#include <JumpSRFD.hh>

Inheritance diagram for core::fragment::DownJumpSRFD:

Collaboration diagram for core::fragment::DownJumpSRFD:

Public Types
typedef utility::vector1 < std::string >	AtomList

Public Member Functions
	DownJumpSRFD (char sequence= 'X')

	DownJumpSRFD (kinematics::RT rt, AtomList downstream_stub_atoms, AtomList upstream_stub_atoms, char sequence)

SingleResidueFragDataOP	clone () const
	clone More...

virtual SingleResidueFragDataOP	create () const
	create a new instance of this object More...

void	set_jump (kinematics::RT setting)
	set value of jump More...

void	set_stub_atoms (AtomList downstream, AtomList upstream)

void	set_standard_stub_atoms ()

virtual bool	apply (pose::Pose &, Size const intra_frame_pos, Frame const &) const
	the seq_pos is hijacked for the rt_nr More...

virtual bool	apply (kinematics::MoveMap const &, pose::Pose &, Size const intra_frame_pos, Frame const &) const
	insert fragment_data into pose at position given by Frame.seqpos( intra_frame_pos ) for dofs that are allowed to move in the MoveMap More...

virtual bool	apply_ss (std::string &, Size, Frame const &) const
	insert fragment_data sec-struct into ss-string at position seq_pos More...

bool	steal (pose::Pose const &, Size pos, Frame const &)
	insert fragment_data into pose at position seq_pos More...

bool	is_compatible (SingleResidueFragData const &) const
	check weather SRFD applies to same dofs and is of same type More...

bool	is_applicable (kinematics::MoveMap const &, Size pos, Frame const &) const
	check weather dofs can be moved More...

virtual bool	apply (pose::Pose &, Size) const
	insert fragment_data into pose at position seq_pos More...

virtual bool	apply (kinematics::MoveMap const &, pose::Pose &, Size const ) const
	for DownJumpSRFD this function should never be called, instead use Frame version More...

virtual bool	apply_ss (std::string &, Size) const
	insert fragment_data sec-struct into ss-string at position seq_pos More...

virtual bool	steal (pose::Pose const &, Size)
	insert fragment_data into pose at position seq_pos More...

virtual bool	is_applicable (kinematics::MoveMap const &, Size) const
	check whether dofs can be moved More...

virtual std::string	type () const

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

virtual void	read (std::istream &in)

Public Member Functions inherited from core::fragment::SingleResidueFragData
virtual	~SingleResidueFragData ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	SingleResidueFragData (char sequence)

	SingleResidueFragData ()

void	set_sequence (char const sequence)

char	sequence () const

virtual char	secstruct () const

virtual void	read_data (std::istream &)
	Default implementation: noop. More...

Static Public Member Functions
static std::string	_static_type_name ()

Static Public Member Functions inherited from core::fragment::SingleResidueFragData
static std::string	_static_type_name ()

Private Types
typedef SingleResidueFragData	Parent

Private Attributes
kinematics::RT	rt_

AtomList	downstream_stub_atoms_

AtomList	upstream_stub_atoms_

Additional Inherited Members
Protected Attributes inherited from core::fragment::SingleResidueFragData
char	sequence_

Detailed Description

Definition at line 130 of file JumpSRFD.hh.

Member Typedef Documentation

typedef utility::vector1<std::string> core::fragment::DownJumpSRFD::AtomList

Definition at line 133 of file JumpSRFD.hh.

typedef SingleResidueFragData core::fragment::DownJumpSRFD::Parent

private

Definition at line 131 of file JumpSRFD.hh.

Constructor & Destructor Documentation

core::fragment::DownJumpSRFD::DownJumpSRFD ( char sequence = 'X')

inline

Definition at line 135 of file JumpSRFD.hh.

References set_standard_stub_atoms().

Referenced by clone(), and create().

core::fragment::DownJumpSRFD::DownJumpSRFD	(	kinematics::RT	rt,
		AtomList	downstream_stub_atoms,
		AtomList	upstream_stub_atoms,
		char	sequence
	)

inline

Definition at line 141 of file JumpSRFD.hh.

Member Function Documentation

static std::string core::fragment::DownJumpSRFD::_static_type_name ( )

inlinestatic

Definition at line 229 of file JumpSRFD.hh.

Referenced by core::fragment::FragFactory::FragFactory(), and type().

bool core::fragment::DownJumpSRFD::apply	(	pose::Pose &	pose,
		Size const	intra_frame_pos,
		Frame const &	frame
	)		const

virtual

the seq_pos is hijacked for the rt_nr

Reimplemented from core::fragment::SingleResidueFragData.

Definition at line 94 of file JumpSRFD.cc.

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_jump_point(), core::pose::named_stub_id_to_stub_id(), core::fragment::Frame::seqpos(), core::conformation::Conformation::set_stub_transform(), and core::fragment::tr().

bool core::fragment::DownJumpSRFD::apply	(	kinematics::MoveMap const &	movemap,
		pose::Pose &	pose,
		Size const	intra_frame_pos,
		Frame const &	frame
	)		const