JumpSRFD.hh

Go to the documentation of this file.

// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
// :noTabs=false:tabSize=4:indentSize=4:
//
// (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   core/fragments/FragData.hh
/// @brief  A fragment as list of SingleResidue Data
/// @author Oliver Lange (olange@u.washington.edu)
/// @date   Wed Oct 20 12:08:31 2007
///
#ifndef INCLUDED_core_fragment_JumpSRFD_HH
#define INCLUDED_core_fragment_JumpSRFD_HH

// Unit Headers
#include <core/fragment/JumpSRFD.fwd.hh>
#include <core/fragment/SingleResidueFragData.hh>

// Package Headers
#include <core/fragment/Frame.fwd.hh>

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

// AUTO-REMOVED #include <core/conformation/Residue.hh> // for ResidueSRFD

// AUTO-REMOVED #include <core/kinematics/types.hh>
#include <core/kinematics/RT.hh>

// AUTO-REMOVED #include <core/id/TorsionID.hh>

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

#include <utility/vector1.hh>



namespace core {
namespace fragment {

class UpJumpSRFD : public SingleResidueFragData {
  typedef SingleResidueFragData Parent;
public:

  UpJumpSRFD( char sequence = 'X'  )
    : SingleResidueFragData( sequence)
  {};

  /// @brief clone
  SingleResidueFragDataOP clone() const {
    return new UpJumpSRFD( *this );
  };

  /// @brief create a new instance of this object
  virtual
  SingleResidueFragDataOP create() const {
    return new UpJumpSRFD();
  }

  virtual bool apply( pose::Pose&, Size const, Frame const& ) const {
    return true;
  }

  virtual bool apply( kinematics::MoveMap const &, pose::Pose &, Size const, Frame const & ) const {
    return true;
  }

  virtual bool apply_ss( std::string&, Size, Frame const& ) const {
    return true;
  };

  bool steal( pose::Pose const&, Size, Frame const& ) {
    return true;
  }

  bool is_compatible( SingleResidueFragData const& ) const;

  bool is_applicable( kinematics::MoveMap const&, Size ) const {
    return true;
  }

  virtual
  std::string type() const {
    return _static_type_name();
  }

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


  // for UpJumpSRFD these functions should never be called
  // might obsolet these completely and only use SRFDs via the func (pose, ipos, Frame ) variant
  virtual bool apply(pose::Pose &, Size) const {
    assert( 0 );
    return false;
  }

  /// @brief for UpJumpSRFD this function should never be called, instead use Frame version
  /// @return always false
  /// @warning will trigger a false runtime assert
  virtual bool apply( kinematics::MoveMap const &, pose::Pose &, Size const ) const {
    runtime_assert( 0 );
    return false;
  }

  // insert fragment_data sec-struct into ss-string at position seq_pos
  virtual bool apply_ss( std::string&, Size) const {
    assert( 0 );
    return false;
  }

  // insert fragment_data into pose at position seq_pos
  virtual bool steal(pose::Pose const&, Size)  {
    assert( 0 );
    return false;
  }

};

//
class DownJumpSRFD : public SingleResidueFragData {
  typedef SingleResidueFragData Parent;
public:
  typedef utility::vector1<std::string> AtomList;

  DownJumpSRFD( char sequence = 'X'  )
    : SingleResidueFragData( sequence)
  {
    set_standard_stub_atoms();
  };

  DownJumpSRFD( kinematics::RT rt, AtomList downstream_stub_atoms, AtomList upstream_stub_atoms, char sequence ) :
    SingleResidueFragData( sequence ),
    rt_( rt ),
    downstream_stub_atoms_( downstream_stub_atoms ),
    upstream_stub_atoms_( upstream_stub_atoms )
  {
    assert( downstream_stub_atoms.size() == 3 || downstream_stub_atoms.size() == 4 );
    assert( upstream_stub_atoms.size() == 3 || upstream_stub_atoms.size() == 4 );
  };

  /// @brief clone
  SingleResidueFragDataOP clone() const {
    return new DownJumpSRFD( *this );
  };

  /// @brief create a new instance of this object
  virtual
  SingleResidueFragDataOP create() const {
    return new DownJumpSRFD();
  }

  /// @brief set value of jump
  void
  set_jump( kinematics::RT setting ) {
    rt_ = setting;
  };

  void
  set_stub_atoms( AtomList downstream, AtomList upstream );

  //@brief set stub atoms to "CA" as center and "N", "CA", "C" as stub atoms
  void
  set_standard_stub_atoms();

  /// @brief the seq_pos is hijacked for the rt_nr

  virtual bool apply( pose::Pose&, Size const intra_frame_pos, Frame const& ) const;
  virtual bool apply( kinematics::MoveMap const &, pose::Pose &, Size const intra_frame_pos, Frame const & ) const;
  virtual bool apply_ss( std::string&, Size, Frame const& ) const { return true; }; //does nothing as jump has no ss

  bool steal( pose::Pose const&, Size pos, Frame const& );
  bool is_compatible( SingleResidueFragData const& ) const;
  bool is_applicable( kinematics::MoveMap const&, Size pos, Frame const& ) const;


  // for DownJumpSRFD these functions should never be called
  // might obsolet these completely and only use SRFDs via the func (pose, ipos, Frame ) variant
  virtual bool apply(pose::Pose &, Size) const {
    assert( 0 );
    return false;
  }

  /// @brief for DownJumpSRFD this function should never be called, instead use Frame version
  /// @return always false
  /// @warning will trigger a false runtime assert
  virtual bool apply( kinematics::MoveMap const &, pose::Pose &, Size const ) const;

  // insert fragment_data sec-struct into ss-string at position seq_pos
  virtual bool apply_ss( std::string&, Size) const {
    assert( 0 );
    return false;
  }

  // insert fragment_data into pose at position seq_pos
  virtual bool steal(pose::Pose const&, Size)  {
    assert( 0 );
    return false;
  }

  //
  virtual bool
  is_applicable( kinematics::MoveMap const&, Size ) const {
    assert( 0 );
    return false;
  }

//  void get_stubs(
//     pose::Pose const& pose,
//    Size downstream_res_nr,
//    id::StubID &up_stub,
//    id::StubID &down_stub
//  ) const;

  virtual
  std::string type() const {
    return _static_type_name();
  }

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

  virtual
  void show( std::ostream &out ) const;

  virtual
  void read( std::istream &in );

private:
  kinematics::RT rt_;
  AtomList downstream_stub_atoms_;
  AtomList upstream_stub_atoms_;
};

}
}

#endif