DisulfPairingLibrary.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_DisulfPairingLibrary_hh
#define INCLUDED_protocols_jumping_DisulfPairingLibrary_hh

// Unit Headers

// Package Headers

// Project Headers
// AUTO-REMOVED #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 <protocols/jumping/DisulfPairingsList.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 <protocols/jumping/DisulfPairingsList.fwd.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace jumping {

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

  //create template with identical set of three upstream and downstream atoms to define their stubs
  DisulfTemplate( std::string const& c, std::string const& s1, std::string const& s2, std::string const& s3);
  DisulfTemplate( 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_;
};


class BaseDisulfPairingLibrary : public utility::pointer::ReferenceCount {
public:
  ///@brief Automatically generated virtual destructor for class deriving directly from ReferenceCount
  virtual ~BaseDisulfPairingLibrary();

  //Not currently using base class as copied from PairingLibrary, it's hanging
  //around because I plan to build into it

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

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

class DisulfPairingLibrary : public BaseDisulfPairingLibrary {
  typedef std::vector< DisulfTemplate > DisulfTemplateList;
  typedef std::map< std::pair< int, int >, DisulfTemplateList > DisulfTemplateMap;
public:
  DisulfPairingLibrary():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();

  void
  create_jump_fragments(
                               bool bWithTorsion,
                               core::fragment::FragDataList& frags
                               ) const;

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

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

private:
  DisulfTemplateMap pairings_;
  DisulfTemplateList all_pairings_;
  core::Size num_of_pairings_;
};


class StandardDisulfPairingLibrary : public DisulfPairingLibrary {
public:
  static StandardDisulfPairingLibrary* get_instance();
private:
  StandardDisulfPairingLibrary() {};
  static StandardDisulfPairingLibrary* instance_;
};


} //protocols
} //jumping

#endif