Rosetta 3.4
Public Member Functions | Static Public Member Functions | Protected Attributes
core::fragment::SingleResidueFragData Class Reference

Base class for SRFD classes Instances of SRFD classes contain information on specific dofs in a single residue or a jump connected to a residue The classes' apply method will now how to implement the specified dofs in the give pose at the given residue position. More...

#include <SingleResidueFragData.hh>

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List of all members.

Public Member Functions

 SingleResidueFragData (char sequence)
 SingleResidueFragData ()
virtual SingleResidueFragDataOP clone () const =0
virtual SingleResidueFragDataOP create () const =0
 create a new instance of this object
virtual bool apply (pose::Pose &, Size seq_pos) const =0
 insert fragment_data into pose at position seq_pos
virtual bool apply (kinematics::MoveMap const &movemap, pose::Pose &pose, Size const seqpos) const =0
 insert fragment_data into pose at position seq_pos for dofs that are allowed to move in the movemap
virtual bool apply_ss (std::string &, Size seq_pos) const =0
 insert fragment_data sec-struct into ss-string at position seq_pos
virtual bool steal (pose::Pose const &, Size seq_pos)=0
 insert fragment_data into pose at position seq_pos
virtual bool apply (pose::Pose &, Size const intra_frame_pos, Frame const &) const
 insert fragment_data into pose at position given by Frame.seqpos( intra_frame_pos );
virtual bool apply (kinematics::MoveMap const &movemap, pose::Pose &pose, Size const intra_frame_pos, Frame const &frame) 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
virtual bool apply_ss (std::string &, Size intra_frame_pos, Frame const &) const
 insert fragment_data sec-struct into ss-string at position seq_pos
virtual bool steal (pose::Pose const &, Size intra_frame_pos, Frame const &)
 insert fragment_data into pose at position seq_pos
virtual bool is_compatible (SingleResidueFragData const &) const =0
 check weather SRFD applies to same dofs and is of same type
virtual bool is_applicable (kinematics::MoveMap const &, Size intra_frame_pos, Frame const &) const
 check weather dofs can be moved
virtual bool is_applicable (kinematics::MoveMap const &, Size pos) const =0
 check whether dofs can be moved
void set_sequence (char const sequence)
char sequence () const
virtual char secstruct () const
virtual void show (std::ostream &out) const
virtual void read_data (std::istream &)
 Default implementation: noop.
virtual std::string type () const

Static Public Member Functions

static std::string _static_type_name ()

Protected Attributes

char sequence_

Detailed Description

Base class for SRFD classes Instances of SRFD classes contain information on specific dofs in a single residue or a jump connected to a residue The classes' apply method will now how to implement the specified dofs in the give pose at the given residue position.

TODO: change SRFD interface such that apply is called like this apply( pose, inframe_pos (1..length), Frame const& ) jumpFrags can then ask the Frame for their upstream residue and check that if they are at position 1 that they do nothgin... can have basic implementation that translates this apply into the old apply


Constructor & Destructor Documentation

core::fragment::SingleResidueFragData::SingleResidueFragData ( char  sequence) [inline]
core::fragment::SingleResidueFragData::SingleResidueFragData ( ) [inline]

Member Function Documentation

std::string core::fragment::SingleResidueFragData::_static_type_name ( ) [static]
virtual bool core::fragment::SingleResidueFragData::apply ( pose::Pose ,
Size  seq_pos 
) const [pure virtual]
bool core::fragment::SingleResidueFragData::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 in core::fragment::UpJumpSRFD, and core::fragment::DownJumpSRFD.

References apply(), and core::fragment::Frame::seqpos().

virtual bool core::fragment::SingleResidueFragData::apply ( kinematics::MoveMap const &  movemap,
pose::Pose pose,
Size const  seqpos 
) const [pure virtual]

insert fragment_data into pose at position seq_pos for dofs that are allowed to move in the movemap

Returns:
True if operation succeeds, False otherwise.

Implemented in core::fragment::BBTorsionAndAnglesSRFD, core::fragment::BBTorsionSRFD, core::fragment::IndependentBBTorsionSRFD, core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

bool core::fragment::SingleResidueFragData::apply ( 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 );

Reimplemented in core::fragment::UpJumpSRFD, and core::fragment::DownJumpSRFD.

References apply(), and core::fragment::Frame::seqpos().

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

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

Reimplemented in core::fragment::UpJumpSRFD, and core::fragment::DownJumpSRFD.

References apply_ss(), and core::fragment::Frame::seqpos().

virtual bool core::fragment::SingleResidueFragData::apply_ss ( std::string &  ,
Size  seq_pos 
) const [pure virtual]

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

Implemented in core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

Referenced by apply_ss().

virtual SingleResidueFragDataOP core::fragment::SingleResidueFragData::clone ( ) const [pure virtual]
virtual SingleResidueFragDataOP core::fragment::SingleResidueFragData::create ( ) const [pure virtual]
bool core::fragment::SingleResidueFragData::is_applicable ( kinematics::MoveMap const &  mm,
Size  intra_frame_pos,
Frame const &  frame 
) const [virtual]

check weather dofs can be moved

Reimplemented in core::fragment::DownJumpSRFD.

References core::fragment::Frame::seqpos().

virtual bool core::fragment::SingleResidueFragData::is_applicable ( kinematics::MoveMap const &  ,
Size  pos 
) const [pure virtual]
virtual bool core::fragment::SingleResidueFragData::is_compatible ( SingleResidueFragData const &  ) const [pure virtual]
void core::fragment::SingleResidueFragData::read_data ( std::istream &  ) [virtual]

Default implementation: noop.

Reimplemented in core::fragment::BBTorsionSRFD, and core::fragment::SecstructSRFD.

Referenced by core::fragment::operator>>().

virtual char core::fragment::SingleResidueFragData::secstruct ( ) const [inline, virtual]

Reimplemented in core::fragment::SecstructSRFD.

char core::fragment::SingleResidueFragData::sequence ( ) const [inline]

References sequence_.

Referenced by set_sequence().

void core::fragment::SingleResidueFragData::set_sequence ( char const  sequence) [inline]
void core::fragment::SingleResidueFragData::show ( std::ostream &  out) const [virtual]
bool core::fragment::SingleResidueFragData::steal ( pose::Pose const &  pose,
Size  seq_pos 
) [pure virtual]
bool core::fragment::SingleResidueFragData::steal ( pose::Pose const &  pose,
Size  intra_frame_pos,
Frame const &  frame 
) [virtual]

insert fragment_data into pose at position seq_pos

Reimplemented in core::fragment::UpJumpSRFD, and core::fragment::DownJumpSRFD.

References core::fragment::Frame::seqpos(), and steal().

std::string core::fragment::SingleResidueFragData::type ( ) const [virtual]

Member Data Documentation

Referenced by sequence(), set_sequence(), and steal().


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