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

#include <VallChunk.hh>

Inheritance diagram for protocols::frag_picker::VallChunk:

Collaboration diagram for protocols::frag_picker::VallChunk:

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< VallResidueOP >	residues_

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

Definition at line 37 of file VallChunk.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 35 of file VallChunk.cc.

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

Definition at line 37 of file VallChunk.cc.

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

Definition at line 65 of file VallChunk.hh.

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

Definition at line 92 of file VallChunk.hh.

References chunk_key_, create_key(), and has_key_.

void protocols::frag_picker::VallChunk::create_key ( )

private

Definition at line 44 of file VallChunk.cc.

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

Definition at line 50 of file VallChunk.hh.

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")

Definition at line 45 of file VallChunk.hh.

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

Definition at line 67 of file VallChunk.cc.

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

Definition at line 62 of file VallChunk.cc.

References my_provider_.

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

returns amino acid sequence of this chunk

Definition at line 52 of file VallChunk.cc.

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

Definition at line 55 of file VallChunk.hh.

References at().

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