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core::fragment::AnnotatedFragData Class Reference

FragData that contains additional information. More...

#include <FragData.hh>

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

 AnnotatedFragData (const std::string &pdb_id, Size start_pos, char chain='_')
 
 AnnotatedFragData (const std::string &pdb_id, Size start_pos, const FragData &frag, char chain='_')
 
FragDataOP clone () const override
 
void copy (FragData const &frag_data) override
 
FragDataOP generate_sub_fragment (Size start, Size stop) const override
 
std::string pdbid () const override
 Returns the PDB identifier if it has been specified, "no_pdb" otherwise. More...
 
Size pdbpos () const override
 
char chain () const override
 Returns the chain if it has been specified, '_' otherwise. More...
 
- Public Member Functions inherited from core::fragment::FragData
 FragData ()
 
 FragData (SingleResidueFragDataOP, core::Size n)
 
 ~FragData () override=default
 
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 &)
 
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 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)
 
void set_score (Real score)
 Set a score value for this fragment. More...
 
Real score () const
 Returns the score for this fragment. More...
 

Private Types

typedef FragData Parent
 

Private Member Functions

void initialize (const std::string &pdb_id, char chain, Size start_pos)
 common initialization routine More...
 

Private Attributes

std::string pdbid_
 
char chain_
 1-letter chain identifier or '' if it was not specified. More...
 
Size startpos_
 

Additional Inherited Members

- Protected Member Functions inherited from core::fragment::FragData
 FragData (Size nr_res)
 
- Protected Attributes inherited from core::fragment::FragData
SRFD_List data_
 

Detailed Description

FragData that contains additional information.

Member Typedef Documentation

Constructor & Destructor Documentation

core::fragment::AnnotatedFragData::AnnotatedFragData ( const std::string &  pdb_id,
Size  start_pos,
char  chain = '_' 
)
inline

References chain(), and initialize().

Referenced by generate_sub_fragment().

core::fragment::AnnotatedFragData::AnnotatedFragData ( const std::string &  pdb_id,
Size  start_pos,
const FragData frag,
char  chain = '_' 
)
inline

References chain(), and initialize().

Member Function Documentation

char core::fragment::AnnotatedFragData::chain ( ) const
inlineoverridevirtual

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

Reimplemented from core::fragment::FragData.

References chain_.

Referenced by AnnotatedFragData(), and initialize().

FragDataOP core::fragment::AnnotatedFragData::clone ( ) const
overridevirtual
void core::fragment::AnnotatedFragData::copy ( FragData const &  frag_data)
overridevirtual
FragDataOP core::fragment::AnnotatedFragData::generate_sub_fragment ( Size  start,
Size  stop 
) const
overridevirtual
void core::fragment::AnnotatedFragData::initialize ( const std::string &  pdb_id,
char  chain,
Size  start_pos 
)
inlineprivate

common initialization routine

References chain(), chain_, pdbid_, and startpos_.

Referenced by AnnotatedFragData().

std::string core::fragment::AnnotatedFragData::pdbid ( ) const
inlineoverridevirtual

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

Reimplemented from core::fragment::FragData.

References pdbid_.

Size core::fragment::AnnotatedFragData::pdbpos ( ) const
inlineoverridevirtual

Reimplemented from core::fragment::FragData.

References startpos_.

Member Data Documentation

char core::fragment::AnnotatedFragData::chain_
private

1-letter chain identifier or '' if it was not specified.

Referenced by chain(), copy(), generate_sub_fragment(), and initialize().

std::string core::fragment::AnnotatedFragData::pdbid_
private
Size core::fragment::AnnotatedFragData::startpos_
private

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