ClassicMatchAlgorithm.hh

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// (c) Copyright Rosetta Commons Member Institutions.
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// (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
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/// @file   protocols/match/downstream/ClassicMatchAlgorithm.hh
/// @brief
/// @author Alex Zanghellini (zanghell@u.washington.edu)
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com), porting to mini

#ifndef INCLUDED_protocols_match_downstream_ClassicMatchAlgorithm_hh
#define INCLUDED_protocols_match_downstream_ClassicMatchAlgorithm_hh

// Unit headers
#include <protocols/match/downstream/ClassicMatchAlgorithm.fwd.hh>

// Package headers
#include <protocols/match/BumpGrid.fwd.hh>
#include <protocols/match/downstream/ActiveSiteGrid.fwd.hh>
#include <protocols/match/downstream/DownstreamAlgorithm.hh>
#include <protocols/match/downstream/DownstreamBuilder.fwd.hh>
#include <protocols/toolbox/match_enzdes_util/ExternalGeomSampler.hh>
// AUTO-REMOVED #include <protocols/match/Hit.hh>

// Project headers
#include <core/types.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
// AUTO-REMOVED #include <core/pose/Pose.fwd.hh>

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

// C++ headers
#include <list>
#include <string>

#include <utility/fixedsizearray1.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace match {
namespace downstream {

/// @brief Produce hits by hashing building the coordinates of the downstream partner
/// The downstream partner is responsible for building itself from the coordinate frame of
/// three of its atoms.  The ExternalGeomSampler describes the ways to orient the downstream
/// partner given the coordinates of the upstream partner.
class ClassicMatchAlgorithm : public DownstreamAlgorithm
{
public:
  typedef DownstreamAlgorithm parent;
  typedef core::Size Size;
  typedef core::Real Real;
  typedef numeric::HomogeneousTransform< Real > HTReal;

public:
  ClassicMatchAlgorithm( Size geom_cst_id );
  virtual ~ClassicMatchAlgorithm();

  virtual
  DownstreamAlgorithmOP
  clone() const;

  virtual
  std::list< Hit >
  build_hits_at_all_positions(
    Matcher & matcher
  );

  /// @brief Reset the occupied space grid for the matcher so that only those
  /// regions which contain hits from this geometric constraint are marked as occupied.
  virtual
  void
  respond_to_primary_hitlist_change( Matcher & matcher, Size round_just_completed );

  /// @brief Delete hits for this geometric constraint if they fall into
  /// now-empty regions of 6D.  This step can be avoided if the occupied-space-grid's
  /// revision ID has not changed since the last time this function was invoked.
  virtual
  void
  respond_to_peripheral_hitlist_change( Matcher & matcher );

  /// @brief Iterate across the external geom samplers that describe the rigid body orientations
  /// of the downstream partner from the coordinates of the upstream partner.
  virtual
  std::list< Hit >
  build(
    Size const scaffold_build_point_id,
    Size const upstream_conf_id,
    core::conformation::Residue const & upstream_residue
  ) const;

  /// @brief This method returns 'false' since the classic match algorithm
  /// builds coordinates of the downstream partner and its hits should
  /// be hashed in 6D to generate matches
  virtual
  bool
  upstream_only() const;

  /// @brief This method returns 'true' since the classic matcher builds the
  /// downstream coordinates from scratch.
  virtual
  bool
  generates_primary_hits() const;


  /// @brief This method should not be invoked on the ClassicMatchAlgorithm,
  /// since it returns "false" in its upstream_only method.
  virtual
  HitPtrListCOP
  hits_to_include_with_partial_match( match_dspos1 const & m ) const;

  virtual
  Size
  n_possible_hits_per_upstream_conformation() const;


  /// @brief This function completes the building of the downstream conformation
  /// once the coordinates of the upstream conformation are known (and deemed
  /// non-colliding or, generally, pass any filter the upstream builder would use).
  std::list< Hit >
  build_from_three_coords(
    Size const which_external_sampler,
    Size const scaffold_build_point_id,
    Size const upstream_conf_id,
    core::conformation::Residue const & upstream_residue
  ) const;

public:

  void set_residue_type( core::chemical::ResidueTypeCOP restype );

  void add_external_geom_sampler(
    toolbox::match_enzdes_util::ExternalGeomSampler const & sampler,
    Size const exgeom_id,
    std::string const & atom1,
    std::string const & atom2,
    std::string const & atom3,
    DownstreamBuilderCOP downstream_builder
  );

  void clear_external_geom_samplers();

public:
  /// Accessors

  core::chemical::ResidueType const &
  restype() const {
    return *restype_;
  }

  toolbox::match_enzdes_util::ExternalGeomSampler const &
  external_sampler( Size external_geom_id ) const
  {
    return external_samplers_[ external_geom_id ];
  }

  Size
  launch_atom( Size external_geom_id, Size which_point ) const {
    return launch_points_[ external_geom_id ][ which_point ];
  }

  Size
  n_external_samplers() const {
    return external_samplers_.size();
  }

private:
  core::chemical::ResidueTypeCOP  restype_;

  utility::vector1< toolbox::match_enzdes_util::ExternalGeomSampler > external_samplers_;
  utility::vector1< utility::fixedsizearray1< Size, 3 > > launch_points_;
  utility::vector1< DownstreamBuilderCOP > dsbuilders_;
  utility::vector1< Size > exgeom_ids_;

  Size occspace_rev_id_at_last_update_;
};

}
}
}

#endif