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protocols::frag_picker::VallChunk Class Reference

represents a chunk of residues extracted from a vall. More...

#include <VallChunk.hh>

Inheritance diagram for protocols::frag_picker::VallChunk:
Inheritance graph
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Public Member Functions

 ~VallChunk () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
 VallChunk (VallProviderAP provider)
 
VallChunkCOP get_self_ptr () const
 
VallChunkOP get_self_ptr ()
 
VallChunkCAP get_self_weak_ptr () const
 
VallChunkAP get_self_weak_ptr ()
 
std::string get_pdb_id () const
 returns a PDB id (a string of four letters, e.g. "4mba") More...
 
char get_chain_id () const
 returns protein chain ID More...
 
core::Size key () const
 returns integer key of this chunk, which is the key of this chunk's first residue More...
 
core::Size size () const
 returns the size of this chunk i.e. the number of residues stored in there More...
 
core::Size vall_key () const
 
void vall_key (core::Size key)
 
VallResidueOP at (core::Size index) const
 returns i-th residue form this chunk. The first residue has index 1 More...
 
void push_back (VallResidueOP what)
 appends a residue to this chunk More...
 
std::string & get_sequence ()
 returns amino acid sequence of this chunk More...
 
core::sequence::SequenceProfileOP get_profile ()
 returns amino acid profile of this chunk More...
 
core::pose::PoseOP get_pose ()
 returns a pose created for this chunk More...
 
std::string get_vall_filename ()
 returns the Vall file used for this chunk More...
 
VallProviderOP get_vall_provider ()
 returns the Vall Provider More...
 
std::string & chunk_key ()
 returns a string that is unique for each chunk in vall More...
 

Private Member Functions

void create_key ()
 

Private Attributes

utility::vector1< VallResidueOPresidues_
 
std::string sequence_
 
VallProviderAP my_provider_
 
std::string chunk_key_
 
core::Size vall_key_
 
bool has_key_
 

Detailed Description

represents a chunk of residues extracted from a vall.

VallChunk contains a vector of VallResidue objects and provides a basic ways to access them

Constructor & Destructor Documentation

protocols::frag_picker::VallChunk::~VallChunk ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

protocols::frag_picker::VallChunk::VallChunk ( VallProviderAP  provider)

References has_key_, my_provider_, and sequence_.

Member Function Documentation

VallResidueOP protocols::frag_picker::VallChunk::at ( core::Size  index) const
inline

returns i-th residue form this chunk. The first residue has index 1

References residues_.

Referenced by create_key(), get_chain_id(), get_pdb_id(), and key().

std::string& protocols::frag_picker::VallChunk::chunk_key ( )
inline

returns a string that is unique for each chunk in vall

References chunk_key_, create_key(), and has_key_.

void protocols::frag_picker::VallChunk::create_key ( )
private
char protocols::frag_picker::VallChunk::get_chain_id ( ) const
inline

returns protein chain ID

References at().

Referenced by create_key().

std::string protocols::frag_picker::VallChunk::get_pdb_id ( ) const
inline

returns a PDB id (a string of four letters, e.g. "4mba")

References at().

Referenced by create_key().

core::pose::PoseOP protocols::frag_picker::VallChunk::get_pose ( )

returns a pose created for this chunk

the pose object is created when this function is called for the first time and then cached within a VallProvider object Every time this method is called for a new chunk, VallProvider caches new data

References get_self_ptr(), and my_provider_.

core::sequence::SequenceProfileOP protocols::frag_picker::VallChunk::get_profile ( )

returns amino acid profile of this chunk

the profile object is created when this function is called for the first time and then cached within a VallProvider object. Every time this method is called for a new chunk, VallProvider caches new data

References get_self_ptr(), and my_provider_.

VallChunkCOP protocols::frag_picker::VallChunk::get_self_ptr ( ) const
inline

Referenced by get_pose(), and get_profile().

VallChunkOP protocols::frag_picker::VallChunk::get_self_ptr ( )
inline
VallChunkCAP protocols::frag_picker::VallChunk::get_self_weak_ptr ( ) const
inline
VallChunkAP protocols::frag_picker::VallChunk::get_self_weak_ptr ( )
inline
std::string & protocols::frag_picker::VallChunk::get_sequence ( )

returns amino acid sequence of this chunk

References residues_, and sequence_.

std::string protocols::frag_picker::VallChunk::get_vall_filename ( )

returns the Vall file used for this chunk

References my_provider_, and vall_key_.

VallProviderOP protocols::frag_picker::VallChunk::get_vall_provider ( )

returns the Vall Provider

References my_provider_.

core::Size protocols::frag_picker::VallChunk::key ( ) const
inline

returns integer key of this chunk, which is the key of this chunk's first residue

References at().

Referenced by vall_key().

void protocols::frag_picker::VallChunk::push_back ( VallResidueOP  what)
inline

appends a residue to this chunk

References residues_.

core::Size protocols::frag_picker::VallChunk::size ( ) const
inline

returns the size of this chunk i.e. the number of residues stored in there

References residues_.

core::Size protocols::frag_picker::VallChunk::vall_key ( ) const
inline

References vall_key_.

void protocols::frag_picker::VallChunk::vall_key ( core::Size  key)
inline

References key(), and vall_key_.

Member Data Documentation

std::string protocols::frag_picker::VallChunk::chunk_key_
private

Referenced by chunk_key(), and create_key().

bool protocols::frag_picker::VallChunk::has_key_
private

Referenced by chunk_key(), create_key(), and VallChunk().

VallProviderAP protocols::frag_picker::VallChunk::my_provider_
private
utility::vector1<VallResidueOP> protocols::frag_picker::VallChunk::residues_
private

Referenced by at(), get_sequence(), push_back(), and size().

std::string protocols::frag_picker::VallChunk::sequence_
private

Referenced by get_sequence(), and VallChunk().

core::Size protocols::frag_picker::VallChunk::vall_key_
private

Referenced by get_vall_filename(), and vall_key().


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