core::fragment::DownJumpSRFD Class Reference

#include <JumpSRFD.hh>

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_

Member Typedef Documentation

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

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

private

Constructor & Destructor Documentation

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

inline

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

Member Function Documentation

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

inlinestatic

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.

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_jump_point(), core::pose::named_stub_id_to_stub_id(), runtime_assert, 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

virtual

insert fragment_data into pose at position given by Frame.seqpos( intra_frame_pos ) for dofs that are allowed to move in the MoveMap

Reimplemented from core::fragment::SingleResidueFragData.

References core::kinematics::MoveMap::get_jump(), and core::fragment::Frame::seqpos().

virtual bool core::fragment::DownJumpSRFD::apply ( pose::Pose &  , Size  seq_pos  ) const

inlinevirtual

insert fragment_data into pose at position seq_pos

Implements core::fragment::SingleResidueFragData.

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

virtual

for DownJumpSRFD this function should never be called, instead use Frame version

Returns

always false

Warning

will trigger a false runtime assert

Implements core::fragment::SingleResidueFragData.

References runtime_assert.

virtual bool core::fragment::DownJumpSRFD::apply_ss ( std::string &  ss, Size  intra_frame_pos, Frame const &  frame  ) const

inlinevirtual

insert fragment_data sec-struct into ss-string at position seq_pos

Reimplemented from core::fragment::SingleResidueFragData.

virtual bool core::fragment::DownJumpSRFD::apply_ss ( std::string &  , Size  seq_pos  ) const

inlinevirtual

insert fragment_data sec-struct into ss-string at position seq_pos

Implements core::fragment::SingleResidueFragData.

SingleResidueFragDataOP core::fragment::DownJumpSRFD::clone ( ) const

inlinevirtual

clone

Implements core::fragment::SingleResidueFragData.

References DownJumpSRFD().

virtual SingleResidueFragDataOP core::fragment::DownJumpSRFD::create ( ) const

inlinevirtual

create a new instance of this object

Implements core::fragment::SingleResidueFragData.

References DownJumpSRFD().

bool core::fragment::DownJumpSRFD::is_applicable ( kinematics::MoveMap const &  mm, Size  intra_frame_pos, Frame const &  frame  ) const

virtual

check weather dofs can be moved

Reimplemented from core::fragment::SingleResidueFragData.

References core::kinematics::MoveMap::get_jump(), runtime_assert, and core::fragment::Frame::seqpos().

virtual bool core::fragment::DownJumpSRFD::is_applicable ( kinematics::MoveMap const &  , Size  pos  ) const

inlinevirtual

check whether dofs can be moved

Implements core::fragment::SingleResidueFragData.

bool core::fragment::DownJumpSRFD::is_compatible ( SingleResidueFragData const &  ) const

virtual

check weather SRFD applies to same dofs and is of same type

Implements core::fragment::SingleResidueFragData.

void core::fragment::DownJumpSRFD::read ( std::istream &  in )

virtual

References getline(), tag, core::fragment::tr, and utility_exit_with_message.

void core::fragment::DownJumpSRFD::set_jump ( kinematics::RT  setting )

inline

set value of jump

References rt_.

void core::fragment::DownJumpSRFD::set_standard_stub_atoms

(

)

Referenced by DownJumpSRFD().

void core::fragment::DownJumpSRFD::set_stub_atoms	(	AtomList	downstream,
		AtomList	upstream
	)

void core::fragment::DownJumpSRFD::show ( std::ostream &  out ) const

virtual

Reimplemented from core::fragment::SingleResidueFragData.

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

virtual

insert fragment_data into pose at position seq_pos

Reimplemented from core::fragment::SingleResidueFragData.

References core::pose::Pose::conformation(), core::conformation::Conformation::get_stub_transform(), core::pose::named_stub_id_to_stub_id(), runtime_assert, and core::fragment::Frame::seqpos().

virtual bool core::fragment::DownJumpSRFD::steal ( pose::Pose const &  pose, Size  seq_pos  )

inlinevirtual

insert fragment_data into pose at position seq_pos

Implements core::fragment::SingleResidueFragData.

virtual std::string core::fragment::DownJumpSRFD::type ( ) const

inlinevirtual

Reimplemented from core::fragment::SingleResidueFragData.

References _static_type_name().

Member Data Documentation

AtomList core::fragment::DownJumpSRFD::downstream_stub_atoms_

private

kinematics::RT core::fragment::DownJumpSRFD::rt_

private

Referenced by set_jump().

AtomList core::fragment::DownJumpSRFD::upstream_stub_atoms_

private

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The documentation for this class was generated from the following files:

• src/core/fragment/JumpSRFD.hh
• src/core/fragment/JumpSRFD.cc