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core::sequence::ABEGOManager Class Reference

manager for abego More...

#include <ABEGOManager.hh>

Inheritance diagram for core::sequence::ABEGOManager:
Inheritance graph
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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< Stringget_symbols (Pose const &pose, Size const level=1)
 get abego sequence from pose More...
 
utility::vector1< Stringget_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, ABEGOname2abego_
 map relating the index to ABEGO class More...
 

Detailed Description

manager for abego

Member Typedef Documentation

Constructor & Destructor Documentation

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

default constructor

References initialize().

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

value constructor

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

copy constructor

Member Function Documentation

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

all output level in current setup

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().

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

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

total number of abego definition

References totnum_abego_.

Member Data Documentation

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

map relating the index to ABEGO class

Referenced by check_rama(), and initialize().

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: