util.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/relax/util.cc
/// @brief initialization protocols for relax and utility functions
/// @detailed
/// @author Mike Tyka, Monica Berrondo
/// @author Roland A. Pache

//Project Headers
#include <protocols/relax/util.hh>

//Core Headers
#include <core/pose/Pose.hh>
#include <core/pose/datacache/CacheableDataType.hh> //pba
#include <core/scoring/MembraneTopology.hh> //pba
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/electron_density/util.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/conformation/Residue.hh>

//Protocol Headers
#include <protocols/relax/RelaxProtocolBase.hh>
#include <protocols/relax/ClassicRelax.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/relax/MiniRelax.hh>
#include <protocols/relax/CentroidRelax.hh>

//Basic Headers
#include <basic/datacache/BasicDataCache.hh> //pba
#include <basic/options/option.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/Tracer.hh>

//Utility Headers
#include <utility/vector0.hh>
#include <utility/vector1.hh>

// ObjexxFCL Headers
#include <ObjexxFCL/string.functions.hh>

#ifdef BOINC_GRAPHICS
#include <protocols/boinc/boinc.hh>
#endif

using basic::T;
using basic::Error;
using basic::Warning;

static basic::Tracer TR("protocols.relax");

using namespace core;
////////////////////////////////////////////////////////////////////////////////////////////////////

namespace protocols {
namespace relax {
////////////////////////////////////////////////////////////////////////////////////////////////////

RelaxProtocolBaseOP
generate_relax_from_cmd( bool NULL_if_no_flag ) {
  using namespace protocols::moves;
  using namespace scoring;
  using namespace basic::options;
  using namespace basic::options::OptionKeys;

  core::scoring::ScoreFunctionOP scorefxn;
  scorefxn = core::scoring::getScoreFunction();
  if ( option[ in::file::fullatom ]() || option[ OptionKeys::constraints::cst_fa_file ].user())
    core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn( *scorefxn );
  else
    core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn( *scorefxn );

  // now add density scores
  if ( option[ edensity::mapfile ].user() ) {
    core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn( *scorefxn );
  }

  RelaxProtocolBaseOP protocol;
  if ( option[ OptionKeys::relax::sequence_file ].user() ) {
    protocol = new FastRelax( scorefxn, option[ OptionKeys::relax::sequence_file ]() );
  } else if ( option[ OptionKeys::relax::script ].user() ) {
    protocol = new FastRelax( scorefxn, option[ OptionKeys::relax::script ]() );
  } else if ( option[ OptionKeys::relax::quick ]() ){
    protocol = new FastRelax( scorefxn, option[ OptionKeys::relax::default_repeats ]() /*default 5*/);
  } else if ( option[ OptionKeys::relax::thorough ]() ){
    protocol = new FastRelax( scorefxn, 15 );
  } else if ( option[ OptionKeys::relax::fast ]() ) {
    protocol = new FastRelax( scorefxn, option[ OptionKeys::relax::default_repeats ]() /*default 5*/);
  } else if ( option[ OptionKeys::relax::classic ]() ) {
    protocol = new ClassicRelax ( scorefxn );
  } else if ( option[ OptionKeys::relax::mini ]() ) {
    protocol = new MiniRelax( scorefxn );
  } else if ( option[ OptionKeys::relax::centroid_mode ]()) {
                protocol = new CentroidRelax();
  } else {
    // default relax should be a quick sequence relax
    if ( NULL_if_no_flag ){
      TR.Debug << "no relax protocol specified at command line" << std::endl;
      return NULL;
    }
    protocol = new FastRelax( scorefxn );
  }

  return protocol;
}

void setup_membrane_topology( pose::Pose & pose, std::string spanfile ) {
  //using core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY;
  core::scoring::MembraneTopologyOP topologyOP = new core::scoring::MembraneTopology;
  pose.data().set( core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY, topologyOP );
  core::scoring::MembraneTopology & topology=*( static_cast< core::scoring::MembraneTopology * >( pose.data().get_ptr( core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY )() ));
  topology.initialize(spanfile);
}

void make_dna_rigid( pose::Pose & pose, core::kinematics::MoveMap & mm){
  using namespace core::conformation;
  //if DNA present set so it doesn't move
  for ( core::Size i=1; i<=pose.total_residue() ; ++i )      {
      if( pose.residue(i).is_DNA()){
    TR << "turning off DNA bb and chi move" << std::endl;
    mm.set_bb( i, false );
    mm.set_chi( i, false );
      }
  }
}

void relax_pose( pose::Pose& pose, core::scoring::ScoreFunctionOP scorefxn, std::string const& tag ) {
  using namespace basic::options;
  RelaxProtocolBaseOP protocol( generate_relax_from_cmd() );
  protocol->set_current_tag( tag );
  protocol->set_scorefxn( scorefxn );
  protocol->apply( pose );
}

}
}