DisulfJumpClaimer.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 DisulfJumpClaimer
/// @brief  Claimer for disulfide jump sampling
/// @detailed responsibilities:
/// @author Robert Vernon


#ifndef INCLUDED_protocols_topology_broker_DisulfJumpClaimer_hh
#define INCLUDED_protocols_topology_broker_DisulfJumpClaimer_hh


// Unit Headers
#include <protocols/topology_broker/DisulfJumpClaimer.fwd.hh>

// Package Headers
#include <protocols/topology_broker/FragmentClaimer.hh>
#include <protocols/topology_broker/DofClaim.fwd.hh>
#include <protocols/topology_broker/weights/AbinitioMoverWeight.hh>

// Project Headers
#include <core/pose/Pose.fwd.hh>
// AUTO-REMOVED #include <protocols/jumping/JumpSetup.hh>
// AUTO-REMOVED #include <protocols/jumping/JumpSample.hh>
#include <protocols/jumping/DisulfPairingsList.hh>
#include <protocols/jumping/DisulfPairingLibrary.hh>

#include <core/fragment/FrameList.hh>
#include <core/fragment/Frame.hh>
// AUTO-REMOVED #include <core/fragment/FrameIteratorWorker_.hh>
// AUTO-REMOVED #include <core/fragment/JumpingFrame.hh>
// AUTO-REMOVED #include <core/fragment/BBTorsionSRFD.hh>
// AUTO-REMOVED #include <core/fragment/JumpSRFD.hh>

// AUTO-REMOVED #include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>

// ObjexxFCL Headers

// Utility headers
//#include <utility/io/izstream.hh>
//#include <utility/io/ozstream.hh>
//#include <utility/io/util.hh>
//#include <basic/Tracer.hh>
//#include <basic/options/option.hh>

#include <utility/pointer/ReferenceCount.hh>

#include <utility/vector1.hh>


//#include <basic/options/option_macros.hh>

//// C++ headers
//#include <fstream>


// option key includes


namespace protocols {
namespace topology_broker {

///@brief Claimer that works with the old system of BaseJumpSetup
/// it supports only JumpFrames of type  [ BBTorsion ] UpJump DownJump [ BBTorsion ]
/// the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored
/// all functionality of JumpSample is not used anymore
class DisulfJumpClaimer : public FragmentClaimer {
  typedef FragmentClaimer Parent;
public:
  DisulfJumpClaimer(); //for factory

  //DisulfJumpClaimer( std::string const& mover_tag = "JumpMove",  weights::AbinitioMoverWeightOP weight = NULL );

  virtual TopologyClaimerOP clone() const {
    return new DisulfJumpClaimer( *this );
  }

void generate_jump_frags(
  protocols::jumping::DisulfPairingLibrary const& lib,
  //core::kinematics::MoveMap const& mm,
  core::fragment::FrameList& all_frames) const;

  //void generate_jump_frames(
  //   core::fragment::FrameList& all_frames,
  // core::kinematics::MoveMap const& mm) const;

  virtual void generate_claims( DofClaims& );

  virtual void new_decoy( core::pose::Pose const& );
  virtual void new_decoy();

  ///@brief type() is specifying the output name of the TopologyClaimer
  virtual std::string type() const {
    return _static_type_name();
  }

  virtual void initialize_dofs( core::pose::Pose&, DofClaims const& init_claims, DofClaims& failed_to_init );

  static std::string _static_type_name() {
    return "DisulfJumpClaimer";
  }

  virtual bool read_tag( std::string tag, std::istream& is );

protected:
//  void set_jump_def( jumping::BaseJumpSetupOP jump_def ) {
//    jump_def_ = jump_def;
//  }

//  jumping::BaseJumpSetupOP jump_def() {
//    return jump_def_;
//  }

private:
  //jumping::BaseJumpSetupOP jump_def_;
  //jumping::JumpSample current_jumps_;


  //std::string secstruct_;
  //size nr_jumps_;
  //ObjexxFCL::FArray2D< std::string > use_jump_atoms_;
  //ObjexxFCL::FArray2D_int use_jumps_;
  //ObjexxFCL::FArray1D_int use_cuts_;
  //core::kinematics::FoldTreeOP use_fold_tree_;

  utility::vector1< protocols::jumping::DisulfPairing > all_jump_pairings_;
  core::fragment::FrameList all_frames_;

  //  abinitio::ClassicFragmentMoverOP init_mover_;
  bool bKeepJumpsFromInputPose_;
}; //class DisulfJumpClaimer

}
}

#endif