ForceDisulfidesMover.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   ForceDisulfidesMover.cc
///
/// @brief
/// @author Sarel Fleishman

// unit headers
#include <protocols/simple_moves/ForceDisulfidesMover.hh>
#include <protocols/simple_moves/ForceDisulfidesMoverCreator.hh>
#include <boost/foreach.hpp>
#define foreach BOOST_FOREACH

// type headers
#include <core/types.hh>
#include <core/id/types.hh>

// project headers
#include <protocols/moves/Mover.hh>
#include <core/pose/util.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/selection.hh>

// utility header
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <utility/exit.hh>
#include <utility/tag/Tag.hh>
#include <utility/string_util.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <protocols/toolbox/task_operations/DesignAroundOperation.hh>
#include <core/pack/task/PackerTask.hh>
#include <protocols/simple_moves/PackRotamersMover.hh>
#include <core/scoring/ScoreFunction.hh>

namespace protocols {
namespace simple_moves {

static basic::Tracer TR("protocols.simple_moves.ForceDisulfidesMover");

std::string
ForceDisulfidesMoverCreator::keyname() const
{
  return ForceDisulfidesMoverCreator::mover_name();
}

protocols::moves::MoverOP
ForceDisulfidesMoverCreator::create_mover() const {
  return new ForceDisulfidesMover;
}

std::string
ForceDisulfidesMoverCreator::mover_name()
{
  return "ForceDisulfides";
}

ForceDisulfidesMover::ForceDisulfidesMover() :
  protocols::moves::Mover("ForceDisulfidesMover"),
  scorefxn_( NULL )
{ disulfides_.clear(); }

ForceDisulfidesMover::~ForceDisulfidesMover() {}

protocols::moves::MoverOP
ForceDisulfidesMover::clone() const
{
  return new ForceDisulfidesMover( *this );
}

protocols::moves::MoverOP
ForceDisulfidesMover::fresh_instance() const
{
  return new ForceDisulfidesMover();
}

void
ForceDisulfidesMover::apply( Pose & pose ) {
  TR<<"Fixing disulfides"<<std::endl;
  pose.conformation().fix_disulfides( disulfides_ );

  using namespace core::pack::task;
  using namespace protocols::toolbox::task_operations;

  DesignAroundOperationOP dao = new DesignAroundOperation;
  dao->design_shell( 0.0 );
  dao->repack_shell( 6.0 );
  for( utility::vector1< std::pair< core::Size, core::Size > > ::const_iterator pair = disulfides_.begin(); pair != disulfides_.end(); ++pair ){
    dao->include_residue( pair->first );
    dao->include_residue( pair->second );
  }
  TaskFactoryOP tf = new TaskFactory;
  tf->push_back( dao );
  tf->push_back( new operation::InitializeFromCommandline );
  PackerTaskOP ptask = tf()->create_task_and_apply_taskoperations( pose );
  PackRotamersMover prm( scorefxn(), ptask );
  TR<<"repacking disulfide surroundings"<<std::endl;
  prm.apply( pose );
}


void
ForceDisulfidesMover::scorefxn( core::scoring::ScoreFunctionOP sf ){
  scorefxn_ = sf;
}

core::scoring::ScoreFunctionOP
ForceDisulfidesMover::scorefxn() const{
  return scorefxn_;
}

std::string
ForceDisulfidesMover::get_name() const {
  return "ForceDisulfidesMover";
}

void
ForceDisulfidesMover::parse_my_tag( utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const & pose )
{
  scorefxn( protocols::rosetta_scripts::parse_score_function( tag, data ) );
  utility::vector1< std::string > const residue_pairs( utility::string_split( tag->getOption< std::string >( "disulfides" ), ',' ) );
  TR<<"Setting fix disulfides on residues: ";
  foreach( std::string const residue_pair, residue_pairs ){
    utility::vector1< std::string > const residues( utility::string_split( residue_pair, ':' ));
    runtime_assert( residues.size() == 2);
    core::Size const res1( core::pose::parse_resnum( residues[ 1 ], pose ) );
    core::Size const res2( core::pose::parse_resnum( residues[ 2 ], pose ) );
    disulfides_.push_back( std::pair< core::Size, core::Size >( res1, res2 ) );
    TR<<res1<<':'<<res2<<',';
  }
  TR<<std::endl;
}

void
ForceDisulfidesMover::disulfides( utility::vector1< std::pair < core::Size, core::Size >  > d ){ disulfides_ = d; }

utility::vector1< std::pair< core::Size, core::Size > >
ForceDisulfidesMover::disulfides() const { return disulfides_; }

} // moves
} // protocols