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core::fragment::FragData Class Reference

#include <FragData.hh>

Inheritance diagram for core::fragment::FragData:
Inheritance graph
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Public Member Functions

 FragData ()
 
 FragData (SingleResidueFragDataOP, core::Size n)
 
 ~FragData () override=default
 
virtual FragDataOP clone () const
 
FragDataCOP get_self_ptr () const
 self pointers More...
 
FragDataOP get_self_ptr ()
 
virtual Size apply (kinematics::MoveMap const &, pose::Pose &, Size start, Size end) const
 
virtual Size apply (kinematics::MoveMap const &, pose::Pose &, Frame const &) const
 
virtual Size apply (pose::Pose &, Frame const &) const
 
virtual Size apply (pose::Pose &, Size start, Size end) const
 
virtual Size apply_ss (kinematics::MoveMap const &, std::string &ss, Frame const &) const
 
virtual Size is_applicable (kinematics::MoveMap const &, Size start, Size end) const
 
virtual Size is_applicable (kinematics::MoveMap const &, Frame const &) const
 
virtual bool steal (pose::Pose const &, Size start, Size end)
 
virtual bool steal (pose::Pose const &, Frame const &)
 
virtual void copy (FragData const &frag_data)
 
bool is_compatible (FragData const &frag_data) const
 
bool is_valid () const
 
Size size () const
 
char secstruct (Size const pos) const
 
char sequence (Size const pos) const
 
std::string secstruct () const
 
std::string sequence () const
 
void set_sequence (Size const pos, char const setting)
 
void set_residue (Size pos, SingleResidueFragDataOP res)
 
void add_residue (SingleResidueFragDataOP res)
 
SingleResidueFragDataCOP get_residue (core::Size pos) const
 
virtual FragDataOP generate_sub_fragment (Size start, Size stop) const
 
virtual void show (std::ostream &out) const
 
virtual void show (std::ostream &out, Frame const &) const
 
virtual void show_classic (std::ostream &out) const
 
void set_valid (bool setting=true)
 
virtual std::string pdbid () const
 Returns the PDB identifier if it has been specified, "no_pdb" otherwise. More...
 
virtual char chain () const
 Returns the chain if it has been specified, '_' otherwise. More...
 
virtual Size pdbpos () const
 
void set_score (Real score)
 Set a score value for this fragment. More...
 
Real score () const
 Returns the score for this fragment. More...
 

Protected Member Functions

 FragData (Size nr_res)
 

Protected Attributes

SRFD_List data_
 

Private Types

typedef utility::vector1
< SingleResidueFragDataOP
SRFD_List
 

Private Attributes

bool valid_
 
Real score_
 

Member Typedef Documentation

typedef utility::vector1< SingleResidueFragDataOP > core::fragment::FragData::SRFD_List
private

Constructor & Destructor Documentation

core::fragment::FragData::FragData ( )
inline

Referenced by clone().

core::fragment::FragData::FragData ( SingleResidueFragDataOP  SRFD,
core::Size  n 
)

References data_.

core::fragment::FragData::~FragData ( )
overridedefault
core::fragment::FragData::FragData ( Size  nr_res)
inlineprotected

Member Function Documentation

void core::fragment::FragData::add_residue ( SingleResidueFragDataOP  res)
inline

References data_.

Size core::fragment::FragData::apply ( kinematics::MoveMap const &  mm,
pose::Pose pose,
Size  start,
Size  end 
) const
virtual
Size core::fragment::FragData::apply ( kinematics::MoveMap const &  mm,
pose::Pose pose,
Frame const &  frame 
) const
virtual
Size core::fragment::FragData::apply ( pose::Pose pose,
Frame const &  frame 
) const
virtual
Size core::fragment::FragData::apply ( pose::Pose pose,
Size  start,
Size  end 
) const
virtual
Size core::fragment::FragData::apply_ss ( kinematics::MoveMap const &  mm,
std::string &  ss,
Frame const &  frame 
) const
virtual

References data_, and is_valid().

Referenced by core::fragment::Frame::apply_ss().

virtual char core::fragment::FragData::chain ( ) const
inlinevirtual

Returns the chain if it has been specified, '_' otherwise.

Reimplemented in core::fragment::AnnotatedFragData.

Referenced by core::fragment::AnnotatedFragData::copy().

FragDataOP core::fragment::FragData::clone ( ) const
virtual
void core::fragment::FragData::copy ( FragData const &  frag_data)
virtual
FragDataOP core::fragment::FragData::generate_sub_fragment ( Size  start,
Size  stop 
) const
virtual
SingleResidueFragDataCOP core::fragment::FragData::get_residue ( core::Size  pos) const
inline

References data_.

FragDataCOP core::fragment::FragData::get_self_ptr ( ) const
inline

self pointers

FragDataOP core::fragment::FragData::get_self_ptr ( )
inline
Size core::fragment::FragData::is_applicable ( kinematics::MoveMap const &  mm,
Size  start,
Size  end 
) const
virtual
Size core::fragment::FragData::is_applicable ( kinematics::MoveMap const &  mm,
Frame const &  frame 
) const
virtual
bool core::fragment::FragData::is_compatible ( FragData const &  frag_data) const

References data_, and size().

Referenced by core::fragment::Frame::is_mergeable().

bool core::fragment::FragData::is_valid ( ) const
inline
virtual std::string core::fragment::FragData::pdbid ( ) const
inlinevirtual

Returns the PDB identifier if it has been specified, "no_pdb" otherwise.

Reimplemented in core::fragment::AnnotatedFragData.

Referenced by core::fragment::AnnotatedFragData::copy(), protocols::fold_from_loops::utils::Nub::fix_fragment(), and show().

virtual Size core::fragment::FragData::pdbpos ( ) const
inlinevirtual
Real core::fragment::FragData::score ( ) const
inline

Returns the score for this fragment.

References score_.

Referenced by set_score().

char core::fragment::FragData::secstruct ( Size const  pos) const
inline
std::string core::fragment::FragData::secstruct ( ) const
inline
char core::fragment::FragData::sequence ( Size const  pos) const
inline

References data_, and sequence().

std::string core::fragment::FragData::sequence ( ) const
inline

References size(), and protocols::kinmatch::str().

Referenced by sequence().

void core::fragment::FragData::set_residue ( Size  pos,
SingleResidueFragDataOP  res 
)
inline

References data_.

void core::fragment::FragData::set_score ( Real  score)
inline

Set a score value for this fragment.

References score(), and score_.

void core::fragment::FragData::set_sequence ( Size const  pos,
char const  setting 
)
inline

References data_.

void core::fragment::FragData::set_valid ( bool  setting = true)
inline

References valid_.

Referenced by steal().

void core::fragment::FragData::show ( std::ostream &  out) const
virtual
void core::fragment::FragData::show ( std::ostream &  out,
Frame const &  frame 
) const
virtual
void core::fragment::FragData::show_classic ( std::ostream &  out) const
virtual

References data_.

Size core::fragment::FragData::size ( ) const
inline
bool core::fragment::FragData::steal ( pose::Pose const &  pose,
Size  start,
Size  end 
)
virtual
bool core::fragment::FragData::steal ( pose::Pose const &  pose,
Frame const &  frame 
)
virtual

Member Data Documentation

SRFD_List core::fragment::FragData::data_
protected
Real core::fragment::FragData::score_
private

Referenced by copy(), score(), and set_score().

bool core::fragment::FragData::valid_
private

Referenced by copy(), is_valid(), and set_valid().


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