DisulfideFilter.cc

Go to the documentation of this file.

// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 sw=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 devel/protein_interface_design/filters/DisulfideFilter.hh
/// @brief Filters for interfaces which could form a disulfide bond between
/// docking partners.
/// @author Spencer Bliven <blivens@u.washington.edu>
/// @date Created 4/30/2009
#include <protocols/protein_interface_design/filters/DisulfideFilter.hh>
#include <protocols/protein_interface_design/filters/DisulfideFilterCreator.hh>


// Project Headers
#include <core/types.hh>


//parsing
#include <utility/tag/Tag.hh>
#include <protocols/filters/Filter.hh>
#include <protocols/moves/Mover.fwd.hh> //Movers_map
#include <protocols/rosetta_scripts/util.hh>
#include <core/pose/selection.hh>
#include <protocols/protein_interface_design/movers/DisulfideMover.hh>

// Utility Headers

// Unit Headers

// C++ headers

#include <core/scoring/disulfides/CentroidDisulfidePotential.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>

namespace protocols {
namespace protein_interface_design {
namespace filters {

using namespace core;
using namespace core::scoring;
using core::pose::Pose;
using namespace std;
using std::pair;
using utility::vector1;
using utility::vector1_int;
using protocols::protein_interface_design::movers::DisulfideMover;

static basic::Tracer TR( "protocols.protein_interface_design.filters.DisulfideFilter" );

const core::scoring::disulfides::CentroidDisulfidePotential DisulfideFilter::potential_;

///@brief default ctor
DisulfideFilter::DisulfideFilter() :
  parent( "DisulfideFilter" ),
  targets_(),
  rb_jump_(1)
{}

///@brief copy ctor
DisulfideFilter::DisulfideFilter(DisulfideFilter const& df) :
  //utility::pointer::ReferenceCount(),
  parent( "DisulfideFilter" ),
  targets_(df.targets_),
  rb_jump_(df.rb_jump_)
{}

///@brief Constructor with a single target residue
DisulfideFilter::DisulfideFilter( core::Size targetResidue ) :
  parent( "DisulfideFilter" ),
  targets_(),
  rb_jump_(1)
{
  targets_.push_back(targetResidue);
}

///@brief Constructor with multiple target residues
DisulfideFilter::DisulfideFilter( utility::vector1<core::Size> const& targetResidues ) :
  parent( "DisulfideFilter" ),
  targets_(targetResidues),
  rb_jump_(1)
{}

DisulfideFilter::~DisulfideFilter() {}

/// @return Whether a disulfide bond is possible between any of the targets
bool DisulfideFilter::apply(Pose const & pose ) const
{
  vector1< pair<Size,Size> > disulfides;
  DisulfideMover::disulfide_list(pose, targets_, rb_jump_, disulfides);
  if( disulfides.empty() ) {
    TR << "Failing."<<std::endl;
    return false;
  } else {
    TR << "Passing."<<std::endl;
    return true;
  }
}

void DisulfideFilter::report( ostream & out, Pose const & pose ) const
{
  vector1< pair<Size,Size> > disulfides;
  DisulfideMover::disulfide_list(pose, targets_, rb_jump_, disulfides);

  out << disulfides.size() << " disulfides possible: ";
  for( vector1< pair<Size,Size> >::const_iterator disulf = disulfides.begin(),
      end_disulf = disulfides.end();
      disulf != end_disulf; ++disulf)
    {
    out << disulf->first << '-' << disulf->second << ", ";
      }
  out << "\n";
    }
/// @return The number of disulfides possible
Real DisulfideFilter::report_sm( Pose const & pose ) const
{
  vector1< pair<Size,Size> > disulfides;
  DisulfideMover::disulfide_list(pose, targets_, rb_jump_, disulfides);

  return disulfides.size();
}

/**
 * @details Parameters recognized:
 *  - targets. A list of possible target residues, seperated by commas.
 */
void DisulfideFilter::parse_my_tag( utility::tag::TagPtr const tag,
    protocols::moves::DataMap &,
    protocols::filters::Filters_map const &,
    protocols::moves::Movers_map const &,
    core::pose::Pose const & pose)
{

  // Set target to the residue specified by "target_pdb_num" or "target_res_num"
  if( tag->hasOption("targets") ) {
    targets_ = core::pose::get_resnum_list(tag, "targets",pose);
  }

  TR.Info << "DisulfideFilter targeting residues ";
  for(vector1<Size>::const_iterator target = targets_.begin();
      target != targets_.end();++target)
  {
    TR.Info<<*target<<", ";
  }
  TR.Info<<std::endl;
}

protocols::filters::FilterOP
DisulfideFilterCreator::create_filter() const { return new DisulfideFilter; }

std::string
DisulfideFilterCreator::keyname() const { return "DisulfideFilter"; }


} // filters
} // protein_interface_design
} // devel