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

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_.