FlexbbRotamerSets.hh

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// vi: set ts=2 noet:
//
// (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/flexpack/rotamer_set/FlexbbRotamerSets.hh
/// @brief  Declaration for a class to hold a set of rotamers for a flexible packing run
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com), Florian Richter (floric@u.washington.edu), oct 08

#ifndef INCLUDED_protocols_flexpack_rotamer_set_FlexbbRotamerSets_hh
#define INCLUDED_protocols_flexpack_rotamer_set_FlexbbRotamerSets_hh

/// Unit headers
#include <protocols/flexpack/rotamer_set/FlexbbRotamerSets.fwd.hh>

/// Package headers
#ifdef WIN32
#include <protocols/flexpack/rotamer_set/FlexbbRotamerSet.hh>
#endif

#include <protocols/flexpack/interaction_graph/FlexbbInteractionGraph.fwd.hh>
#include <protocols/flexpack/interaction_graph/OTFFlexbbInteractionGraph.fwd.hh>
#include <protocols/flexpack/interaction_graph/PrecomputedFlexbbInteractionGraph.fwd.hh>

/// Project headers
#include <core/conformation/Residue.fwd.hh>
#include <core/fragment/Frame.fwd.hh>
#include <core/graph/Graph.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/rotamer_set/RotamerSetsBase.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/methods/LongRangeTwoBodyEnergy.fwd.hh>
#include <core/types.hh>

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

#include <protocols/flexpack/rotamer_set/FlexbbRotamerSet.fwd.hh>
#include <utility/vector1.hh>



namespace protocols {
namespace flexpack {
namespace rotamer_set {

class FlexbbRotamerSets : public core::pack::rotamer_set::RotamerSetsBase
{
public:
  typedef core::Size Size;
  typedef core::PackerEnergy PackerEnergy;
  typedef core::pose::Pose Pose;
  typedef core::scoring::ScoreFunction ScoreFunction;
  typedef core::scoring::methods::LongRangeTwoBodyEnergy LongRangeTwoBodyEnergy;
  typedef core::pack::task::PackerTaskCOP PackerTaskCOP;

public:
  FlexbbRotamerSets( PackerTaskCOP task );

  virtual ~FlexbbRotamerSets();

  void
  set_frames(
    Pose const & pose,
    utility::vector1< core::fragment::FrameCOP > const & frames
  );

  core::graph::GraphOP
  flexpack_neighbor_graph(
    Pose const & pose,
    ScoreFunction const & sfxn,
    PackerTaskCOP task
  ) const;

  core::Distance
  determine_res_cb_deviation(
    Pose const & pose,
    Size resid
  ) const;

  void build_rotamers(
    Pose const & pose,
    ScoreFunction const & sfxn,
    core::graph::Graph const & flexpack_neighbor_graph
  );

  void
  dump_pdbs( core::pose::Pose const & pose, std::string const & filename_base ) const;

  void
  precompute_energies(
    Pose const & pose,
    ScoreFunction const & sfxn,
    core::graph::GraphCOP flexpack_neighbor_graph,
    interaction_graph::FlexbbInteractionGraph & flexbb_ig
  ) const;

  void precompute_all_energies(
    Pose const & pose,
    ScoreFunction const & sfxn,
    core::graph::GraphCOP flexpack_neighbor_graph,
    interaction_graph::PrecomputedFlexbbInteractionGraph & flexbb_ig
  ) const;

  /* void compute_one_body_energies_for_precomputed_ig(
    Pose const & pose,
    ScoreFunction const & sfxn,
    core::graph::GraphCOP flexpack_neighbor_graph,
    interaction_graph::FlexbbInteractionGraph & flexbb_ig
  ) const; */

  void compute_one_body_energies_for_otf_ig(
    Pose const & pose,
    ScoreFunction const & sfxn,
    core::graph::GraphCOP flexpack_neighbor_graph,
    interaction_graph::OTFFlexbbInteractionGraph & flexbb_ig
  ) const;

  /* void compute_two_body_energies(
    Pose const & pose,
    ScoreFunction const & sfxn,
    core::graph::Graph const & flexpack_neighbor_graph,
    interaction_graph::PrecomputedFlexbbInteractionGraph & flexbb_ig
  ) const; */

  //void prepare_sets_for_packing( Pose const & pose, ScoreFunction const &);

  /// Virtual functions from base class
  virtual core::uint nrotamers() const;
  virtual core::uint nrotamers_for_moltenres( core::uint ) const;

  virtual core::uint nmoltenres() const;

  virtual core::uint total_residue() const;

  virtual
  core::uint
  moltenres_2_resid( core::uint ) const;

  virtual
  core::uint
  resid_2_moltenres( core::uint ) const;

  virtual
  core::uint
  moltenres_for_rotamer( core::uint ) const;

  virtual
  core::uint
  res_for_rotamer( core::uint ) const;

  virtual
  core::conformation::ResidueCOP
  rotamer( core::uint ) const;

  virtual
  core::conformation::ResidueCOP
  rotamer_for_moltenres( core::uint moltenres_id, core::uint rotamerid ) const;

  virtual
  core::uint
  nrotamer_offset_for_moltenres( core::uint ) const;

  /// @brief convert rotid in full rotamer enumeration into rotamer id on its source residue
  virtual
  core::uint
  rotid_on_moltenresidue( core::uint rotid ) const;

  /// @brief convert moltenres rotid to id in full rotamer enumeration
  virtual
  core::uint
  moltenres_rotid_2_rotid( core::uint moltenres, core::uint moltenresrotid ) const;

  Size
  nmolten_res() const
  { return nmoltenres_;}

  //Size
  //moltenres_2_resid( Size molten_resid ) const
  //{ return moltenres_2_resid_[ molten_resid ]; }

  //Size
  //resid_2_moltenres( Size resid ) const
  //{ return resid_2_moltenres_[ resid ]; }

  /// @brief The total number of rotamers across all residues and all backbone conformations
  //Size
  //nrotamers() const {
  //  return nrotamers_;
  //}

  //Size
  //nrotamers_for_moltenres( Size molten_resid ) const
  //{ return nrotamers_for_moltenres_[ molten_resid ]; }

  Size
  nrotamers_for_res( Size resid ) const
  { return nrotamers_for_moltenres_[ resid_2_moltenres_[ resid ] ]; }

  Size
  nbbconfs_for_moltenres( core::Size moltenres ) const;

  Size
  nbbconfs_for_flexseg( core::Size flex_segment_id ) const
  { return nbbconfs_for_flexseg_[ flex_segment_id ]; }

  /// @brief the "total" number of backbone conformations, counting the input conformation
  /// for all flexible segments (but not counting the input conformation for residues with only a single
  /// backbone conformation)
  Size
  nbackbone_conformations() const;

  Size
  nbbconfs_for_res( core::Size resid ) const;

  utility::vector1< Size > const &
  num_states_per_backbone_for_moltenres( Size moltenres ) const {
    return nrots_for_moltenres_bbconf_[ moltenres ];
  }

  Size
  nrotamers_for_moltenres_in_bbconf( Size moltenres, Size bbconf ) const
  { return nrots_for_moltenres_bbconf_[moltenres][bbconf]; }

  Size
  nrotamers_for_resid_in_bbconf( Size resid, Size bbconf ) const
  { return nrots_for_moltenres_bbconf_[ resid_2_moltenres_[ resid ] ][ bbconf ]; }

  Size
  global_rotid_start_for_moltenres_in_bbconf( Size moltenres, Size bbconf ) const
  { return nrotoffset_for_moltenres_bbconf_[ moltenres ][ bbconf ] ;}

  Size
  local_rotid_start_for_moltenres_in_bbconf( Size moltenres, Size bbconf ) const
  { return nrotoffset_for_moltenres_bbconf_[ moltenres ][ bbconf ] - nrotoffset_for_moltenres_[ moltenres ]; }

  //virtual
  //uint
  //nrotamer_offset_for_moltenres( uint moltenresid ) const {
  //  return nrotoffset_for_moltenres_[ moltenresid ];
  //}

  /// @brief Input: rotid in global enumeration, Output rotid in local enumeration
  Size
  local_rotid_for_rotamer_on_moltenres( Size moltenres, Size rotamer_id ) const
  { return rotamer_id - nrotoffset_for_moltenres_[ moltenres ] ; }


  Size
  local_rotid_for_rotamer( Size rotamer_id ) const
  { return rotamer_id - nrotoffset_for_moltenres_[ moltenres_for_rotamer_[ rotamer_id ] ]; }

  Size
  nflexible_segments() const
  { return flexsegment_span_.size(); }

  Size
  flexsegment_start_moltenresid( Size flex_segment_id ) const
  { return resid_2_moltenres_[ flexsegment_span_[ flex_segment_id ].first ]; }

  Size
  flexsegment_stop_moltenresid( Size flex_segment_id ) const
  { return resid_2_moltenres_[ flexsegment_span_[ flex_segment_id ].second ]; }

  Size
  flexsegment_size( Size flex_segment_id ) const
  { return flexsegment_span_[ flex_segment_id ].second - flexsegment_span_[ flex_segment_id ].first + 1; }

  Size
  flexsegment_start_resid( Size flex_segment_id ) const
  { return flexsegment_span_[ flex_segment_id ].first; }

  Size
  flexsegment_stop_resid( Size flex_segment_id ) const
  { return flexsegment_span_[ flex_segment_id ].second; }

  Size
  flexsegid_for_moltenres( Size molten_resid ) const
  { return moltenres_2_flexseg_[ molten_resid ]; }

  Size
  flexsegid_for_res( Size resid ) const
  { return moltenres_2_flexseg_[ resid_2_moltenres_[ resid ] ]; }

  bool
  moltenres_part_of_flexsegment( Size molten_resid ) const
  { return moltenres_2_flexseg_[ molten_resid ] != 0; }

  bool
  res_part_of_flexsegment( Size resid ) const
  { return moltenres_2_flexseg_[ resid_2_moltenres_[ resid ] ] != 0; }

  FlexbbRotamerSetCOP
  rotset_for_moltenres( Size molten_resid, Size bbconf = 1 ) const;

  FlexbbRotamerSetCOP
  rotset_for_residue( Size resid, Size bbconf = 1 ) const;

  /// @brief Rotamer indexed locally
  core::conformation::ResidueCOP
  rotamer_for_residue( Size resid, Size rotindex_on_residue ) const;

  /// @brief Rotamer indexed locally
  //core::conformation::ResidueCOP
  //rotamer_for_moltenres( Size moltenres, Size rotindex_on_residue ) const;

  /// @brief Rotamer indexed globally.
  //core::conformation::ResidueCOP
  //rotamer( Size rotindex ) const;

  core::conformation::Residue const &
  backbone_for_resid_bbconf( Size resid, Size bbconf ) const
  { return *conformations_for_flexible_segments_[ resid_2_moltenres_[ resid ] ][ bbconf ]; }

  core::conformation::Residue const &
  backbone_for_moltenres_bbconf( Size moltenres, Size bbconf ) const
  { return *conformations_for_flexible_segments_[ moltenres ][ bbconf ]; }


  /// @brief rotamer_id in the global enumeration of rotamers.
  //Size
  //moltenres_for_rotamer( Size rotamer_id ) const {
  //  return moltenres_for_rotamer_[ rotamer_id ];
  //}

  Size
  bbconf_for_rotamer( Size rotamer_id ) const {
    Size moltenres = moltenres_for_rotamer_[ rotamer_id ];
    return bbconf_for_rotamer_of_moltenres_[ moltenres ][ local_rotid_for_rotamer_on_moltenres( moltenres, rotamer_id ) ];
  }

  Size
  bbconf_for_rotamer_on_moltenres( Size moltenres, Size rotamer_id ) const {
    return bbconf_for_rotamer_of_moltenres_[ moltenres ][ rotamer_id ];
  }

  /// @brief Do two rotamers originate from the same backbone conformation?
  /// Local enumeration for both rot1 and rot2; rot1 and rot2 must be rotamers of the
  /// same molten residue.
  bool
  rotamers_on_same_bbconf( Size moltenres, Size rot1, Size rot2 ) const {
    utility::vector1< Size > const & bbconf( bbconf_for_rotamer_of_moltenres_[ moltenres ] );
    return bbconf[ rot1 ] == bbconf[ rot2 ];
  }

protected:

  void
  build_residue_vector_from_fragment(
    Pose & pose,
    core::fragment::FrameCOP frame,
    Size frag_num,
    utility::vector1< core::conformation::ResidueOP > & fragment_res
  );

private:
  void update_offset_data();

  void
  compute_sr_one_body_energies_for_flexsets(
    Size lowermoltenres,
    Size uppermoltenres,
    utility::vector1< utility::vector1< Size > > const & regular_representatives,
    utility::vector1< utility::vector1< Size > > const & proline_representatives,
    utility::vector1< utility::vector1< Size > > const & glycine_representatives,
    Pose const & pose,
    ScoreFunction const & sfxn,
    interaction_graph::OTFFlexbbInteractionGraph & flexbb_ig
  ) const;

  void
  compute_onebody_interactions_with_background(
    Size moltenres,
    Pose const & pose,
    ScoreFunction const & sfxn,
    core::graph::GraphCOP flexpack_neighbor_graph,
    interaction_graph::FlexbbInteractionGraph & flexbb_ig
  ) const;


private:

  //not derived from fixbb RotamerSets, so we need to copy some of the basic data structs
  Size nmoltenres_;
  Size total_residue_;
  Size nbbconfs_;

  PackerTaskCOP task_;  // initialized at construction

  utility::vector1< utility::vector1< rotamer_set::FlexbbRotamerSetOP > > rotamers_;
  Size nrotamers_;
  utility::vector1< Size > nrotamers_for_moltenres_;
  utility::vector1< Size > moltenres_2_resid_;
  utility::vector1< Size > resid_2_moltenres_;

  //andrew, did you forget to put these two vectors in?
  utility::vector1< Size > moltenres_for_rotamer_;
  utility::vector1< utility::vector1< Size > > bbconf_for_rotamer_of_moltenres_;

  //why is this a vector of vector of residues?
  utility::vector1< utility::vector1< core::conformation::ResidueCOP > > conformations_for_flexible_segments_;
  utility::vector1< std::pair< Size, Size > > flexsegment_span_;
  utility::vector1< Size > nbbconfs_for_flexseg_;
  utility::vector1< Size > moltenres_2_flexseg_;
  utility::vector1< Size > nrotoffset_for_moltenres_;
  utility::vector1< utility::vector1< Size > > nrots_for_moltenres_bbconf_;
  utility::vector1< utility::vector1< Size > > nrotoffset_for_moltenres_bbconf_;

};


}
}
}

#endif