WorkUnit_LoopHash.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/wum/WorkUnitBase.cc
/// @brief
/// @author Mike Tyka

#include <protocols/loophash/WorkUnit_LoopHash.hh>
// AUTO-REMOVED #include <protocols/loophash/Exceptions.hh>
#include <protocols/wum/WorkUnitBase.hh>
#include <protocols/wum/SilentStructStore.hh>

#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>

// AUTO-REMOVED #include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
// AUTO-REMOVED #include <core/import_pose/pose_stream/util.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/ProteinSilentStruct.hh>
#include <core/io/silent/BinaryProteinSilentStruct.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
// AUTO-REMOVED #include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/lh.OptionKeys.gen.hh>
#include <basic/options/keys/wum.OptionKeys.gen.hh>
// AUTO-REMOVED #include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <basic/options/option.hh>
// AUTO-REMOVED #include <core/pose/Pose.hh>
// AUTO-REMOVED #include <core/pose/util.hh>
// AUTO-REMOVED #include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
// AUTO-REMOVED #include <basic/Tracer.hh>
// AUTO-REMOVED #include <protocols/relax/FastRelax.hh>
#include <protocols/loophash/LocalInserter.hh>
#include <protocols/loophash/LoopHashSampler.hh>

//Auto Headers
#include <utility/vector1.hh>
//Auto Headers
#include <core/io/silent/ProteinSilentStruct.tmpl.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <utility/excn/Exceptions.hh>




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

namespace protocols {
namespace loophash {


static basic::Tracer TR("WorkUnit_LoopHash");



WorkUnit_LoopHash::WorkUnit_LoopHash( core::Size start_ir, core::Size end_ir, core::Size ssid ):
  WorkUnit_SilentStructStore()
{
  set_defaults();
  set_start(start_ir);
  set_end(end_ir);
  set_ssid(ssid);
}

void
WorkUnit_LoopHash::set_defaults()
{
  TR.Debug << "Setting type to WU_Type_LoopHash" << std::endl;
}

void
WorkUnit_LoopHash::init_from_cmd( const core::Size mpi_rank )
{
  using namespace basic::options;
  using namespace basic::options::OptionKeys;

  utility::vector1 < core::Size > loop_sizes = option[ OptionKeys::lh::loopsizes]();
    core::Size num_partitions = option[ OptionKeys::wum::n_slaves_per_master](); 
    if( option[ OptionKeys::lh::num_partitions].user() )
        num_partitions = option[ OptionKeys::lh::num_partitions]();
    core::Size assigned_num = mpi_rank % num_partitions;
  try{
    library_ = new LoopHashLibrary( loop_sizes, num_partitions, assigned_num );
    // load initial library from disk
    library_->load_mergeddb();
  }
  catch( utility::excn::EXCN_Msg_Exception e ){
    e.show( std::cout );
    e.show( std::cerr );
    throw;
  }
  library_->mem_foot_print();
}

void
WorkUnit_LoopHash::run()
{
  using namespace core::pose;
  using namespace protocols::loops;
  using namespace basic::options;
  using namespace basic::options::OptionKeys;

  if( decoys().size() == 0 ){
    TR << "Empty WorkUnit ! Cannot execute run() " << std::endl;
    return;
  }

  core::io::silent::SilentStructCOP start_struct = decoys().get_struct(0);
  core::pose::Pose pose;
  decoys().get_pose( 0, pose );

  // clear the sotre of structures
  decoys().clear();

  runtime_assert( library_ );

  TR << "Executing WorkUnit_LoopHash_Mover..." << std::endl;
  LocalInserter_SimpleMinOP simple_inserter( new LocalInserter_SimpleMin() );
  LoopHashSampler  lsampler( library_, simple_inserter );
  lsampler.set_start_res( get_start()  );
  lsampler.set_stop_res ( get_end() );
  lsampler.set_min_bbrms( 20.0   );
  lsampler.set_max_bbrms( 1400.0 );
  lsampler.set_min_rms( 0.5 );
  lsampler.set_max_rms( 4.0 );
  if( option[ OptionKeys::lh::bss]() ) lsampler.set_nonideal(true);

  // convert pose to centroid pose:
  if( pose.is_fullatom() ){
    core::util::switch_to_residue_type_set( pose, core::chemical::CENTROID);
  }
  core::pose::set_ss_from_phipsi( pose );

  TR.Info << "Running loophash function: Start: " << get_start() << " End: " << get_end() << std::endl;
  core::Size starttime = time(NULL);

  lsampler.build_structures( pose, decoys().store() );

  core::Size endtime = time(NULL);
  TR.Info << "Build " << decoys().size() << " structures in " << endtime - starttime << " s " << std::endl;

  // transfer any tags from input structure:

  const core::io::silent::SilentStruct *ss2 = &( *start_struct );

  for ( protocols::wum::SilentStructStore::iterator it = decoys().begin();
        it != decoys().end(); ++ it ){
    
    core::io::silent::SilentStruct *ss = &(*(*it));
    // preserve the centroid score!
    core::Real censcore = (*it)->get_energy("censcore");
    (*it)->copy_scores( *start_struct );
    (*it)->add_energy("censcore", censcore );
    std::string new_usid = protocols::wum::generate_unique_structure_id();
    (*it)->add_string_value( "husid", (*it)->get_string_value("husid") + "." + new_usid );
    (*it)->add_string_value( "usid", new_usid );
    (*it)->add_energy( "state", 1 );

  if( option[ OptionKeys::lh::bss]() ) {
      const core::io::silent::BinaryProteinSilentStruct *pss2 = dynamic_cast< const core::io::silent::BinaryProteinSilentStruct* > ( ss2 );
      core::io::silent::BinaryProteinSilentStruct *pss = dynamic_cast< core::io::silent::BinaryProteinSilentStruct* > ( ss );
      if( (pss != NULL) && (pss2 != NULL) ){
        TR.Debug << "LoophashResult: " << pss->CA_rmsd( *pss2 ) << "  " <<  pss->get_energy("censcore") << std::endl;
      } else {
        TR << "LoophashResult: ERROR, dynamic cast to BSS failed"  << std::endl;
      }
    } else {
      const core::io::silent::ProteinSilentStruct *pss2 = dynamic_cast< const core::io::silent::ProteinSilentStruct* > ( ss2 );
      core::io::silent::ProteinSilentStruct *pss = dynamic_cast< core::io::silent::ProteinSilentStruct* > ( ss );
      if( (pss != NULL) && (pss2 != NULL) ){
        TR.Debug << "LoophashResult: " << pss->CA_rmsd( *pss2 ) << "  " <<  pss->get_energy("censcore") << std::endl;
      } else {
        TR << "LoophashResult: ERROR, dynamic cast to PSS failed"  << std::endl;
      }
    }
  }
}





}
}