain_moves::SidechainMCMoverOP scm(new protocols::simple_moves::sidechain_moves::SidechainMCMover());
    TaskFactoryOP main_task_factory = new TaskFactory;
    operation::RestrictToRepackingOP rtrop = new operation::RestrictToRepacking;
    main_task_factory->push_back( rtrop );
    scm->set_temperature( csm->get_temp() );
    scm->set_scorefunction(  *sfxn );
    scm->setup( sfxn );
    scm->set_task_factory(main_task_factory);
    scm->set_prob_uniform(options::option[ options::OptionKeys::canonical_sampling::probabilities::sc_prob_uniform ]);
    scm->set_prob_withinrot(options::option[ options::OptionKeys::canonical_sampling::probabilities::sc_prob_withinrot ]);
    scm->set_prob_random_pert_current(options::option[ options::OptionKeys::canonical_sampling::probabilities::sc_prob_perturbcurrent ]);
    scm->set_preserve_detailed_balance( csm->detailed_balance() );
    scm->set_ntrials( options::option[ options::OptionKeys::canonical_sampling::probabilities::fast_sc_moves_ntrials ] );

    csm->add_mover(scm,options::option[options::OptionKeys::canonical_sampling::probabilities::sc]);

  }
  //add move-map to bbg-mover
  core::kinematics::MoveMapOP movemap = new core::kinematics::MoveMap;
  if( options::option[in::file::movemap].user() ){
    movemap->init_from_file(options::option[in::file::movemap]);
  }else{
    movemap->set_bb( true );
    movemap->set_chi( true );
  }
  simple_moves::BBG8T3AMoverOP bbg8t3mover = new simple_moves::BBG8T3AMover();
  bbg8t3mover->movemap(movemap);
  tr << "probability of executing bbg move: " << (options::option[options::OptionKeys::canonical_sampling::probabilities::localbb]*
                                                  (1-options::option[options::OptionKeys::canonical_sampling::probabilities::backrub]-options::option[options::OptionKeys::canonical_sampling::probabilities::conrot]())) << std::endl;
  runtime_assert(1-options::option[options::OptionKeys::canonical_sampling::probabilities::backrub]-options::option[options::OptionKeys::canonical_sampling::probabilities::conrot] >= 0);
  csm->add_mover( bbg8t3mover, options::option[options::OptionKeys::canonical_sampling::probabilities::localbb]*(1-options::option[options::OptionKeys::canonical_sampling::probabilities::backrub]-options::option[options::OptionKeys::canonical_sampling::probabilities::conrot]()) );

  //setup conrot mover
  if( options::option[options::OptionKeys::canonical_sampling::probabilities::conrot]() > 0 ) {
    simple_moves::BBConRotMoverOP conrotmover = new simple_moves::BBConRotMover();
    conrotmover->movemap( movemap );
    csm->add_mover( conrotmover, options::option[options::OptionKeys::canonical_sampling::probabilities::localbb]*options::option[options::OptionKeys::canonical_sampling::probabilities::conrot]());
  }


  //setup backrub mover
  if( options::option[options::OptionKeys::canonical_sampling::probabilities::backrub]() > 0 ) {
    protocols::backrub::BackrubMoverOP backrubmover = new protocols::backrub::BackrubMover;
    core::scoring::methods::EnergyMethodOptions energymethodoptions(sfxn->energy_method_options());
    if (energymethodoptions.bond_angle_residue_type_param_set()) {
      backrubmover->branchopt().bond_angle_residue_type_param_set(energymethodoptions.bond_angle_residue_type_param_set());
    }
    backrubmover->set_preserve_detailed_balance( csm->detailed_balance() );
    backrubmover->init_with_options();
    //backrubmover->add_mainchain_segments_from_options();
    //if( !option[in::file::fullatom] ) {
    //  backrubmover->optimize_branch_angles(pose);
    //}
    tr << "probability of executing backrub move: " << (options::option[options::OptionKeys::canonical_sampling::probabilities::localbb]*(options::option[options::OptionKeys::canonical_sampling::probabilities::backrub])) << std::endl;
    csm->add_mover((MoverOP)(backrubmover),(core::Real)(options::option[options::OptionKeys::canonical_sampling::probabilities::localbb]*options::option[options::OptionKeys::canonical_sampling::probabilities::backrub]));
  }


  tr.Info << "using regular pool-rmsd" << std::endl;
  //protocols::jd2::JobDistributor* jd2 = protocols::jd2::JobDistributor::get_instance();
  mc_convergence_checks::Pool_RMSD_OP pool_ptr =
    new mc_convergence_checks::Pool_RMSD(options::option[mc::known_structures]);
  csm->set_poolrmsd(pool_ptr);
  if( no_jd2_output ) {
    protocols::jd2::JobDistributor::get_instance()->go( csm, new protocols::jd2::NoOutputJobOutputter );
  } else {
    protocols::jd2::JobDistributor::get_instance()->go( csm );
  }
  return 0;
}

}
}