Vector candidate says which X-mer from vall fits to a query sequence. More...

#include <FragmentCandidate.hh>

Inheritance diagram for protocols::frag_picker::FragmentCandidate:

Public Member Functions
	FragmentCandidate (core::Size queryPosition, core::Size inChunkPosition, VallChunkOP chunk, core::Size fragmentLength)

	~FragmentCandidate () override

VallChunkOP	get_chunk () const
	returns a pointer to the original chunk from vall the fragment comes from More...

VallResidueOP	get_residue (core::Size whichOne) const
	returns a given residue from this fragment More...

std::string	sequence ()
	creates a new string object that contains a sequence of this fragment More...

core::Size	key () const
	returns an integer key identifying a fragment More...

std::string	get_pdb_id () const
	returns a PDB id of a protein from which the fragment has been extracted More...

char	get_chain_id () const
	returns a chain id of a protein from which the fragment has been extracted More...

core::Size	get_first_index_in_query () const
	returns the index of a very first residue in a query sequence that is covered by this fragment More...

core::Size	get_first_index_in_vall () const
	returns the index of a very first residue in a Vall chunk that is covered by this fragment More...

core::Size	get_vall_middle_res_id ()
	returns a vall index of a middle residue in this fragment More...

core::Size	get_query_middle_res_id ()
	returns a query index of a middle residue in this fragment More...

VallResidueOP	get_middle_residue () const
	returns the middle residue of this fragment candidate More...

char	get_middle_ss () const
	returns secondary structure assigned to the middle residue of this fragment candidate More...

core::Size	get_length () const
	returns the length of this fragment More...

core::fragment::FragDataOP	get_frag_data ()

void	print_fragment_index (std::ostream &out, bool vall_index_database_exists)

void	print_fragment (std::ostream &out, scores::FragmentScoreMapOP sc=nullptr, scores::FragmentScoreManagerOP ms=nullptr)
	Prints fragment data, the output can be directly loaded to minirosetta. More...

void	print_fragment_seq (std::ostream &out)
	Prints fragment sequence, used for generating structure based sequence profiles. More...

void	output_silent (core::io::silent::SilentFileData &sfd, std::string const &sequence, std::string const &silent_file_name, std::string const &tag, scores::FragmentScoreMapOP sc, scores::FragmentScoreManagerOP ms)
	Prints fragment to silent struct. More...

void	set_pool_name (std::string const &pool_name)

std::string	get_pool_name ()

bool	same_chain (FragmentCandidateCOP fr)

Protected Attributes
VallChunkOP	chunk_

core::Size	vallResidueIndex_

core::Size	queryResidueIndex_

core::Size	fragmentLength_

Private Attributes
std::string *	pool_name_

Static Private Attributes
static const std::string	unknown_pool_name_ = "UNKNOWN_POOL_NAME"

Detailed Description

Vector candidate says which X-mer from vall fits to a query sequence.

Scores for a given fragment are stored separately in a FragmentScoreMap object Therefore fragment containers hold std::pair<FragmentCandidateOP,FragmentScoreMapOP>

Constructor & Destructor Documentation

◆ FragmentCandidate()

protocols::frag_picker::FragmentCandidate::FragmentCandidate	(	core::Size	queryPosition,
		core::Size	inChunkPosition,
		VallChunkOP	chunk,
		core::Size	fragmentLength
	)

inline

References fragmentLength_, pool_name_, queryResidueIndex_, and vallResidueIndex_.

◆ ~FragmentCandidate()

protocols::frag_picker::FragmentCandidate::~FragmentCandidate ( )

inlineoverride

References pool_name_.

Member Function Documentation

◆ get_chain_id()

char protocols::frag_picker::FragmentCandidate::get_chain_id ( ) const

inline

returns a chain id of a protein from which the fragment has been extracted

References chunk_.

◆ get_chunk()

VallChunkOP protocols::frag_picker::FragmentCandidate::get_chunk ( ) const

inline

returns a pointer to the original chunk from vall the fragment comes from

References chunk_.

◆ get_first_index_in_query()

core::Size protocols::frag_picker::FragmentCandidate::get_first_index_in_query ( ) const

inline

returns the index of a very first residue in a query sequence that is covered by this fragment

References queryResidueIndex_.

Referenced by protocols::frag_picker::operator<<().

◆ get_first_index_in_vall()

core::Size protocols::frag_picker::FragmentCandidate::get_first_index_in_vall ( ) const

inline

returns the index of a very first residue in a Vall chunk that is covered by this fragment

References vallResidueIndex_.

Referenced by protocols::frag_picker::operator<<().

◆ get_frag_data()

core::fragment::FragDataOP protocols::frag_picker::FragmentCandidate::get_frag_data ( )

inline

References chunk_, fragmentLength_, get_pdb_id(), queryResidueIndex_, and vallResidueIndex_.

◆ get_length()

core::Size protocols::frag_picker::FragmentCandidate::get_length ( ) const

inline

returns the length of this fragment

References fragmentLength_.

◆ get_middle_residue()

VallResidueOP protocols::frag_picker::FragmentCandidate::get_middle_residue ( ) const

inline

returns the middle residue of this fragment candidate

References fragmentLength_, and get_residue().

◆ get_middle_ss()

char protocols::frag_picker::FragmentCandidate::get_middle_ss ( ) const

inline

returns secondary structure assigned to the middle residue of this fragment candidate

Returns: secondary structure of the middle residue of this fragment, as extracted from Vall data

References fragmentLength_, and get_residue().

◆ get_pdb_id()

std::string protocols::frag_picker::FragmentCandidate::get_pdb_id ( ) const

inline

returns a PDB id of a protein from which the fragment has been extracted

References chunk_.

Referenced by get_frag_data(), and protocols::frag_picker::operator<<().

◆ get_pool_name()

std::string protocols::frag_picker::FragmentCandidate::get_pool_name ( )

inline

References pool_name_, and unknown_pool_name_.

◆ get_query_middle_res_id()

core::Size protocols::frag_picker::FragmentCandidate::get_query_middle_res_id ( )

inline

returns a query index of a middle residue in this fragment

Returns: a position of the middle residue of this fragment in the query sequence

References fragmentLength_, and queryResidueIndex_.

◆ get_residue()

VallResidueOP protocols::frag_picker::FragmentCandidate::get_residue ( core::Size whichOne ) const

inline

returns a given residue from this fragment

the irgument is in the range [1,fragmentLength]

References chunk_, fragmentLength_, and vallResidueIndex_.

Referenced by get_middle_residue(), and get_middle_ss().

◆ get_vall_middle_res_id()

core::Size protocols::frag_picker::FragmentCandidate::get_vall_middle_res_id ( )

inline

returns a vall index of a middle residue in this fragment

Returns: a position of the middle residue of this fragment in the vall sequence

References fragmentLength_, and vallResidueIndex_.

◆ key()

core::Size protocols::frag_picker::FragmentCandidate::key ( ) const

inline

returns an integer key identifying a fragment

References chunk_, and vallResidueIndex_.

◆ output_silent()

void protocols::frag_picker::FragmentCandidate::output_silent	(	core::io::silent::SilentFileData &	sfd,
		std::string const &	sequence,
		std::string const &	silent_file_name,
		std::string const &	tag,
		scores::FragmentScoreMapOP	sc,
		scores::FragmentScoreManagerOP	ms
	)

Prints fragment to silent struct.

References core::pose::add_score_line_string(), protocols::minimization_packing::PackRotamersMover::apply(), core::scoring::CA_rmsd(), core::pack::task::TaskFactory::create_packer_task(), core::chemical::FULL_ATOM_t, protocols::relax::generate_relax_from_cmd(), core::pose::full_model_info::get_residue(), core::scoring::get_score_function(), core::fragment::make_pose_from_frags(), protocols::relax::relax_pose(), core::optimization::AtomTreeMinimizer::run(), core::pose::setPoseExtraScore(), core::util::switch_to_residue_type_set(), and core::io::silent::SilentFileData::write_silent_struct().

◆ print_fragment()

void protocols::frag_picker::FragmentCandidate::print_fragment	(	std::ostream &	out,
		scores::FragmentScoreMapOP	sc = `nullptr`,
		scores::FragmentScoreManagerOP	ms = `nullptr`
	)

Prints fragment data, the output can be directly loaded to minirosetta.

References core::chemical::element::F, core::pose::full_model_info::get_residue(), core::chemical::element::I, and core::conformation::membrane::out.

◆ print_fragment_index()

void protocols::frag_picker::FragmentCandidate::print_fragment_index	(	std::ostream &	out,
		bool	vall_index_database_exists
	)

References core::chemical::element::F, core::pose::full_model_info::get_residue(), and core::conformation::membrane::out.

◆ print_fragment_seq()

void protocols::frag_picker::FragmentCandidate::print_fragment_seq ( std::ostream & out )

Prints fragment sequence, used for generating structure based sequence profiles.

Prints fragment data, the output can be directly loaded to minirosetta.

References core::pose::full_model_info::get_residue(), core::chemical::element::I, core::conformation::membrane::out, and protocols::hybridization::r1.

◆ same_chain()

bool protocols::frag_picker::FragmentCandidate::same_chain ( FragmentCandidateCOP fr )

◆ sequence()

std::string protocols::frag_picker::FragmentCandidate::sequence ( )

inline

creates a new string object that contains a sequence of this fragment

References chunk_, fragmentLength_, and vallResidueIndex_.

◆ set_pool_name()

void protocols::frag_picker::FragmentCandidate::set_pool_name ( std::string const & pool_name )

inline

References pool_name_.

Member Data Documentation

◆ chunk_

VallChunkOP protocols::frag_picker::FragmentCandidate::chunk_

protected

Referenced by get_chain_id(), get_chunk(), get_frag_data(), get_pdb_id(), get_residue(), key(), and sequence().

◆ fragmentLength_

core::Size protocols::frag_picker::FragmentCandidate::fragmentLength_

protected

Referenced by FragmentCandidate(), get_frag_data(), get_length(), get_middle_residue(), get_middle_ss(), get_query_middle_res_id(), get_residue(), get_vall_middle_res_id(), and sequence().

◆ pool_name_

std::string* protocols::frag_picker::FragmentCandidate::pool_name_

private

Referenced by FragmentCandidate(), get_pool_name(), set_pool_name(), and ~FragmentCandidate().

◆ queryResidueIndex_

core::Size protocols::frag_picker::FragmentCandidate::queryResidueIndex_

protected

Referenced by FragmentCandidate(), get_first_index_in_query(), get_frag_data(), and get_query_middle_res_id().

◆ unknown_pool_name_

const std::string protocols::frag_picker::FragmentCandidate::unknown_pool_name_ = "UNKNOWN_POOL_NAME"

staticprivate

Referenced by get_pool_name().

◆ vallResidueIndex_

core::Size protocols::frag_picker::FragmentCandidate::vallResidueIndex_

protected

Referenced by FragmentCandidate(), get_first_index_in_vall(), get_frag_data(), get_residue(), get_vall_middle_res_id(), key(), and sequence().

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

src/protocols/frag_picker/FragmentCandidate.hh
src/protocols/frag_picker/FragmentCandidate.cc

Public Member Functions

Protected Attributes

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FragmentCandidate()

◆ ~FragmentCandidate()

Member Function Documentation

◆ get_chain_id()

◆ get_chunk()

◆ get_first_index_in_query()

◆ get_first_index_in_vall()

◆ get_frag_data()

◆ get_length()

◆ get_middle_residue()

◆ get_middle_ss()

◆ get_pdb_id()

◆ get_pool_name()

◆ get_query_middle_res_id()

◆ get_residue()

◆ get_vall_middle_res_id()

◆ key()

◆ output_silent()

◆ print_fragment()

◆ print_fragment_index()

◆ print_fragment_seq()

◆ same_chain()

◆ sequence()

◆ set_pool_name()

Member Data Documentation

◆ chunk_

◆ fragmentLength_

◆ pool_name_

◆ queryResidueIndex_

◆ unknown_pool_name_

◆ vallResidueIndex_