DoubleLayerKinematicAbinitio.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 KinematicTaskCenter
/// @brief  this class will be handled to a SampleProtocol as a control instance
/// @detailed
/// this class will have two LOOP definitions:
/// loops ( defines which part has missing density and should start "extended"
/// rigids ( defines which part should be kept as a rigid (minimal) core )
/// the extended part will be sampled with stage1
/// following on this the non-rigid part will be sampled with stage2-stage4 and loop-closing

/// @author Oliver Lange


#ifndef INCLUDED_protocols_abinitio_DoubleLayerKinematicAbinitio_hh
#define INCLUDED_protocols_abinitio_DoubleLayerKinematicAbinitio_hh

// Unit Headers
#include <protocols/abinitio/DoubleLayerKinematicAbinitio.fwd.hh>
#include <protocols/abinitio/LoopJumpFoldCst.hh>

// Package Headers
#include <protocols/jumping/JumpSetup.hh>
#include <protocols/abinitio/KinematicControl.hh>
#include <protocols/abinitio/Protocol.hh>
#include <protocols/abinitio/ResolutionSwitcher.hh>

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

#include <protocols/loops/Loops.hh>

// ObjexxFCL Headers
//#include <ObjexxFCL/FArray1D.hh>
//#include <ObjexxFCL/FArray2D.hh>

// Utility headers
// AUTO-REMOVED #include <utility/vector1.hh>
#include <utility/pointer/ReferenceCount.hh>

//// C++ headers
#include <cstdlib>
#include <string>

#include <utility/vector1.hh>



namespace protocols {
namespace abinitio {


class DoubleLayerKinematicAbinitio : public LoopJumpFoldCst {
public:
  DoubleLayerKinematicAbinitio(
    jumping::BaseJumpSetupOP jump_def,
    loops::Loops extended_loops,
    loops::Loops rigid_core,
    ProtocolOP sampler,
    ProtocolOP extended_chain_sampler,
    core::fragment::SecondaryStructureOP ss_def,
    core::Real coord_cst_weight,
    bool bCstAllAtom = false //false = CA atoms only
  ) :
    LoopJumpFoldCst( jump_def, extended_loops, sampler, ss_def, coord_cst_weight, bCstAllAtom ),
    rigid_loops_( rigid_core ),
    extended_loops_( extended_loops ),
    stage1_sampler_( extended_chain_sampler )
  {}

  ~DoubleLayerKinematicAbinitio();

  //@brief make a new KinematicControl...
  virtual KinematicControlOP new_kinematics( core::pose::Pose &pose );

  virtual std::string get_name() const;

  //  virtual void init( core::pose::Pose const& pose );

protected:
  ///@brief heuristic to select subset of loops from loops_
  virtual void select_core_loops( loops::Loops& loops_select ) const;

  virtual bool inner_loop( core::pose::Pose& pose );
private:
  loops::Loops rigid_loops_; //if empty rebuild whole structure
  loops::Loops extended_loops_;
  ProtocolOP stage1_sampler_;
};

}
}
#endif