minirosetta.cc

Go to the documentation of this file.

// -*- 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

#ifdef BOINC
#include <utility/io/ozstream.hh>
#include <utility/boinc/boinc_util.hh>
#include <utility/file/file_sys_util.hh>
#include <protocols/boinc/boinc.hh>
#include "boinc_zip.h"
#endif // BOINC

/// Must have this after BOINC stuff to avoid windows build error
#include <core/io/silent/util.hh>
#include <protocols/abinitio/AbrelaxApplication.hh>
#include <protocols/abinitio/IterativeAbrelax.hh>
#include <protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.hh>
#include <protocols/jd2/archive/ArchiveManager.hh>
#include <protocols/abinitio/BrokerMain.hh>
#include <protocols/boinc/util.hh>
#include <protocols/comparative_modeling/cm_main.hh>
#include <protocols/medal/MedalMain.hh>
#include <protocols/symmetric_docking/SymDockProtocol.hh>
#include <protocols/rbsegment_relax/RBSegmentRelax_main.hh>
#include <protocols/loop_build/LoopBuild.hh>
#include <protocols/loophash/Mover_LoopHashRefine.hh>
#include <protocols/abinitio/vs_test.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/ligand_docking/ligand_dock_impl.hh>
#include <protocols/flxbb/FlxbbDesign_main.hh>
#include <protocols/ddg/ddG_main.hh>
#include <protocols/canonical_sampling/CanonicalSamplingApplication.hh>
#include <protocols/canonical_sampling/CanonicalSamplingMover.hh>
#include <protocols/frag_picker/nonlocal/NonlocalFragsMain.hh>
#include <protocols/star/StarAbinitioMain.hh>

#ifdef BOINC
#include <protocols/boinc/boinc.hh>
#include <protocols/init/init.hh>
#endif

#ifdef WIN32
#include <protocols/init/init.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#endif

#include <core/types.hh>

#ifndef BOINC
#ifndef WIN32
#include <devel/init.hh>
#endif
#endif

#ifdef BOINC
#include <core/pose/Pose.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/util.hh>
#include <core/pose/util.hh>
#endif

#include <basic/options/option.hh>
#include <utility/exit.hh>
#include <utility/excn/Exceptions.hh>

// option key includes
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/jd2.OptionKeys.gen.hh>
#include <basic/options/keys/boinc.OptionKeys.gen.hh>

#include <protocols/checkpoint/Checkpoint.hh>
#include <protocols/jd2/BOINCJobDistributor.hh>
#include <protocols/relax/relax_main.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>

class DummyMover : public protocols::moves::Mover {
public:
  DummyMover() : protocols::moves::Mover( "DummyMover" ) {}
  virtual ~DummyMover(){}
  virtual void apply( core::pose::Pose & ) {
    std::cerr << "DummyMover::apply() should never have been called!"
      << " (JobDistributor/Parser should have replaced DummyMover.)" << std::endl;
    runtime_assert(false); // will enable a backtrace in gdb
  }
  virtual std::string get_name() const { return "DummyMover"; }
};

int
main( int argc, char * argv [] )
{
  try {

    using namespace basic::options;
    using namespace basic::options::OptionKeys;
    using std::string;
    using utility::vector1;

#ifdef BOINC // BOINC STUFF

  // initialize boinc
  using namespace protocols::boinc;
  Boinc boinc_wu = Boinc::instance();
  boinc_wu.initialize_worker(); //The shared memory gets created here.

  // make sure -use_filters flag is not ambiguous
  for (int i=0; i<argc; ++i) {
    if (!strcmp(argv[i], "-use_filters")) {
      std::cerr << "Fixing ambiguous flag " << argv[i];
      char tmpstr[] = "-abinitio::use_filters";
      argv[i] = tmpstr;
      std::cerr << " to " << argv[i] << std::endl;
    }
  }
  // print command to stderr
  std::cerr << "command:";
  for ( int i=0; i< argc; ++i ) {
    std::cerr << ' ' <<  argv[i];
  }
  std::cerr  << std::endl;

#endif

    // has to be called before core::init::init. Which is really stupid.
#ifdef BOINC // BOINC STUFF
  std::cerr << "Registering options.. " << std::endl;std::cerr.flush();
#endif
    protocols::abinitio::AbrelaxApplication::register_options();
    protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::register_options();
    protocols::abinitio::IterativeAbrelax::register_options();
    protocols::jd2::archive::ArchiveManager::register_options();
    //protocols::canonical_sampling::register_options();
    protocols::canonical_sampling::CanonicalSamplingMover::register_options();


#ifdef BOINC // BOINC STUFF
  std::cerr << "Initializing broker options ..." << std::endl;std::cerr.flush();
#endif
    protocols::abinitio::register_options_broker();
    // options, random initialization
#ifdef BOINC // BOINC STUFF
  std::cerr << "Initializing core..." << std::endl;std::cerr.flush();
#endif

#ifndef BOINC
#ifndef WIN32
    // No devel in BOINC builds
    devel::init( argc, argv );
#endif
#endif

#ifdef BOINC
  protocols::init::init( argc, argv );
#endif
#ifdef WIN32
    protocols::init::init( argc, argv );
#endif

#ifdef BOINC // BOINC STUFF

#ifdef BOINC_GRAPHICS
  // read the work unit description file if one exists
  std::cerr << "Setting WU description ..." << std::endl;std::cerr.flush();
  Boinc::set_wu_desc();
  Boinc::set_randomly_cycle_appearance( option[run::protocol]() != "simple_cycpep_predict" );  // Set whether the app should randomly cycle the graphics
#endif

  // unzip an archive?
  if (option[ in::file::zip ].user()) {
    std::string resolvedfile = option[ in::file::zip ]();
    bool is_database = false;
    if (resolvedfile == "minirosetta_database.zip") {
      is_database = true;
    }
    if (is_database && utility::file::file_exists( "minirosetta_database.zip.is_extracted" )) {
      std::cerr << "Using previously extracted minirosetta_database." << std::endl;std::cerr.flush();
    } else {
      utility::boinc::resolve_filename( resolvedfile );
      if (!utility::file::file_exists( resolvedfile )) {
        utility_exit_with_message("in::file::zip "+
          option[ in::file::zip ]()+" does not exist!");
      } else {
        std::cerr << "Unpacking zip data: " << resolvedfile << std::endl;std::cerr.flush();
        boinc_zip(UNZIP_IT, resolvedfile, "./");
        if (is_database) {
          utility::io::ozstream data( "minirosetta_database.zip.is_extracted" );
        }
      }
    }
  }

  // unzip an archive of files specific to a given BOINC workunit.
  if ( option[ in::file::boinc_wu_zip ].user() ) {
    std::cerr << "Unpacking WU data ..." << std::endl; std::cerr.flush();
    vector1< string > files = option[ in::file::boinc_wu_zip ]();
    for( vector1< string >::const_iterator it = files.begin(), end = files.end(); it != end; ++it ) {
      std::string resolvedfile = *it;
      utility::boinc::resolve_filename( resolvedfile );
      if ( !utility::file::file_exists( resolvedfile ) ) {
        utility_exit_with_message( "in::file::boinc_wu_zip " +
          *it + " does not exist!"
        );
      } else {
        std::cerr << "Unpacking data: " << resolvedfile << std::endl;std::cerr.flush();
        boinc_zip(UNZIP_IT, resolvedfile, "./");
      }
    }
  }

  // override database option and set to current directory
  std::cerr << "Setting database description ..." << std::endl;std::cerr.flush();

  option[in::path::database].value("minirosetta_database");

  std::cerr << "Setting up checkpointing ..." << std::endl;std::cerr.flush();
#endif
    if ( option[ run::checkpoint ] || option[ run::checkpoint_interval ].user() ) {
      protocols::checkpoint::checkpoint_with_interval( option[ run::checkpoint_interval ] );
    }

#ifdef BOINC_GRAPHICS
    std::cerr << "Setting up graphics native ..." << std::endl;std::cerr.flush();
    // set native for graphics
    if ( option[ in::file::native ].user() ) {
      core::pose::PoseOP native_pose_( new core::pose::Pose );
      core::import_pose::pose_from_file( *native_pose_, option[ in::file::native ]() , core::import_pose::PDB_file);
      if ( native_pose_->total_residue() <= protocols::boinc::MAX_NATIVE_POSE_RESIDUES ) {
        core::pose::set_ss_from_phipsi( *native_pose_ );
        protocols::boinc::Boinc::set_graphics_native_pose( *native_pose_ );
      }
    }

    protocols::boinc::Boinc::set_shared_memory_fully_initialized(); //Signal that the shared memory is fully initialized at this point, and can be used by the graphics app.
#endif


    // RUN PROTOCOL
    // catch *any* exception.
    try{
      if ( option[ run::protocol ]() == "abrelax" ) {
        protocols::abinitio::AbrelaxApplication abrelax;
        abrelax.run();
      } else if ( option[run::protocol]() == "simple_cycpep_predict" ) {
        protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication peppredict;
        peppredict.run();
      } else if ( option[ run::protocol ]() == "symdock" ) {
        protocols::symmetric_docking::SymDock_main();
      } else if ( option[ run::protocol ]() == "broker" ) {
        protocols::abinitio::Broker_main();
      } else if ( option[ run::protocol ]() == "loophash" ) {
        protocols::loophash::loophash_main();
      } else if ( option[ run::protocol ]() == "ligand_dock" ) {
        ligand_dock_main();
      } else if ( option[ run::protocol ]() == "relax" ) {
        protocols::relax::Relax_main( true );
      } else if ( option[ run::protocol ]() == "looprelax" ) {
        protocols::loop_build::LoopBuild_main( true );
      } else if ( option[ run::protocol ]() == "threading" ) {
        protocols::comparative_modeling::cm_main();
      } else if ( option[ run::protocol ]() == "medal" ) {
        protocols::medal::Medal_main(NULL);
      } else if ( option[ run::protocol ]() == "medal_exchange" ) {
        protocols::medal::MedalExchange_main(NULL);
      } else if ( option[ run::protocol ]() == "star" ) {
        protocols::star::StarAbinitio_main(NULL);
      } else if ( option[ run::protocol ]() == "rbsegmentrelax" ) {
        protocols::RBSegmentRelax_main( );
      } else if ( option[ run::protocol ]() == "boinc_debug" ) {
        protocols::abinitio::run_boinc_debug();
      } else if ( option[ run::protocol ]() == "flxbb" ) {
        protocols::flxbb::FlxbbDesign_main();
      } else if ( option[ run::protocol ]() == "jd2_scripting" ) {
        protocols::moves::MoverOP mover( new DummyMover );
        option[ jd2::dd_parser ].value( true ); // This option MUST be set true if we're using rosetta_scripts.
        // To avoid accidental crashes, we'll do so programatically
        protocols::jd2::BOINCJobDistributor::get_instance()->go( mover );
      } else if ( option[run::protocol]() == "ddg" ) {
        protocols::ddG_main();
      } else if ( option[run::protocol]() == "canonical_sampling" ) {
        protocols::canonical_sampling::canonical_sampling_main();
      } else if ( option[run::protocol]() == "nonlocal_frags" ) {
        protocols::frag_picker::nonlocal::NonlocalFrags_main();
      } else {
        utility_exit_with_message(
          "Invalid protocol requested: "+ option[ run::protocol ]()
        );
        return 0; // makes compiler happy
      }
      //---code to do a in spot score cut necessary for running centroid abinitio through boinc
#ifdef BOINC
  double runtime = protocols::boinc::Boinc::get_boinc_wu_cpu_time();
#else
      double runtime = -1; //-1 does not do filtering
#endif
      if ( option[boinc::score_cut_pct].user() ) {
        double minTimePerModel = 61;  //seconds per model min time for boinc.
        protocols::boinc::boincOutputFilter(runtime,minTimePerModel); //ideally score cut alone, but an additional filter that allows only 1 structure every 61 seconds.
      }
#ifdef BOINC

  // gzip the output silent files.
  std::cerr << "reached end of minirosetta::main()" << std::endl;
  core::io::silent::gzip();

  // ideally these would be called in the dtor but the way we have the singleton pattern set up the dtors don't get
  // called
  protocols::boinc::Boinc::worker_finish_summary( protocols::boinc::Boinc::decoy_count() + 2 , protocols::boinc::Boinc::decoy_count() + 2 , 2 );
  protocols::boinc::Boinc::worker_shutdown(); // Does not return.
  utility_exit_with_message( "reached end of minirosetta::main() after worker_shutdown(); " );
#endif
    } catch ( utility::excn::EXCN_Base& excn ) {
      std::cerr << "std::cerr: Exception was thrown: " << std::endl;
      excn.show( std::cerr );
      std::cout << "std::cout: Exception was thrown: " << std::endl;
      excn.show( std::cout ); //so its also seen in a >LOG file
#ifdef USEMPI
    MPI_Abort( MPI_COMM_WORLD, 911 );
#endif
      return 1;    // MUST return non-0 - otherwise BOINC does not abort!
    }

  } catch ( utility::excn::EXCN_Base const & e ) {
    std::cout << "caught exception " << e.msg() << std::endl;
    return -1;
  }
  return 0;
}

#ifdef BOINC
#ifdef _WIN32

/*******************************************************
 * Windows: Unix applications begin with main() while Windows applications
 * begin with WinMain, so this just makes WinMain() process the command line
 * and then invoke main()
 */
int WINAPI WinMain(HINSTANCE hInst, HINSTANCE hPrevInst,
                   LPSTR Args, int WinMode)
{
    LPSTR command_line;
    char* argv[1024];
    int argc;

    command_line = GetCommandLine();
    argc = parse_command_line( command_line, argv );
    return main(argc, argv);
}
#endif
#endif