BrokerMain.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 protocols/abinitio/BrokerMain.cc
/// @author Oliver Lange
/// @author Christopher Miles (cmiles@uw.edu)

// keep these headers first for compilation with Visual Studio C++

// Package Headers
#include <protocols/abinitio/AbrelaxMover.hh>

// Project Headers
// AUTO-REMOVED #include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
// AUTO-REMOVED #include <core/scoring/constraints/NamedAtomPairConstraint.hh>

#include <core/scoring/constraints/BoundConstraint.hh>
#include <protocols/constraints_additional/AdditionalConstraintCreators.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <core/scoring/constraints/FuncFactory.hh>

//archive headers
#include <protocols/abinitio/IterativeAbrelax.hh>
#include <protocols/jd2/archive/MPIArchiveJobDistributor.hh>
// AUTO-REMOVED #include <numeric/random/random.hh>

// Utility headers
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/frags.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/jumps.OptionKeys.gen.hh>
#include <basic/options/keys/loopfcst.OptionKeys.gen.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/templates.OptionKeys.gen.hh>
#include <basic/options/keys/chunk.OptionKeys.gen.hh>
#include <basic/options/keys/broker.OptionKeys.gen.hh>

// C/C++ headers
#include <iostream>

#include <utility/vector1.hh>


static basic::Tracer tr("main");

namespace protocols  {
namespace abinitio {

void register_options_broker() {
  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  using namespace core;

  option.add_relevant(broker::setup);

  option.add_relevant(chunk::pdb2);
  option.add_relevant(chunk::loop2);

  option.add_relevant(in::file::native);
  option.add_relevant(in::file::silent);
  option.add_relevant(in::file::frag3);
  option.add_relevant(in::file::frag9);
  option.add_relevant(in::file::fasta);
  option.add_relevant(in::file::native_exclude_res);
  option.add_relevant(in::file::tags);

  option.add_relevant(out::file::silent);
  option.add_relevant(out::nstruct);

  option.add_relevant(run::proc_id);
  option.add_relevant(run::nproc);
  option.add_relevant(run::condor);

  option.add_relevant(OptionKeys::abinitio::fastrelax);
  option.add_relevant(OptionKeys::abinitio::relax);
  option.add_relevant(OptionKeys::abinitio::multifastrelax);
  option.add_relevant(OptionKeys::abinitio::relax_with_jumps);
  option.add_relevant(OptionKeys::abinitio::use_filters);
  option.add_relevant(OptionKeys::abinitio::detect_disulfide_before_relax);
  option.add_relevant(OptionKeys::abinitio::debug);
  option.add_relevant(OptionKeys::abinitio::number_3mer_frags);
  option.add_relevant(OptionKeys::abinitio::number_9mer_frags);
  option.add_relevant(OptionKeys::abinitio::process_store);
  option.add_relevant(OptionKeys::abinitio::fix_residues_to_native);
  option.add_relevant(OptionKeys::abinitio::return_full_atom);
  option.add_relevant(OptionKeys::abinitio::rerun);
  option.add_relevant(OptionKeys::abinitio::jdist_rerun);

  // starting conditions
  option.add_relevant(OptionKeys::abinitio::start_native);
  option.add_relevant(OptionKeys::abinitio::perturb);
  option.add_relevant(OptionKeys::abinitio::close_loops);

  // evaluation
  option.add_relevant(OptionKeys::abinitio::rmsd_residues);
  option.add_relevant(OptionKeys::abinitio::bGDT);
  option.add_relevant(OptionKeys::run::no_prof_info_in_silentout);

  // use fragments from native structure
  option.add_relevant(OptionKeys::abinitio::steal_3mers);
  option.add_relevant(OptionKeys::abinitio::steal_9mers);
  option.add_relevant(OptionKeys::abinitio::dump_frags);
  option.add_relevant(OptionKeys::abinitio::no_write_failures);

  option.add_relevant(loopfcst::use_general_protocol);
  option.add_relevant(loopfcst::coord_cst_weight);
  option.add_relevant(loopfcst::coord_cst_all_atom);
  option.add_relevant(loopfcst::coord_cst_weight_array);
  option.add_relevant(loopfcst::dump_coord_cst_weight_array);

  option.add_relevant(OptionKeys::in::file::pca);
  option.add_relevant(OptionKeys::out::sf);

  // jumping
  option.add_relevant(jumps::fix_jumps);
  option.add_relevant(jumps::jump_lib);
  option.add_relevant(jumps::fix_chainbreak);
  option.add_relevant(jumps::pairing_file);
  option.add_relevant(jumps::sheets);
  option.add_relevant(jumps::random_sheets);
  option.add_relevant(jumps::evaluate);
  option.add_relevant(jumps::extra_frags_for_ss);
  option.add_relevant(jumps::loop_definition_from_file);
  option.add_relevant(jumps::no_chainbreak_in_relax);
  option.add_relevant(jumps::residue_pair_jump_file);
  option.add_relevant(jumps::topology_file);

  //loop closure
  option.add_relevant(OptionKeys::loops::loop_file);
  option.add_relevant(OptionKeys::loops::alternative_closure_protocol);
  option.add_relevant(OptionKeys::loops::short_frag_cycles);
  option.add_relevant(OptionKeys::loops::scored_frag_cycles);
  option.add_relevant(OptionKeys::loops::debug_loop_closure);
  option.add_relevant(OptionKeys::loops::non_ideal_loop_closing);
  option.add_relevant(OptionKeys::loops::chainbreak_max_accept);
  option.add_relevant(OptionKeys::loops::extended);

  // constraints
  option.add_relevant(constraints::cst_file);
  option.add_relevant(constraints::forest_file);
  option.add_relevant(constraints::compute_total_dist_cst);
  option.add_relevant(constraints::no_linearize_bounded);
  option.add_relevant(constraints::dump_cst_set);
  option.add_relevant(constraints::no_cst_in_relax);
  option.add_relevant(constraints::evaluate_max_seq_sep);
  option.add_relevant(constraints::cull_with_native);
  option.add_relevant(constraints::named);
  option.add_relevant(constraints::viol);
  option.add_relevant(constraints::viol_level);
  option.add_relevant(constraints::viol_type);

  // homologs
  option.add_relevant(templates::config);
  option.add_relevant(templates::pairings);

  //large default number means all frags are used if this option is not specified
  option.add_relevant(templates::min_nr_large_frags);
  option.add_relevant(templates::min_nr_small_frags);

  option.add_relevant(templates::nr_large_copies);
  option.add_relevant(templates::nr_small_copies);
  option.add_relevant(templates::vary_frag_size);
  option.add_relevant(templates::fix_aligned_residues);
  option.add_relevant(templates::fix_margin);
  option.add_relevant(templates::fix_frag_file);
  option.add_relevant(templates::no_pick_fragments);
  option.add_relevant(templates::pick_multiple_sizes);
  option.add_relevant(templates::strand_constraint);

  option.add_relevant(frags::nr_large_copies);
  option.add_relevant(frags::annotate);

#ifdef BOINC
  std::cerr << "Registered extra options." << std::endl;
  std::cerr.flush();
#endif
}

void common_setup() {
  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  using core::scoring::constraints::BoundFunc;
  using core::scoring::constraints::ConstraintFactory;
  using core::scoring::constraints::ConstraintIO;
  using protocols::constraints_additional::NamedAtomPairConstraintCreator;

  if ( option[ constraints::no_linearize_bounded ] ) {
    tr.Info << "use fully harmonic potential for BOUNDED " << std::endl;
    ConstraintIO::get_func_factory().add_type("BOUNDED", new BoundFunc(0,0,0,1000,"dummy") );
  }

  if ( option[ constraints::named ] ) {
    tr.Info << "use named constraints in AtomPairConstraint to avoid problems with cutpoint-variants " << std::endl;
    ConstraintFactory::get_instance()->replace_creator(
      new NamedAtomPairConstraintCreator());
  }
}

// note: initialization now takes place in AbrelaxMover::set_defaults()
void Broker_main() {
  common_setup();
  AbrelaxMoverOP m = new AbrelaxMover();
  protocols::jd2::JobDistributor* jd2( protocols::jd2::JobDistributor::get_instance() );
  protocols::jd2::archive::MPIArchiveJobDistributor* archive_jd = dynamic_cast< protocols::jd2::archive::MPIArchiveJobDistributor* >( jd2 );
  if ( archive_jd && archive_jd->is_archive_rank() ) {
    archive_jd->set_archive( new IterativeAbrelax );
  }
  protocols::jd2::JobDistributor::get_instance()->go(m);
}

}
}