NonSequentialNeighborsFilter.hh

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/// @file protocols/simple_filters/NonSequentialNeighborsFilter.hh
/// @brief Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint
/// @author Gabi Pszolla & Sarel Fleishman

#ifndef INCLUDED_protocols_simple_filters_NonSequentialNeighborsFilter_hh
#define INCLUDED_protocols_simple_filters_NonSequentialNeighborsFilter_hh

//unit headers
#include <protocols/simple_filters/NonSequentialNeighborsFilter.fwd.hh>

// Project Headers
#include <core/types.hh>
#include <protocols/filters/Filter.hh>
#include <core/pose/Pose.fwd.hh>
#include <protocols/moves/DataMap.fwd.hh>
#include <protocols/moves/Mover.fwd.hh>

namespace protocols {
namespace simple_filters {

class NonSequentialNeighborsFilter : public filters::Filter
{
public:
  //default ctor
  NonSequentialNeighborsFilter();
  bool apply( core::pose::Pose const & pose ) const;
  filters::FilterOP clone() const {
    return new NonSequentialNeighborsFilter( *this );
  }
  filters::FilterOP fresh_instance() const{
    return new NonSequentialNeighborsFilter();
  }

  void report( std::ostream & out, core::pose::Pose const & pose ) const;
  core::Real report_sm( core::pose::Pose const & pose ) const;
  core::Real compute( core::pose::Pose const &pose ) const;
  virtual ~NonSequentialNeighborsFilter();
  void 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 & );

  core::Real distance_threshold() const { return distance_threshold_; }
  void distance_threshold( core::Real const r ){ distance_threshold_ = r; }
  core::Size neighbor_cutoff() const {return neighbor_cutoff_; }
  void neighbor_cutoff( core::Size const n ) { neighbor_cutoff_ = n; }
  bool bound() const{ return bound_; }
  void bound( bool const b ) { bound_ = b;}
  core::Size resnum() const{ return resnum_; }
  void resnum( core::Size const s ){ resnum_ = s; }
  void jump( core::Size const j ){ jump_ = j; }
  core::Size jump() const { return jump_; }
  core::Size residue_neighbors( core::pose::Pose const & pose, core::Size const resi ) const; // number of residue neighbours outside the sequence neighbours.
private:
  core::Real distance_threshold_; // dflt 8.0A; sphere around the residue
  core::Size neighbor_cutoff_; // dflt 10; how many residues in the sequence around the target residue to ignore in computing neighbours
  bool bound_; // dflt false; treat the bound or unbound pose
  core::Size resnum_; // dflt 0; 0 - means all residues in the pose; any other number targets a particular residue
  core::Size jump_; // dflt 1;
};

}
}

#endif