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

#include <FragmentCandidate.hh>

Inheritance diagram for protocols::frag_picker::FragmentCandidate:

Collaboration diagram for protocols::frag_picker::FragmentCandidate:

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

virtual	~FragmentCandidate ()

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

VallResidueOP	get_residue (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...

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...

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...

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...

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

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...

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

FragDataOP	get_frag_data ()

void	print_fragment (std::ostream &out, scores::FragmentScoreMapOP sc=NULL, scores::FragmentScoreManagerOP ms=NULL)
	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, const std::string sequence, const std::string silent_file_name, const std::string tag, scores::FragmentScoreMapOP sc, scores::FragmentScoreManagerOP ms)
	Prints fragment to silent struct. More...

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_

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.

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

Definition at line 50 of file FragmentCandidate.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 53 of file FragmentCandidate.hh.

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

inlinevirtual

Definition at line 65 of file FragmentCandidate.hh.

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

Definition at line 95 of file FragmentCandidate.hh.

Referenced by output_silent(), 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

Definition at line 68 of file FragmentCandidate.hh.

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

Definition at line 100 of file FragmentCandidate.hh.

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

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

Definition at line 105 of file FragmentCandidate.hh.

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

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

inline

Definition at line 137 of file FragmentCandidate.hh.

Referenced by output_silent().

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

inline

returns the length of this fragment

Definition at line 133 of file FragmentCandidate.hh.

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

inline

returns the middle residue of this fragment candidate

Definition at line 122 of file FragmentCandidate.hh.

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

Definition at line 127 of file FragmentCandidate.hh.

Referenced by output_silent().

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

Definition at line 90 of file FragmentCandidate.hh.

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

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

inline

Definition at line 167 of file FragmentCandidate.hh.

Referenced by output_silent().

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

Definition at line 117 of file FragmentCandidate.hh.

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]

Definition at line 74 of file FragmentCandidate.hh.

Referenced by output_silent(), 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

Definition at line 111 of file FragmentCandidate.hh.

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

inline

returns an integer key identifying a fragment

Definition at line 85 of file FragmentCandidate.hh.

Referenced by output_silent().

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

Prints fragment to silent struct.

Definition at line 230 of file FragmentCandidate.cc.

References core::pose::add_score_line_string(), protocols::simple_moves::PackRotamersMover::apply(), core::scoring::CA_rmsd(), core::scoring::Energies::clear(), core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_packer_task(), core::pose::Pose::data(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::pose::Pose::energies(), core::chemical::FA_STANDARD, protocols::relax::generate_relax_from_cmd(), get_chain_id(), get_first_index_in_query(), get_frag_data(), core::io::silent::SilentStructFactory::get_instance(), get_middle_ss(), get_pdb_id(), get_pool_name(), get_residue(), core::io::silent::SilentStructFactory::get_silent_struct_out(), core::scoring::getScoreFunction(), core::pose::Pose::is_fullatom(), key(), core::fragment::make_pose_from_frags(), protocols::relax::relax_pose(), core::optimization::AtomTreeMinimizer::run(), core::pose::setPoseExtraScores(), core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), and core::io::silent::SilentFileData::write_silent_struct().

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

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

Definition at line 172 of file FragmentCandidate.cc.

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.

Definition at line 215 of file FragmentCandidate.cc.

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

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

Definition at line 324 of file FragmentCandidate.cc.

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

Definition at line 82 of file FragmentCandidate.hh.

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

inline

Definition at line 162 of file FragmentCandidate.hh.

Member Data Documentation

VallChunkOP protocols::frag_picker::FragmentCandidate::chunk_

protected

Definition at line 175 of file FragmentCandidate.hh.

Size protocols::frag_picker::FragmentCandidate::fragmentLength_

protected

Definition at line 178 of file FragmentCandidate.hh.

Referenced by print_fragment(), and print_fragment_seq().

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

private

Definition at line 181 of file FragmentCandidate.hh.

Size protocols::frag_picker::FragmentCandidate::queryResidueIndex_

protected

Definition at line 177 of file FragmentCandidate.hh.

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

staticprivate

Definition at line 180 of file FragmentCandidate.hh.

Size protocols::frag_picker::FragmentCandidate::vallResidueIndex_

protected

Definition at line 176 of file FragmentCandidate.hh.

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

Member Function Documentation

Member Data Documentation