#include <EnzymeManager.hh>

Inheritance diagram for core::enzymes::EnzymeManager:

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

References core::enzymes::AA, core::enzymes::EnzymeData::consensus_residues, core::enzymes::EnzymeData::consensus_sequence, core::enzymes::EnzymeData::cs_type, core::enzymes::get_3_letter_codes_from_NA_consensus_sequence(), core::enzymes::get_3_letter_codes_from_peptide_consensus_sequence(), core::enzymes::get_codes_from_saccharide_consensus_sequence(), core::enzymes::NA, and core::enzymes::SACCHARIDE.

Referenced by specific_enzyme_data().

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

private

References enzymes_, is_enzyme_not_yet_loaded(), parse_consensus_sequence(), core::enzymes::read_enzyme_data_from_file(), and TR().

Friends And Related Function Documentation

friend class utility::SingletonBase< EnzymeManager >

friend

Member Data Documentation

EnzymeDataSet core::enzymes::EnzymeManager::enzymes_

private

Referenced by is_enzyme_not_yet_loaded(), and specific_enzyme_data().

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

src/core/enzymes/EnzymeManager.hh
src/core/enzymes/EnzymeManager.cc

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation