Protocol.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
/// @detailed
///
///
///
/// @author Oliver Lange

// Unit Headers
#include <protocols/abinitio/Protocol.hh>

// Package Headers
#include <protocols/evaluation/PoseEvaluator.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentStructFactory.hh>

// AUTO-REMOVED #include <core/pose/Pose.hh>

// Utility Headers
#include <basic/Tracer.hh>

#include <basic/options/option.hh>


// option key includes

#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>

#include <protocols/jobdist/Jobs.hh>
#include <utility/vector1.hh>



static basic::Tracer tr("protocols");
using namespace core;

void
protocols::abinitio::Protocol::register_options() {
  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  option.add_relevant( OptionKeys::abinitio::debug_structures );
}

namespace protocols {
namespace abinitio {
// Project Header


protocols::abinitio::Protocol::Protocol() :
  checkpoints_("Protocol"),
  evaluator_( NULL ),
  return_centroid_( true )
{
  if ( basic::options::option[ basic::options::OptionKeys::out::file::silent ].user() ) {
    silentout_file_name_ = basic::options::option[ basic::options::OptionKeys::out::file::silent ]();
  }
}

void
protocols::abinitio::Protocol::evaluate_pose(
  core::pose::Pose &pose,
  std::string tag,
  core::io::silent::SilentStruct &pss) const
{
  if ( evaluator_) {
    evaluator_->apply( pose, tag, pss );
  }
}

void
protocols::abinitio::Protocol::add_evaluation( evaluation::PoseEvaluatorOP ev ) {
  if ( !evaluator_ ) {
    evaluator_ = new evaluation::MetaPoseEvaluator;
  }
  evaluator_->add_evaluation( ev );
}

void
protocols::abinitio::Protocol::set_evaluation( evaluation::MetaPoseEvaluatorOP ev ) {
  evaluator_ = ev;
}

void
protocols::abinitio::Protocol::output_debug_structure( core::pose::Pose & pose, std::string prefix ) {
  using namespace core::io::silent;
  using namespace basic::options;
  if ( option[ basic::options::OptionKeys::out::file::silent ].user() ) {
    std::string silent_file="_"+prefix;
    if ( get_current_job() && get_current_job()->output_file_name() != "" ) {
      silent_file = get_current_job()->output_file_name()+silent_file;
    } else silent_file = silentout_file_name_+silent_file;

    SilentFileData sfd;
    //filename might have been changed -- e.g., to also have an MPI rank in there

    //    ProteinSilentStruct pss;
    io::silent::SilentStructOP pss = io::silent::SilentStructFactory::get_instance()->get_silent_struct_out();
    pss->fill_struct( pose, get_current_tag() );

    evaluate_pose( pose, get_current_tag(), *pss );

    sfd.write_silent_struct( *pss, silent_file, !option[ OptionKeys::abinitio::debug_structures ]()  /* bWriteScoresOnly */ );
  } // if option[ out::file::silent ].user()
}
void
protocols::abinitio::Protocol::apply( core::pose::Pose& ) {
  reset_status();
  //  structure_store().clear(); // keep this to avoid memory leaks
  // if (! bInitialized_ ) {
//    tr.Warning << "WARNING: ClassicAbinitio::apply is called without previous call to init(). Will self-initialize now... this overrides any"
//               << " custom settings if they existed... ;" << std::endl; // could call init at
//    init( pose );
//  }
}

std::string
protocols::abinitio::Protocol::get_name() const {
  return "Protocol";
}


}
}