Rosetta 3.5: core::util::ABEGOManager Class Reference

manager for abego More...

#include <ABEGOManager.hh>

Inheritance diagram for core::util::ABEGOManager:

Inheritance graph

Collaboration diagram for core::util::ABEGOManager:

Collaboration graph

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...

virtual	~ABEGOManager ()
	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...

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

Definition at line 170 of file ABEGOManager.hh.

Member Typedef Documentation

typedef core::pose::Pose core::util::ABEGOManager::Pose

Definition at line 177 of file ABEGOManager.hh.

typedef core::Real core::util::ABEGOManager::Real

Definition at line 175 of file ABEGOManager.hh.

typedef core::Size core::util::ABEGOManager::Size

Definition at line 174 of file ABEGOManager.hh.

typedef std::string core::util::ABEGOManager::String

Definition at line 176 of file ABEGOManager.hh.

Constructor & Destructor Documentation

core::util::ABEGOManager::ABEGOManager ( )

default constructor

Definition at line 87 of file ABEGOManager.cc.

References initialize().

core::util::ABEGOManager::~ABEGOManager ( )

virtual

value constructor

Definition at line 27 of file ABEGOManager.cc.

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

copy constructor

Definition at line 93 of file ABEGOManager.cc.

Member Function Documentation

Size core::util::ABEGOManager::alllevel ( )

inline

all output level in current setup

Definition at line 223 of file ABEGOManager.hh.

bool core::util::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

Definition at line 144 of file ABEGOManager.cc.

References name2abego_, and symbol2index().

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

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

get abego string

Definition at line 439 of file ABEGOManager.cc.

Referenced by protocols::fldsgn::filters::SecondaryStructureFilter::apply(), and protocols::fldsgn::filters::SecondaryStructureFilter::parse_my_tag().

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

get abego sequence from pose

Definition at line 431 of file ABEGOManager.cc.

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

Referenced by core::util::get_abego().

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

get abego sequence from pose

Definition at line 415 of file ABEGOManager.cc.

References core::sequence::end, index2symbol(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), torsion2index(), and core::pose::Pose::total_residue().

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

transform abego index to symbol

Definition at line 324 of file ABEGOManager.cc.

References core::util::TR().

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

void core::util::ABEGOManager::initialize ( )

initialize

intialize ABEGOManager

Definition at line 100 of file ABEGOManager.cc.

References protocols::comparative_modeling::features::A, core::util::ABEGO::add_line(), protocols::comparative_modeling::features::B, core::id::D, protocols::comparative_modeling::features::E, protocols::comparative_modeling::features::G, protocols::forge::build::SegmentInsertConnectionScheme::N, name2abego_, protocols::comparative_modeling::features::O, totnum_abego_, and core::scoring::rna::X.

Referenced by ABEGOManager().

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

transform abego symbol to index

Definition at line 363 of file ABEGOManager.cc.

References core::util::TR().

Referenced by check_rama(), and protocols::jd2::parser::BluePrint::read_blueprint().

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

get abego index from torsion angles

get abego

Definition at line 153 of file ABEGOManager.cc.

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

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

Size core::util::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

Definition at line 174 of file ABEGOManager.cc.

Referenced by torsion2index().

Size core::util::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

Definition at line 197 of file ABEGOManager.cc.

References protocols::swa::psi().

Referenced by torsion2index().

Size core::util::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

Definition at line 233 of file ABEGOManager.cc.

References protocols::swa::psi().

Referenced by torsion2index().

Size core::util::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

Definition at line 276 of file ABEGOManager.cc.

References protocols::swa::psi().

Referenced by torsion2index().

Size core::util::ABEGOManager::total_number_abego ( )

inline

total number of abego definition

Definition at line 195 of file ABEGOManager.hh.

References totnum_abego_.

Member Data Documentation

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

private

map relating the index to ABEGO class

Definition at line 247 of file ABEGOManager.hh.

Referenced by check_rama(), and initialize().

Size core::util::ABEGOManager::totnum_abego_

private

total number of abego symbols

Definition at line 244 of file ABEGOManager.hh.

Referenced by initialize(), and total_number_abego().

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

src/core/util/ABEGOManager.hh
src/core/util/ABEGOManager.cc