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Static Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
core::enzymes::EnzymeManager Class Reference

#include <EnzymeManager.hh>

Inheritance diagram for core::enzymes::EnzymeManager:
Inheritance graph
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Static Public Member Functions

static std::string const & get_consensus_sequence (std::string const &family, std::string const &species, std::string const &enzyme)
 Return the consensus sequence of the requested enzyme. More...
 
static ConsensusSequenceType get_consensus_sequence_type (std::string const &family, std::string const &species, std::string const &enzyme)
 Return the consensus sequence type of the requested enzyme. More...
 
static core::Real get_efficiency (std::string const &family, std::string const &species, std::string const &enzyme)
 Return the efficiency of the requested enzyme. More...
 
static utility::vector1
< std::string > const & 
get_second_substrates_or_byproducts (std::string const &family, std::string const &species, std::string const &enzyme)
 Return the second substrates or byproducts of the requested enzyme. More...
 
static utility::vector1
< utility::vector1
< std::string > > const & 
get_consensus_residues (std::string const &family, std::string const &species, std::string const &enzyme)
 Return the identifiers (such as 3-letter codes) of the residues of the consensus sequence. More...
 
static core::uint get_reactive_residue_consensus_sequence_position (std::string const &family, std::string const &species, std::string const &enzyme)
 Return the position in the consensus sequence of the reactive residue. More...
 
static std::string const & get_reactive_atom (std::string const &family, std::string const &species, std::string const &enzyme)
 Return the name of the reactive site atom. More...
 

Private Member Functions

 EnzymeManager ()=default
 
bool is_enzyme_not_yet_loaded (std::string const &family, std::string const &species, std::string const &enzyme)
 
void parse_consensus_sequence (EnzymeData &enzyme_data) const
 
EnzymeData const & specific_enzyme_data (std::string const &family, std::string const &species, std::string const &enzyme)
 

Private Attributes

EnzymeDataSet enzymes_
 

Friends

class utility::SingletonBase< EnzymeManager >
 

Detailed Description

This class is a singleton and manages enzyme data that should only be read from the database one time as needed and shared among all instances of EnzymeMovers.

Constructor & Destructor Documentation

core::enzymes::EnzymeManager::EnzymeManager ( )
privatedefault

Member Function Documentation

utility::vector1< utility::vector1< std::string > > const & core::enzymes::EnzymeManager::get_consensus_residues ( std::string const &  family,
std::string const &  species,
std::string const &  enzyme 
)
static

Return the identifiers (such as 3-letter codes) of the residues of the consensus sequence.

Returns
a vector of vectors of strings, because each position may have more than one possible match.
Note
This function is designed to be threadsafe.
std::string const & core::enzymes::EnzymeManager::get_consensus_sequence ( std::string const &  family,
std::string const &  species,
std::string const &  enzyme 
)
static

Return the consensus sequence of the requested enzyme.

Note
This function is designed to be threadsafe.
ConsensusSequenceType core::enzymes::EnzymeManager::get_consensus_sequence_type ( std::string const &  family,
std::string const &  species,
std::string const &  enzyme 
)
static

Return the consensus sequence type of the requested enzyme.

Note
This function is designed to be threadsafe.
Returns
a ConsensusSequenceType enum value
core::Real core::enzymes::EnzymeManager::get_efficiency ( std::string const &  family,
std::string const &  species,
std::string const &  enzyme 
)
static

Return the efficiency of the requested enzyme.

Note
This function is designed to be threadsafe.

Referenced by protocols::enzymatic_movers::EnzymaticMover::set_efficiency().

std::string const & core::enzymes::EnzymeManager::get_reactive_atom ( std::string const &  family,
std::string const &  species,
std::string const &  enzyme 
)
static

Return the name of the reactive site atom.

Note
This function is designed to be threadsafe.
core::uint core::enzymes::EnzymeManager::get_reactive_residue_consensus_sequence_position ( std::string const &  family,
std::string const &  species,
std::string const &  enzyme 
)
static

Return the position in the consensus sequence of the reactive residue.

Note
This function is designed to be threadsafe.
utility::vector1< std::string > const & core::enzymes::EnzymeManager::get_second_substrates_or_byproducts ( std::string const &  family,
std::string const &  species,
std::string const &  enzyme 
)
static

Return the second substrates or byproducts of the requested enzyme.

Depending on whether this is a transferase or hydrolase, this will return a list of possible substrates or possible byproducts, respectively.

Note
This function is designed to be threadsafe.

Referenced by protocols::enzymatic_movers::EnzymaticMover::set_available_co_substrates().

bool core::enzymes::EnzymeManager::is_enzyme_not_yet_loaded ( std::string const &  family,
std::string const &  species,
std::string const &  enzyme 
)
private

References enzymes_.

Referenced by specific_enzyme_data().

void core::enzymes::EnzymeManager::parse_consensus_sequence ( EnzymeData enzyme_data) const
private
EnzymeData const & core::enzymes::EnzymeManager::specific_enzyme_data ( std::string const &  family,
std::string const &  species,
std::string const &  enzyme 
)
private

Friends And Related Function Documentation

friend class utility::SingletonBase< EnzymeManager >
friend

Member Data Documentation

EnzymeDataSet core::enzymes::EnzymeManager::enzymes_
private

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