Rosetta Core  2014.35
Public Member Functions | Static Public Member Functions | Protected Attributes | List of all members
core::fragment::SingleResidueFragData Class Referenceabstract

Base class for SRFD classes. More...

#include <SingleResidueFragData.hh>

Public Member Functions

virtual ~SingleResidueFragData ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
 SingleResidueFragData (char sequence)
 
 SingleResidueFragData ()
 
virtual SingleResidueFragDataOP clone () const =0
 
virtual SingleResidueFragDataOP create () const =0
 create a new instance of this object More...
 
virtual bool apply (pose::Pose &, Size seq_pos) const =0
 insert fragment_data into pose at position seq_pos More...
 
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 More...
 
virtual bool apply_ss (std::string &, Size seq_pos) const =0
 insert fragment_data sec-struct into ss-string at position seq_pos More...
 
virtual bool steal (pose::Pose const &, Size seq_pos)=0
 insert fragment_data into pose at position seq_pos More...
 
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 ); More...
 
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 More...
 
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 More...
 
virtual bool steal (pose::Pose const &, Size intra_frame_pos, Frame const &)
 insert fragment_data into pose at position seq_pos More...
 
virtual bool is_compatible (SingleResidueFragData const &) const =0
 check weather SRFD applies to same dofs and is of same type More...
 
virtual bool is_applicable (kinematics::MoveMap const &, Size intra_frame_pos, Frame const &) const
 check weather dofs can be moved More...
 
virtual bool is_applicable (kinematics::MoveMap const &, Size pos) const =0
 check whether dofs can be moved More...
 
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. More...
 
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 positionTODO: 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 ( )
virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

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

insert fragment_data into pose at position seq_pos

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

Referenced by apply().

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::DownJumpSRFD, core::fragment::BBTorsionSRFD, core::fragment::IndependentBBTorsionSRFD, core::fragment::UpJumpSRFD, core::fragment::BBTorsionAndAnglesSRFD, 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::DownJumpSRFD, and core::fragment::UpJumpSRFD.

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

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

References apply(), 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::DownJumpSRFD, core::fragment::UpJumpSRFD, and core::fragment::SecstructSRFD.

Referenced by apply_ss().

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

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

virtual SingleResidueFragDataOP core::fragment::SingleResidueFragData::clone ( ) const
pure virtual

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

virtual SingleResidueFragDataOP core::fragment::SingleResidueFragData::create ( ) const
pure virtual

create a new instance of this object

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

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

check whether dofs can be moved

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

virtual bool core::fragment::SingleResidueFragData::is_compatible ( SingleResidueFragData const &  ) const
pure virtual

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

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

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
inlinevirtual

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

References sequence(), and sequence_.

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

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

References type().

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

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

insert fragment_data into pose at position seq_pos

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

References core::conformation::Residue::aa(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::residue(), and sequence_.

Referenced by steal().

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

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

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

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

Referenced by show().

Member Data Documentation

char core::fragment::SingleResidueFragData::sequence_
protected

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

The documentation for this class was generated from the following files:
Generated on Wed Sep 10 2014 11:27:17 for Rosetta Core by   doxygen 1.8.7