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protocols::frag_picker::FragmentCandidate Class Reference

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

#include <FragmentCandidate.hh>

Inheritance diagram for protocols::frag_picker::FragmentCandidate:
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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

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

References pool_name_.

Member Function Documentation

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_.

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

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

References chunk_.

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<<().

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<<().

core::fragment::FragDataOP protocols::frag_picker::FragmentCandidate::get_frag_data ( )
inline
core::Size protocols::frag_picker::FragmentCandidate::get_length ( ) const
inline

returns the length of this fragment

References fragmentLength_.

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

returns the middle residue of this fragment candidate

References fragmentLength_, and get_residue().

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().

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<<().

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

References pool_name_, and unknown_pool_name_.

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_.

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().

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_.

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

returns an integer key identifying a fragment

References chunk_, and vallResidueIndex_.

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 
)
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(), and core::chemical::element::I.

void protocols::frag_picker::FragmentCandidate::print_fragment_index ( std::ostream &  out,
bool  vall_index_database_exists 
)
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, and protocols::hybridization::r1.

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

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

References pool_name_.

Member Data Documentation

VallChunkOP protocols::frag_picker::FragmentCandidate::chunk_
protected
core::Size protocols::frag_picker::FragmentCandidate::fragmentLength_
protected
std::string* protocols::frag_picker::FragmentCandidate::pool_name_
private
core::Size protocols::frag_picker::FragmentCandidate::queryResidueIndex_
protected
const std::string protocols::frag_picker::FragmentCandidate::unknown_pool_name_ = "UNKNOWN_POOL_NAME"
staticprivate

Referenced by get_pool_name().

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

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