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

#include <VallChunk.hh>

Inheritance diagram for protocols::frag_picker::VallChunk:

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< VallResidueOP >	residues_

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

References at(), chunk_key_, get_chain_id(), get_pdb_id(), has_key_, and core::conformation::membrane::out.

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

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