Rosetta: core::sequence::ABEGOManager Class Reference

Rosetta

manager for abego More...

#include <ABEGOManager.hh>

Inheritance diagram for core::sequence::ABEGOManager:

Inheritance graph

[legend]

Public Types
typedef core::Size	Size

typedef core::Real	Real

typedef std::string	String

typedef core::pose::Pose	Pose

Public Member Functions
	ABEGOManager ()
	default constructor More...

	~ABEGOManager () override
	value constructor More...

	ABEGOManager (ABEGOManager const &rval)
	copy constructor More...

Size	total_number_abego ()
	total number of abego definition More...

void	initialize ()
	initialize More...

bool	check_rama (char const &symbol, Real const &phi, Real const &psi, Real const &omega)
	check input torsion angle are in a given abego region More...

Size	torsion2index (Real const phi, Real const psi, Real const omega, Size const level=1)
	get abego index from torsion angles More...

Size	torsion2index_level1 (Real const phi, Real const psi, Real const omega)
	get abego index from torsion angles at level 1 More...

Size	torsion2index_level2 (Real const phi, Real const psi, Real const omega)
	get abego index from torsion angles at level 2 More...

Size	torsion2index_level3 (Real const phi, Real const psi, Real const omega)
	get abego index from torsion angles at level 3 More...

Size	torsion2index_level4 (Real const phi, Real const psi, Real const omega)
	get abego index from torsion angles at level 3 More...

Size	alllevel ()
	all output level in current setup More...

Size	symbol2index (char const &symbol)
	transform abego symbol to index More...

Size	symbolString2base5index (std::string symbolString)
	transform abego symbol string to base5 index More...

std::string	base5index2symbolString (Size base5index, Size length)
	transform abego string to abego base5 index More...

char	index2symbol (Size const &idx)
	transform abego index to symbol More...

utility::vector1< String >	get_symbols (Pose const &pose, Size const level=1)
	get abego sequence from pose More...

utility::vector1< String >	get_symbols (Pose const &pose, Size const begin, Size const end, Size const level)
	get abego sequence from pose More...

String	get_abego_string (utility::vector1< String > abego)
	get abego string More...

Private Attributes
Size	totnum_abego_
	total number of abego symbols More...

std::map< Size, ABEGO >	name2abego_
	map relating the index to ABEGO class More...

Detailed Description

manager for abego

Member Typedef Documentation

◆ Pose

typedef core::pose::Pose core::sequence::ABEGOManager::Pose

◆ Real

typedef core::Real core::sequence::ABEGOManager::Real

◆ Size

typedef core::Size core::sequence::ABEGOManager::Size

◆ String

typedef std::string core::sequence::ABEGOManager::String

Constructor & Destructor Documentation

◆ ABEGOManager() [1/2]

core::sequence::ABEGOManager::ABEGOManager ( )

default constructor

References initialize().

◆ ~ABEGOManager()

core::sequence::ABEGOManager::~ABEGOManager ( )

overridedefault

value constructor

◆ ABEGOManager() [2/2]

core::sequence::ABEGOManager::ABEGOManager ( ABEGOManager const & rval )

copy constructor

Member Function Documentation

◆ alllevel()

Size core::sequence::ABEGOManager::alllevel ( )

inline

all output level in current setup

◆ base5index2symbolString()

std::string core::sequence::ABEGOManager::base5index2symbolString	(	Size	base5index,
		Size	length
	)

transform abego string to abego base5 index

transform abego symbol string to base5 index. This is used to quickly pool the abego from Alex's hd5 database

References index2symbol().

◆ check_rama()

bool core::sequence::ABEGOManager::check_rama	(	char const &	symbol,
		Real const &	phi,
		Real const &	psi,
		Real const &	omega
	)

check input torsion angle are in a given abego region

References name2abego_, core::scoring::omega, and symbol2index().

Referenced by protocols::fldsgn::filters::SecondaryStructureFilter::compute().

◆ get_abego_string()

std::string core::sequence::ABEGOManager::get_abego_string ( utility::vector1< String > abego )

get abego string

References core::scoring::abego.

Referenced by protocols::pose_length_moves::PossibleLoop::check_loop_abego(), protocols::fldsgn::filters::SecondaryStructureFilter::compute(), protocols::pose_length_moves::NearNativeLoopCloser::get_additional_output_with_rmsd(), core::scoring::dssp::Dssp::get_dssp_plus_abego_L_def(), and protocols::fldsgn::filters::SecondaryStructureFilter::parse_my_tag().

◆ get_symbols() [1/2]

utility::vector1< std::string > core::sequence::ABEGOManager::get_symbols	(	Pose const &	pose,
		Size const	begin,
		Size const	end,
		Size const	level
	)

get abego sequence from pose

References core::sequence::end, index2symbol(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and torsion2index().

◆ get_symbols() [2/2]

utility::vector1< std::string > core::sequence::ABEGOManager::get_symbols	(	Pose const &	pose,
		Size const	level = `1`
	)

get abego sequence from pose

References core::pose::Pose::size().

Referenced by protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(), core::sequence::get_abego(), core::scoring::dssp::Dssp::get_dssp_plus_abego_L_def(), and core::energy_methods::Abego::setup_for_scoring().

◆ index2symbol()

char core::sequence::ABEGOManager::index2symbol ( Size const & idx )

transform abego index to symbol

References TR().

Referenced by base5index2symbolString(), get_symbols(), and protocols::forge::remodel::RemodelLoopMover::loophash_stage().

◆ initialize()

void core::sequence::ABEGOManager::initialize ( )

initialize

intialize ABEGOManager

References protocols::comparative_modeling::features::A, core::chemical::element::B, core::id::D, protocols::comparative_modeling::features::E, protocols::comparative_modeling::features::G, core::chemical::element::N, name2abego_, core::chemical::element::O, core::chemical::element::S, totnum_abego_, protocols::comparative_modeling::features::X, and core::chemical::element::Y.

Referenced by ABEGOManager().

◆ symbol2index()

Size core::sequence::ABEGOManager::symbol2index ( char const & symbol )

transform abego symbol to index

References TR().

Referenced by check_rama(), protocols::parser::BluePrint::read_blueprint_stream(), and symbolString2base5index().

◆ symbolString2base5index()

Size core::sequence::ABEGOManager::symbolString2base5index ( std::string symbolString )

transform abego symbol string to base5 index

transform abego symbol string to base5 index. This is used to quickly pool the abego from Alex's hd5 database

References symbol2index().

◆ torsion2index()

Size core::sequence::ABEGOManager::torsion2index	(	Real const	phi,
		Real const	psi,
		Real const	omega,
		Size const	level = `1`
	)

get abego index from torsion angles

get abego

References core::scoring::omega, torsion2index_level1(), torsion2index_level2(), torsion2index_level3(), torsion2index_level4(), and TR().

Referenced by get_symbols(), and protocols::forge::remodel::RemodelLoopMover::loophash_stage().

◆ torsion2index_level1()

Size core::sequence::ABEGOManager::torsion2index_level1	(	Real const	phi,
		Real const	psi,
		Real const	omega
	)

get abego index from torsion angles at level 1

get abegeo index from torsion angles: ABEGO

References core::scoring::omega.

Referenced by torsion2index().

◆ torsion2index_level2()

Size core::sequence::ABEGOManager::torsion2index_level2	(	Real const	phi,
		Real const	psi,
		Real const	omega
	)

get abego index from torsion angles at level 2

get abego index from torsion angles: ABEGOD

References core::scoring::omega.

Referenced by torsion2index().

◆ torsion2index_level3()

Size core::sequence::ABEGOManager::torsion2index_level3	(	Real const	phi,
		Real const	psi,
		Real const	omega
	)

get abego index from torsion angles at level 3

get abego index from torsion angles: ASPZYD

References core::scoring::omega.

Referenced by torsion2index().

◆ torsion2index_level4()

Size core::sequence::ABEGOManager::torsion2index_level4	(	Real const	phi,
		Real const	psi,
		Real const	omega
	)

get abego index from torsion angles at level 3

get abego index from torsion angles: MNSPZYD

References core::scoring::omega.

Referenced by torsion2index().

◆ total_number_abego()

Size core::sequence::ABEGOManager::total_number_abego ( )

inline

total number of abego definition

References totnum_abego_.

Member Data Documentation

◆ name2abego_

std::map< Size, ABEGO > core::sequence::ABEGOManager::name2abego_

private

map relating the index to ABEGO class

Referenced by check_rama(), and initialize().

◆ totnum_abego_

Size core::sequence::ABEGOManager::totnum_abego_

private

total number of abego symbols

Referenced by initialize(), and total_number_abego().

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

src/core/sequence/ABEGOManager.hh
src/core/sequence/ABEGOManager.cc