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Rosetta
2021.07
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manager for abego More...
#include <ABEGOManager.hh>
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... | |
manager for abego
typedef std::string core::sequence::ABEGOManager::String |
core::sequence::ABEGOManager::ABEGOManager | ( | ) |
default constructor
References initialize().
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overridedefault |
value constructor
core::sequence::ABEGOManager::ABEGOManager | ( | ABEGOManager const & | rval | ) |
copy constructor
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inline |
all output level in current setup
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().
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_, and symbol2index().
Referenced by protocols::fldsgn::filters::SecondaryStructureFilter::compute().
std::string core::sequence::ABEGOManager::get_abego_string | ( | utility::vector1< String > | abego | ) |
get abego string
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().
utility::vector1< std::string > core::sequence::ABEGOManager::get_symbols | ( | Pose const & | pose, |
Size const | level = 1 |
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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().
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().
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().
void core::sequence::ABEGOManager::initialize | ( | ) |
initialize
intialize ABEGOManager
References protocols::comparative_modeling::features::A, core::sequence::ABEGO::add_line(), 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().
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().
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().
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 torsion2index_level1(), torsion2index_level2(), torsion2index_level3(), torsion2index_level4(), and TR().
Referenced by get_symbols(), and protocols::forge::remodel::RemodelLoopMover::loophash_stage().
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
Referenced by torsion2index().
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
Referenced by torsion2index().
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
Referenced by torsion2index().
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
Referenced by torsion2index().
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inline |
total number of abego definition
References totnum_abego_.
map relating the index to ABEGO class
Referenced by check_rama(), and initialize().
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private |
total number of abego symbols
Referenced by initialize(), and total_number_abego().