DownstreamBuilder.hh

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// (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
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/// @file   protocols/match/downstream/DownstreamBuilder.hh
/// @brief
/// @author Alex Zanghellini (zanghell@u.washington.edu)
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com), porting to mini
/// @author Florian Richter (floric@u.washington.edu)

#ifndef INCLUDED_protocols_match_downstream_DownstreamBuilder_hh
#define INCLUDED_protocols_match_downstream_DownstreamBuilder_hh

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

// Package headers
#include <protocols/match/BumpGrid.fwd.hh>
// AUTO-REMOVED #include <protocols/match/Hit.hh>
#include <protocols/match/OccupiedSpaceHash.fwd.hh>
#include <protocols/match/downstream/ActiveSiteGrid.fwd.hh>
#include <protocols/match/downstream/RigidLigandBuilder.fwd.hh>
#include <protocols/match/downstream/LigandConformerBuilder.fwd.hh>
#include <protocols/toolbox/match_enzdes_util/LigandConformer.fwd.hh>

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

// Numeric headers
#include <numeric/HomogeneousTransform.fwd.hh>

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

// C++ headers
#include <list>

#include <core/id/AtomID.fwd.hh>
#include <protocols/match/Hit.fwd.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace match {
namespace downstream {

class DownstreamBuilder : public utility::pointer::ReferenceCount {
public:
  typedef utility::pointer::ReferenceCount      parent;
  typedef core::id::AtomID                      AtomID;
  typedef core::Vector                          Vector;
  typedef core::Real                            Real;
  typedef numeric::HomogeneousTransform< Real > HTReal;

public:
  DownstreamBuilder();

  DownstreamBuilder( DownstreamBuilder const & );

  virtual ~DownstreamBuilder();

  virtual
  DownstreamBuilderOP
  clone() const = 0;

  virtual
  std::list< Hit >
  build(
    HTReal const & atom6_frame,
    Size const scaffold_build_point_id,
    Size const upstream_conf_id,
    Size const external_geometry_id,
    core::conformation::Residue const & upstream_residue
  ) const = 0;

  virtual
  void
  set_bb_grid(
    BumpGridCOP bbgrid
  );

  void
  set_occupied_space_hash(
    OccupiedSpaceHashCOP occ_space
  );

  void
  set_active_site_grid(
    ActiveSiteGridCOP active_site_grid
  );

  /// @brief In case downstream builders can return hits that
  /// are incompatible with each other (e.g. different ligand
  /// conformations ) the matcher needs to know about this to
  /// allow for speedy match enumeration
  virtual bool
  hits_potentially_incompatible() const = 0;

  virtual bool compatible(
    Hit const & my_hit,
    DownstreamBuilder const & other,
    Hit const & other_hit,
    bool first_dispatch = true
  ) const;

  virtual bool compatible(
    Hit const & my_hit,
    RigidLigandBuilder const & other,
    Hit const & other_hit,
    bool first_dispatch = true
  ) const;

  virtual bool compatible(
    Hit const & my_hit,
    LigandConformerBuilder const & other,
    Hit const & other_hit,
    bool first_dispatch = true
  ) const;

  virtual
  void
  require_atom_to_reside_in_active_site(
    core::id::AtomID const & id
  ) = 0;

  virtual
  ProbeRadius
  atom1_radius() const = 0;

  virtual
  ProbeRadius
  atom2_radius() const = 0;

  virtual
  ProbeRadius
  atom3_radius() const = 0;

  virtual
  bool
  atom1_belongs_in_active_site() const = 0;

  virtual
  bool
  atom2_belongs_in_active_site() const = 0;

  virtual
  bool
  atom3_belongs_in_active_site() const = 0;


  virtual
  Real
  atom1_atom2_distance() const = 0;

  virtual
  Real
  atom2_atom3_distance() const = 0;

  /// @brief Returns an angle in degrees between the three downstream atoms.
  virtual
  Real
  atom1_atom2_atom3_angle() const = 0;

  virtual
  void
  coordinates_from_hit(
    Hit const & hit,
    utility::vector1< AtomID > const & atom_indices, // these are the indices of the atoms whose coordinates are requested
    utility::vector1< Vector > & atom_coords       // ouput coordinates are placed in this array.
  ) const = 0;

  virtual
  toolbox::match_enzdes_util::LigandConformerOP
  get_lig_conformers(core::Size conf_id) const = 0;

//  virtual
//  utility::vector1< utility::vector1< std::pair< core::Size, core::Real > > >
//  get_min_sep_d2_from_upstream_atoms() const = 0;

  virtual
  core::chemical::ResidueTypeCOP
  get_upstream_restype() const = 0;

  virtual
  core::pose::PoseCOP
  downstream_pose_from_hit(
    Hit const & hit
  ) const = 0;

  virtual
  Size
  n_possible_hits_per_at3frame() const = 0;


protected:
  bool
  bbgrid_set() const {
    return bb_grid_.get() != 0;
  }

  BumpGrid const &
  bbgrid() const {
    return *bb_grid_;
  }

  bool
  occ_space_set() const {
    return space_ != 0;
  }

  OccupiedSpaceHash const &
  occ_space() const {
    return *space_;
  }

  bool
  active_site_grid_set() const {
    return active_site_grid_ != 0;
  }

  ActiveSiteGrid const &
  active_site_grid() const {
    return *active_site_grid_;
  }

private:
  BumpGridCOP bb_grid_;
  OccupiedSpaceHashCOP space_;
  ActiveSiteGridCOP active_site_grid_;

};

}
}
}

#endif