Rosetta 3.4
Public Member Functions | Protected Attributes
protocols::frag_picker::FragmentCandidate Class Reference

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

#include <FragmentCandidate.hh>

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List of all members.

Public Member Functions

 FragmentCandidate (Size queryPosition, Size inChunkPosition, VallChunkOP chunk, Size fragmentLength)
 ~FragmentCandidate ()
VallChunkOP get_chunk () const
 returns a pointer to the original chunk from vall the fragment comes from
VallResidueOP get_residue (Size whichOne) const
 returns a given residue from this fragment
std::string sequence ()
 creates a new string object that contains a sequence of this fragment
Size key () const
 returns an integer key identifying a fragment
std::string get_pdb_id () const
 returns a PDB id of a protein from which the fragment has been extracted
char get_chain_id () const
 returns a chain id of a protein from which the fragment has been extracted
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
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
Size get_vall_middle_res_id ()
 returns a vall index of a middle residue in this fragment
Size get_query_middle_res_id ()
 returns a query index of a middle residue in this fragment
VallResidueOP get_middle_residue () const
 returns the middle residue of this fragment candidate
char get_middle_ss () const
 returns secondary structure assigned to the middle residue of this fragment candidate
Size get_length () const
 returns the length of this fragment
FragDataOP get_frag_data ()
void print_fragment (std::ostream &out)
 Prints fragment data, the output can be directly loaded to minirosetta.
void print_fragment_seq (std::ostream &out)
 Prints fragment sequence, used for generating structure based sequence profiles.
void set_pool_name (std::string pool_name)
std::string get_pool_name ()
bool same_chain (FragmentCandidateCOP fr)

Protected Attributes

VallChunkOP chunk_
Size vallResidueIndex_
Size queryResidueIndex_
Size fragmentLength_

Detailed Description

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

Detailed: 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 ( Size  queryPosition,
Size  inChunkPosition,
VallChunkOP  chunk,
Size  fragmentLength 
) [inline]
protocols::frag_picker::FragmentCandidate::~FragmentCandidate ( ) [inline]

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

Referenced by print_fragment(), print_fragment_seq(), and same_chain().

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

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

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

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

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

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

FragDataOP protocols::frag_picker::FragmentCandidate::get_frag_data ( ) [inline]
Size protocols::frag_picker::FragmentCandidate::get_length ( ) const [inline]

returns the length of this fragment

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

returns the middle residue of this fragment candidate

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
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

Referenced by protocols::frag_picker::operator<<(), print_fragment(), print_fragment_seq(), and same_chain().

std::string protocols::frag_picker::FragmentCandidate::get_pool_name ( ) [inline]
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
VallResidueOP protocols::frag_picker::FragmentCandidate::get_residue ( Size  whichOne) const [inline]

returns a given residue from this fragment

Detailed: the irgument is in the range [1,fragmentLength]

Referenced by print_fragment(), and print_fragment_seq().

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
Size protocols::frag_picker::FragmentCandidate::key ( ) const [inline]

returns an integer key identifying a fragment

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

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

References fragmentLength_, get_chain_id(), get_pdb_id(), and get_residue().

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 fragmentLength_, get_chain_id(), get_pdb_id(), and get_residue().

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

References get_chain_id(), and get_pdb_id().

std::string protocols::frag_picker::FragmentCandidate::sequence ( ) [inline]

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

void protocols::frag_picker::FragmentCandidate::set_pool_name ( std::string  pool_name) [inline]

Member Data Documentation


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