core::fragment::AnnotatedFragData Class Reference

FragData that contains additional information. More...

#include <FragData.hh>

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='_')
virtual FragDataOP	clone () const
virtual void	copy (FragData const &frag_data)
virtual FragDataOP	generate_sub_fragment (Size start, Size stop)
virtual std::string	pdbid () const
	Returns the PDB identifier if it has been specified, "no_pdb" otherwise. More...
virtual Size	pdbpos () const
virtual char	chain () const
	Returns the chain if it has been specified, '_' otherwise. More...
Public Member Functions inherited from core::fragment::FragData
	FragData ()
	FragData (SingleResidueFragDataOP, core::Size n)
virtual	~FragData ()
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 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)
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

typedef FragData core::fragment::AnnotatedFragData::Parent

private

Constructor & Destructor Documentation

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

inline

References chain(), and initialize().

Referenced by clone(), and 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

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

inlinevirtual

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

virtual

Reimplemented from core::fragment::FragData.

References AnnotatedFragData(), core::fragment::FragData::clone(), pdbid_, and startpos_.

void core::fragment::AnnotatedFragData::copy ( FragData const &  frag_data )

virtual

Reimplemented from core::fragment::FragData.

References core::fragment::FragData::chain(), chain_, core::fragment::FragData::copy(), core::fragment::FragData::pdbid(), pdbid_, core::fragment::FragData::pdbpos(), and startpos_.

FragDataOP core::fragment::AnnotatedFragData::generate_sub_fragment ( Size  start, Size  stop  )

virtual

References AnnotatedFragData(), chain_, core::fragment::FragData::data_, pdbid_, runtime_assert, core::fragment::FragData::size(), and startpos_.

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().

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

inlinevirtual

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

Reimplemented from core::fragment::FragData.

References pdbid_.

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

inlinevirtual

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

Referenced by clone(), copy(), generate_sub_fragment(), initialize(), and pdbid().

Size core::fragment::AnnotatedFragData::startpos_

private

Referenced by clone(), copy(), generate_sub_fragment(), initialize(), and pdbpos().

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

• src/core/fragment/FragData.hh
• src/core/fragment/FragData.cc