MotifSearch.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (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 MotifSearch.hh
/// @brief Class declaration for motif searching protocol
/// @author sthyme (sthyme@gmail.com)

#ifndef INCLUDED_protocols_motifs_MotifSearch_hh
#define INCLUDED_protocols_motifs_MotifSearch_hh

// Unit Headers
#include <protocols/motifs/MotifSearch.fwd.hh>

// Package Headers
#include <protocols/dna/DnaDesignDef.fwd.hh>
#include <protocols/motifs/BuildPosition.fwd.hh>
#include <protocols/motifs/Motif.fwd.hh>
#include <protocols/motifs/MotifHit.fwd.hh>
#include <protocols/motifs/MotifLibrary.fwd.hh>

// Project Headers
#include <core/conformation/Residue.fwd.hh>
#include <core/pack/rotamer_set/RotamerSet.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>

// Utility Headers
#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.hh>

// C++ Headers
#include <map>
#include <set>
#include <string>

#ifdef WIN32
  #include <protocols/motifs/BuildPosition.hh>
#endif

namespace protocols {
namespace motifs {

class MotifSearch : public utility::pointer::ReferenceCount
{

public:

  typedef core::Real Real;
  typedef core::Size Size;
  typedef utility::vector1< Size > Sizes;
  typedef core::pose::Pose Pose;
  typedef protocols::dna::DnaDesignDefOP DnaDesignDefOP;
  typedef protocols::dna::DnaDesignDefOPs DnaDesignDefOPs;

  // Constructor
  MotifSearch();

  // Destructor
  virtual ~MotifSearch();

  // Copy constructor
  MotifSearch(
    MotifSearch const & src
  );

  MotifSearch const &
  operator = (
    MotifSearch const & src
  );

  //
  void run(
    Pose & pose,
    Sizes & input_BPs
  );

  //
  void initialize(
    Pose & pose,
    Sizes & input_BPs
  );

  void
  incorporate_motifs(
    Pose const & pose
  );

  core::pack::rotamer_set::Rotamers
  bp_rotamers(
    Size const seqpos
  );

  protocols::motifs::MotifHitCOPs
  bp_motifhits(
    Size const seqpos
  );


  bool
  protein_dna_motif();

  void
  position_vector_setup(
    Pose const & pose
  );

  void
  identify_motif_build_positions(
    Pose const & pose,
    Sizes & build_positions
  );

  void identify_motif_BuildPositions(
    Pose const & pose
  );

  void
  BuildPosition_from_Size(
    Pose const & pose,
    Size const input_BP
  );

  void
  defs2BuildPositions(
    Pose const & pose,
    protocols::dna::DnaDesignDefOPs const & defs
  );

  void
  defs2BuildPositions_findts(
    Pose const & pose,
    protocols::dna::DnaDesignDefOPs const & defs
  );

  utility::vector1< Size >
  map2keyvector(
    std::map< Size, std::set< std::string > > mappositions
  );

  utility::vector1< Size >
  shorten_target_list(
    Pose const & pose,
    Size const bp,
    Sizes & full_tl
  );

  void
  protein_DNA_motif_build_positions_JA(
    Pose const & pose,
    Sizes & build_positions,
    Sizes & target_positions
  );

  void
  protein_DNA_motif_target_positions_JA(
    Pose const & pose,
    Sizes & build_positions,
    Sizes & target_positions,
    Sizes & short_tl
  );

  void
  override_option_input(
    Real const & r1,
    Real const & z1,
    Real const & r2,
    Real const & z2,
    Real const & d1,
    Size const & rlevel,
    bool const bpdata,
    bool const bump_check
  );

  void
  reset_option_input();

  void
  set_motif_library(
    MotifLibrary & motiflibrary
  );

  // Accessors
  MotifCOPs const & motif_library() const { return motif_library_; }
  Sizes const & dna_positions() const { return dna_positions_; }
  Sizes const & protein_positions() const { return protein_positions_; }
  std::map< Size, std::set< std::string > > const & target_positions() const { return target_positions_; }
  BuildPositionOPs const & build_positionOPs() const { return build_positionOPs_; }
  std::map< std::string, core::conformation::ResidueOPs > const & target_conformers_map() const { return target_conformers_map_; }
  Real const & ztest_cutoff_1() const { return ztest_cutoff_1_;}
  Real const & ztest_cutoff_2() const { return ztest_cutoff_2_;}
  Real const & rmsd_cutoff_1() const { return rmsd_cutoff_1_;}
  Real const & rmsd_cutoff_2() const { return rmsd_cutoff_2_;}
  Real const & dtest_cutoff() const { return dtest_cutoff_;}
  Size const & rot_level() const { return rot_level_;}
  bool const & minimize() const { return minimize_;}

private:
  void init_options();

private:
  MotifCOPs motif_library_;
  Sizes dna_positions_;
  Sizes protein_positions_;
  std::map< Size, std::set< std::string > > target_positions_;
  BuildPositionOPs build_positionOPs_;
  std::map< std::string, core::conformation::ResidueOPs > target_conformers_map_;

  // inputs used for scoring motif, 1s are broader first limit and 2s are a tighter cutoff for final selection
  Real ztest_cutoff_1_;
  Real ztest_cutoff_2_;
  Real rmsd_cutoff_1_;
  Real rmsd_cutoff_2_;
  Real dtest_cutoff_;

  // input rotamer level (4 = all chis explosion, 8 is extra deviations of explosion on all 4 chis)
  Size rot_level_;

  bool minimize_;

  // options set in init_options
  bool bpdata_;
  std::string bpdata_filename_;
  bool output_;
  std::string output_filename_;
  bool data_;
  std::string data_filename_;
  bool quick_and_dirty_;
  bool dump_motifs_;
  bool clear_bprots_;
  Size rots2add_;
  bool restrict_to_wt_;
  bool rerun_motifsearch_;
  bool bump_check_;

};

} // namespace motifs
} // namespace protocols

#endif // INCLUDED_protocols_motifs_MotifSearch