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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:
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Public Member Functions

virtual ~VallChunk ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
 VallChunk (VallProviderAP provider)
 
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...
 
Size key () const
 returns integer key of this chunk, which is the key of this chunk's first residue More...
 
Size size () const
 returns the size of this chunk i.e. the number of residues stored in there More...
 
VallResidueOP at (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 & 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_
 
bool has_key_
 

Detailed Description

represents a chunk of residues extracted from a vall.

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

Constructor & Destructor Documentation

protocols::frag_picker::VallChunk::~VallChunk ( )
virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

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 ( 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

References at(), chunk_key_, get_chain_id(), get_pdb_id(), and has_key_.

Referenced by chunk_key().

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

Detailed: 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 my_provider_.

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

returns amino acid profile of this chunk

Detailed: 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 my_provider_.

std::string & protocols::frag_picker::VallChunk::get_sequence ( )

returns amino acid sequence of this chunk

References residues_, and sequence_.

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().

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

appends a residue to this chunk

References residues_.

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_.

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

Referenced by get_pose(), get_profile(), and VallChunk().

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().


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