UpstreamCollisionFilter.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
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// :noTabs=false:tabSize=4:indentSize=4:
//
// (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/match/output/UpstreamCollisionFilter.hh
/// @brief  Declaration for class to filter matches where the upstream residues collide.
/// @author Alex Zanghellini (zanghell@u.washington.edu)
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com), porting to mini

#ifndef INCLUDED_protocols_match_output_UpstreamCollisionFilter_hh
#define INCLUDED_protocols_match_output_UpstreamCollisionFilter_hh

// Unit headers
#include <protocols/match/output/UpstreamCollisionFilter.fwd.hh>

// Package headers
#include <protocols/match/BumpGrid.hh>
#include <protocols/match/output/MatchFilter.hh>
#include <protocols/match/output/UpstreamHitCacher.fwd.hh>

// Project headers
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/methods/ShortRangeTwoBodyEnergy.fwd.hh>


// Utility headers
#include <utility/pointer/ReferenceCount.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace match {
namespace output {


class MatchCollisionFilter : public MatchFilter {

public:
  typedef core::Real Real;

public:
  //MatchCollisionFilter( std::string filter_name );
  MatchCollisionFilter( std::string filter_name, UpstreamHitCacherOP coordinate_cacher );

  virtual
  ~MatchCollisionFilter();

  virtual
  bool
  passes_filter(
    match const & m
  ) const = 0;

  virtual
  bool
  passes_filter(
    match_dspos1 const & m
  ) const = 0;

  //setters
  void set_filter_by_lj( bool setting );
  void set_lj_cutoff( Real setting );
  void set_lj_atr_weight( Real setting );
  void set_lj_rep_weight( Real setting );
  void set_lj_sol_weight( Real setting );

  virtual
  void set_tolerated_overlap( Real setting );

  //getters
  bool filter_by_lj() const;
  Real wfa_atr() const;
  Real wfa_rep() const;
  Real wfa_sol() const;
  Real lj_cutoff() const;
  Real tolerated_overlap() const;

  core::pose::PoseCOP empty_pose() const;
  core::scoring::ScoreFunctionOP empty_sfxn() const;
  core::scoring::methods::ShortRangeTwoBodyEnergyCOP etable_energy() const;
  BumpGridCOP bump_grid() const;


protected:
  UpstreamHitCacherOP cacher_;

private:
  bool filter_by_lj_;
  Real wfa_atr_;
  Real wfa_rep_;
  Real wfa_sol_;
  Real lj_cutoff_;
  Real tolerated_overlap_;

  core::pose::PoseOP empty_pose_;
  core::scoring::ScoreFunctionOP empty_sfxn_;

  core::scoring::methods::ShortRangeTwoBodyEnergyOP   etable_energy_;
  BumpGridOP bump_grid_;



};

/// @brief This class is used to detect collisions between the upstream residues
/// and filter out matches that have too much collision.  It can perform either
/// hard-sphere collision detection, or score-function (Etable) driven collision
/// detection.  Four command-line flags are read by the MatcherTask to initialize
/// this class:
/// match::filter_colliding_upstream_residues
/// match::upstream_residue_collision_tolerance
/// match::upstream_residue_collision_score_cutoff
/// match::upstream_residue_collision_Wfa_atr
/// match::upstream_residue_collision_Wfa_rep
/// match::upstream_residue_collision_Wfa_sol
class UpstreamCollisionFilter : public MatchCollisionFilter {
public:
  typedef core::Real Real;
  typedef MatchCollisionFilter parent;

public:
  //UpstreamCollisionFilter( std::string filter_name );
  UpstreamCollisionFilter( std::string filter_name, UpstreamHitCacherOP coordinate_cacher );

  virtual
  ~UpstreamCollisionFilter();

  /// @brief Returns true if the given match does not contain too much residue-pair collision.
  virtual
  bool
  passes_filter(
    match const & m
  ) const;

  /// @brief Returns true if the given match does not contain too much residue-pair collision.
  virtual
  bool
  passes_filter(
    match_dspos1 const & m
  ) const;

  bool
  passes_hardsphere_filter(
    core::Size geomcst_a,
    core::Size geomcst_b,
    Hit const & upstream_hit_a,
    Hit const & upstream_hit_b
  ) const;

  inline
  bool
  passes_hardsphere_filter(
    core::conformation::Residue const & resA,
    core::conformation::Residue const & resB
  ) const
  {
    for ( Size ii = resA.first_sidechain_atom(); ii <= resA.nheavyatoms(); ++ii ) {
      ProbeRadius ii_rad = probe_radius_for_atom_type( resA.atom_type_index( ii ) );
      for ( Size jj = resB.first_sidechain_atom(); jj <= resB.nheavyatoms(); ++jj ) {
        ProbeRadius jj_rad = probe_radius_for_atom_type( resB.atom_type_index( jj ) );
        Real minsep = bump_grid()->required_separation_distance( ii_rad, jj_rad );
        if ( resA.xyz( ii ).distance_squared( resB.xyz( jj )) < minsep * minsep ) {
          return false;
        }
      }
    }
    return true;
  }

private:

};


}
}
}

#endif