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core::fragment::DownJumpSRFD Class Reference

#include <JumpSRFD.hh>

Inheritance diagram for core::fragment::DownJumpSRFD:
Inheritance graph
[legend]

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 override
 clone More...
 
SingleResidueFragDataOP create () const override
 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 ()
 
bool apply (pose::Pose &, Size const intra_frame_pos, Frame const &) const override
 the seq_pos is hijacked for the rt_nr More...
 
bool apply (kinematics::MoveMap const &, pose::Pose &, Size const intra_frame_pos, Frame const &) const override
 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...
 
bool apply_ss (std::string &, Size, Frame const &) const override
 insert fragment_data sec-struct into ss-string at position seq_pos More...
 
bool steal (pose::Pose const &, Size pos, Frame const &) override
 insert fragment_data into pose at position seq_pos More...
 
bool is_compatible (SingleResidueFragData const &) const override
 check weather SRFD applies to same dofs and is of same type More...
 
bool is_applicable (kinematics::MoveMap const &, Size pos, Frame const &) const override
 check weather dofs can be moved More...
 
bool apply (pose::Pose &, Size) const override
 insert fragment_data into pose at position seq_pos More...
 
bool apply (kinematics::MoveMap const &, pose::Pose &, Size const ) const override
 for DownJumpSRFD this function should never be called, instead use Frame version More...
 
bool apply_ss (std::string &, Size) const override
 insert fragment_data sec-struct into ss-string at position seq_pos More...
 
bool steal (pose::Pose const &, Size) override
 insert fragment_data into pose at position seq_pos More...
 
bool is_applicable (kinematics::MoveMap const &, Size) const override
 check whether dofs can be moved More...
 
std::string type () const override
 
void show (std::ostream &out) const override
 
virtual void read (std::istream &in)
 
- Public Member Functions inherited from core::fragment::SingleResidueFragData
 ~SingleResidueFragData () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. 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

Constructor & Destructor Documentation

core::fragment::DownJumpSRFD::DownJumpSRFD ( char  sequence = 'X')
inline
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
bool core::fragment::DownJumpSRFD::apply ( pose::Pose pose,
Size const  intra_frame_pos,
Frame const &  frame 
) const
overridevirtual
bool core::fragment::DownJumpSRFD::apply ( kinematics::MoveMap const &  movemap,
pose::Pose pose,
Size const  intra_frame_pos,
Frame const &  frame 
) const
overridevirtual

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().

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

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
overridevirtual

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.

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

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

Reimplemented from core::fragment::SingleResidueFragData.

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

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

Implements core::fragment::SingleResidueFragData.

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

create a new instance of this object

Implements core::fragment::SingleResidueFragData.

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

check weather dofs can be moved

Reimplemented from core::fragment::SingleResidueFragData.

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

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

check whether dofs can be moved

Implements core::fragment::SingleResidueFragData.

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

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

insert fragment_data into pose at position seq_pos

Implements core::fragment::SingleResidueFragData.

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

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

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