PairingLibrary.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 src/protocols/jumping/PairingTemplate
/// @brief header file for ClassicAbinitio protocol
/// @detailed
///  from converting jumping_pairings.cc of rosetta++ into mini
///
///
///
/// @author Oliver Lange



#ifndef INCLUDED_protocols_jumping_PairingLibrary_hh
#define INCLUDED_protocols_jumping_PairingLibrary_hh

// Unit Headers

// Package Headers

// Project Headers
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>

#include <core/fragment/FragData.fwd.hh>
#include <core/fragment/FragSet.fwd.hh>

// AUTO-REMOVED #include <core/scoring/dssp/PairingsList.hh>

// ObjexxFCL Headers
#include <ObjexxFCL/FArray1D.hh>

// Utility headers
#include <utility/pointer/ReferenceCount.hh>
// AUTO-REMOVED #include <utility/vector1.hh>
#include <core/kinematics/RT.hh>
#include <core/kinematics/MoveMap.fwd.hh>

//// C++ headers
#include <cstdlib>
#include <string>
#include <map>
// AUTO-REMOVED #include <vector>

#include <core/scoring/dssp/PairingsList.fwd.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace jumping {


class PairingTemplate  {
  typedef utility::vector1<std::string> AtomList;
public:

  //create template with identical set of three upstream and downstream atoms to define their stubs
  PairingTemplate( std::string const& c, std::string const& s1, std::string const& s2, std::string const& s3);
  PairingTemplate( std::string const& s1, std::string const& s2, std::string const& s3);
  core::kinematics::RT rt_;
  ObjexxFCL::FArray1D_float phi;
  ObjexxFCL::FArray1D_float psi;
  ObjexxFCL::FArray1D_float omega;
  ObjexxFCL::FArray1D_char secstruct;
  AtomList atoms_downstream_;
  AtomList atoms_upstream_;
};

/// @brief returns relative orientation of chains at res1 and res2
/// this is the inner product of the respective N-C vectors.
//void compute_orientation_and_pleating( core::pose::Pose const&, core::Size res1, core::Size res2, core::Size &orientation, core::Size &pleating);

class BasePairingLibrary : public utility::pointer::ReferenceCount {
public:
  virtual ~BasePairingLibrary();

  virtual void
  create_jump_fragments(
    int const orientation,
    int const pleating,
    bool bWithTorsion,
    core::fragment::FragDataList &
  ) const = 0;

  virtual void
  generate_jump_frags(
    core::scoring::dssp::PairingsList const& pairings,
    core::kinematics::MoveMap const& mm,
    bool bWithTorsion,
    core::fragment::FragSet& frags_accumulator
  ) = 0;
};

class PairingLibrary : public BasePairingLibrary {
  typedef std::vector< PairingTemplate > PairingTemplateList;
  typedef std::map< std::pair< int, int >, PairingTemplateList > PairingTemplateMap;
public:
  PairingLibrary():num_of_pairings_(0) {};
  void read_from_file( std::string const& fn);
  void read_from_file_no_filters( std::string const& fn); /*Version which does not assume the jump is a beta sheet */
  //void read_from_database();

  /// @brief classic rosetta++ accessor
  core::kinematics::RT get_random_beta_sheet_jump(
    int const orientation,
    int const pleating
  ) const;
  /// @brief classic rosetta++ accessor
  core::kinematics::RT get_random_tmh_jump(int const orientation,
                       int const pos1,
                       int const pos2
                      ) const;
  void
  set_tmh_jump(core::pose::Pose pose,
        int const jump_number,
        int const orientation,
        int const pos1,
        int const pos2
  ) const;
  /// @brief puts all jump-geometries that fit the orientation and pleating into
  /// list of FragData's. Try to reuse these FragData for different Frames that have same orientation and pleating
  /// This creates Fragments with single JumpSRFD --- PairingLibrary also stores phi/psi/omega of start and end residue
  /// use bWithTorsion = true to get FragData with BBTorsionSRFD and JumpSRFD
  /// length of single FragData is
  ///   noTorsion 1
  ///   withTorsion 3
  /// bWithTorsion = true length of single FragData is 3   start jump end
  void
  create_jump_fragments(
    int const orientation,
    int const pleating,
    bool bWithTorsion,
    core::fragment::FragDataList &
  ) const;

  core::Size
  size() const {
    return num_of_pairings_;
  }

  void
  generate_jump_frags(
    core::scoring::dssp::PairingsList const & pairings,
    core::kinematics::MoveMap const & mm,
    bool bWithTorsion,
    core::fragment::FragSet & frags_accumulator
  );

private:
  PairingTemplateMap pairings_;
  core::Size num_of_pairings_;
};

class SpecificGeometryLibrary : public PairingLibrary {
public:

private:
};

class StandardPairingLibrary : public PairingLibrary {
public:
  static StandardPairingLibrary* get_instance();
private:
  StandardPairingLibrary() {};
  static StandardPairingLibrary* instance_;
};


} //protocols
} //jumping

#endif