rotamer_recovery.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 apps/performance_benchmark/scientific/rotamer_recovery.cc
/// @brief this determines the percent of rotamers correctly predictied during a repack
/// @author Matthew O'Meara (mattjomeara@gmail.com)


// Unit Headers
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/rotamer_recovery/RotamerRecoveryMover.hh>
#include <protocols/rotamer_recovery/RotamerRecovery.hh>
#include <protocols/rotamer_recovery/RotamerRecoveryFactory.hh>


// Project Headers
#include <devel/init.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>

// Utility Headers
#include <utility/excn/EXCN_Base.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/exit.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>

// c++ Headers
#include <fstream>

using std::endl;
using std::ofstream;
using std::string;
using basic::Tracer;
using core::pose::PoseOP;
using core::import_pose::pose_from_pdb;
using core::pack::task::TaskFactory;
using core::pack::task::TaskFactoryOP;
using core::pack::task::operation::InitializeFromCommandline;
using core::pack::task::operation::ReadResfile;
using core::pack::task::operation::RestrictToRepacking;
using core::scoring::get_score_function;
using core::scoring::ScoreFunctionOP;
using protocols::rotamer_recovery::RotamerRecoveryOP;
using protocols::rotamer_recovery::RotamerRecoveryFactory;
using protocols::rotamer_recovery::RotamerRecoveryMover;
using protocols::rotamer_recovery::RotamerRecoveryMoverOP;
using protocols::jd2::JobDistributor;
using utility::excn::EXCN_Base;

static Tracer TR("apps.benchmark.scientific.rotamer_recovery");

OPT_1GRP_KEY( String, rotamer_recovery, protocol )
OPT_1GRP_KEY( String, rotamer_recovery, comparer )
OPT_1GRP_KEY( String, rotamer_recovery, reporter )
//OPT_2GRP_KEY( File, rotamer_recovery, native_vs_decoy )
//OPT_2GRP_KEY( File, out, rotamer_recovery, method )
OPT_2GRP_KEY( File, out, file, rotamer_recovery )

void
register_options() {
  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  OPT( in::file::s );
  OPT( in::file::l );
  OPT( in::file::silent );
  OPT( in::file::native );
  OPT( packing::use_input_sc );
  OPT( packing::resfile );
  NEW_OPT( rotamer_recovery::protocol, "Rotamer Recovery Protocol component.", "RRProtocolMinPack");
  NEW_OPT( rotamer_recovery::comparer, "Rotamer Recovery Comparer component.", "RRComparerAutomorphicRMSD");
  NEW_OPT( rotamer_recovery::reporter, "Rotamer Recovery Reporter component.", "RRReporterHuman");
  // NEW_OPT( rotamer_recovery::native_vs_decoy, "Table of describing which native structures the decoys are modeling.  The first column is native pdb filename and the second column is the decoy pdb filename.", "");
  NEW_OPT( out::file::rotamer_recovery, "Output File  Name for reporters that write their results to a file.", "");

}

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

    devel::init(argc, argv);

    using namespace basic::options;
    using namespace basic::options::OptionKeys;
    using namespace basic::options::OptionKeys::out::file;
    using namespace core::pack::task::operation;

    string const & protocol( option[ rotamer_recovery::protocol ].value() );
    string const & reporter( option[ rotamer_recovery::reporter ].value() );
    string const & output_fname( option[ out::file::rotamer_recovery ].value() );
    string const & comparer( option[ rotamer_recovery::comparer ].value() );
    ScoreFunctionOP scfxn( get_score_function() );
    TaskFactoryOP task_factory( new TaskFactory );
    task_factory->push_back( TaskOperationCOP( new InitializeFromCommandline ) );
    if ( option.has(OptionKeys::packing::resfile) && option[OptionKeys::packing::resfile].user() ) {
      task_factory->push_back( TaskOperationCOP( new ReadResfile ) );
    }
    task_factory->push_back( TaskOperationCOP( new RestrictToRepacking ) );

    RotamerRecoveryOP rotamer_recovery(
      RotamerRecoveryFactory::get_instance()->get_rotamer_recovery(
      protocol, comparer, reporter));

    RotamerRecoveryMoverOP rotamer_recovery_mover( new RotamerRecoveryMover(rotamer_recovery, scfxn, task_factory) );


    try{
      JobDistributor::get_instance()->go( rotamer_recovery_mover );

      rotamer_recovery_mover->show();

      // if requsted write output to disk
      if ( option[ out::file::rotamer_recovery].user() ) {
        ofstream fout;
        fout.open( output_fname.c_str(), std::ios::out );
        if ( !fout.is_open() ) {
          TR << "Unable to open output file '" << output_fname << "'." << endl;
          utility_exit();
        }
        rotamer_recovery_mover->show( fout );
        fout.close();
      }
    } catch (EXCN_Base & excn ) {
      TR.Error << "Exception: " << endl;
      excn.show( TR.Error );

      TR << "Exception: " << endl;
      excn.show( TR ); //so its also seen in a >LOG file
    }

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

  return 0;
}