#include <metabolicnetwork.h>

Public Member Functions
	MetabolicNetwork ()
	MetabolicNetwork (MetabolicNetwork &metab_network)
	MetabolicNetwork (Options options)
BitEfm &	get_bit_efm ()
int	get_num_reacs ()
	Returns number of reactions in the network.
unsigned long	get_num_modes ()
vector< string > &	get_reacs_names ()
map< string, int > &	get_substrate_names ()
map< string, int > &	get_target_names ()
map< string, int > &	get_transport_names ()
map< string, int > &	get_init_knocks_names ()
map< string, double > &	get_yields ()
map< string, double > &	get_max_yields ()
vector< vector< double > > &	get_core_efms ()
vector< vector< double > > &	get_efm_yields ()
vector< long > &	get_eff_efm_indices ()
vector< long > &	get_ineff_efm_indices ()
vector< long > &	get_core_efm_indices ()
vector< long > &	get_knock_cand_reacs ()
Options &	get_options ()
int	init_efm_yields ()
int	init_max_yields ()
	Scan the preloaded array of elementary mode yields in 'efm_yields' and find maximal target reaction yields.
int	init_yields ()
	Given the name of the file containing precomputed yields of the target reactions for given substrate reactions, load the yield values into the member of the class object 'efm_yields'.
int	load_efm_full (string efm_bit_fname, t_UnsignedInt num_ems, vector< vector< double > > &stoich)
double	get_efm_elem (unsigned long index, int reac)
int	remove_zero_substrate_modes ()
	Remove elementary modes with zero-flux for the substrate reactions.
int	extract_production_eff_efms ()
	Given the minimal yield values for growth-efficient modes, extract them into member variable 'eff_efm_indices'.
int	extract_growth_eff_and_ineff_modes ()
	Given the minimal yield values for growth-efficient modes, extract them into member variable 'eff_efm_indices'.
int	is_efm_elem_zero (unsigned long index, int reac, int &is_zero)
	Check if elementary flux mode has zero value for given reaction.
int	is_core_efms_collapsed (map< int, string > knock_reacs, int &cnt_not_collapsed)
	Finds out if the set of reaction collapses all the production-efficient modes and how many modes remain.
Protected Attributes
vector< vector< double > >	core_efms
	production-efficient modes
vector< vector< double > >	efm_yields
	array with yield values for all modes across all specified target reactions
vector< string >	reacs_names
	list of reaction names
map< string, int >	target_names
	list of target reaction names
map< string, int >	substrate_names
	list of substrate reaction names
map< string, int >	init_knocks_names
	list of of reactions knocked out prior to executing search algorithm
map< string, int >	transport_names
	list of transport/exchange reaction names
map< string, double >	yields
map< string, double >	max_yields
Options	options
	program execution options
long	num_modes
int	num_reacs
int	num_metabs
int	compressed_mode
vector< long >	eff_efm_indices
	growth-efficient modes
vector< long >	ineff_efm_indices
	inefficient modes
vector< long >	knock_cand_reacs
vector< double >	core_min_yields
vector< long >	core_efm_indices
BitEfm	bit_efm

Detailed Description

Metabolic network class contains members loaded from configuration options file with data related to metabolic network, algorithm options, reaction names etc.

Definition at line 24 of file metabolicnetwork.h.

Constructor & Destructor Documentation

MetabolicNetwork::MetabolicNetwork ( )

Definition at line 16 of file metabolicnetwork.cpp.

MetabolicNetwork::MetabolicNetwork ( MetabolicNetwork & metab_network )

Definition at line 17 of file metabolicnetwork.cpp.

MetabolicNetwork::MetabolicNetwork ( Options options )

Definition at line 35 of file metabolicnetwork.cpp.

Member Function Documentation

int MetabolicNetwork::extract_growth_eff_and_ineff_modes ( )

Given the minimal yield values for growth-efficient modes, extract them into member variable 'eff_efm_indices'.

Also assign inefficient modes into variable 'ineff_efm_indices'.

Returns:: return indicator of success of execution

See also:: MetabolicNetwork()

Definition at line 485 of file metabolicnetwork.cpp.

int MetabolicNetwork::extract_production_eff_efms ( )

Given the minimal yield values for growth-efficient modes, extract them into member variable 'eff_efm_indices'.

Also assign inefficient modes into variable 'ineff_efm_indices'.

Returns:: return indicator of success of execution

See also:: MetabolicNetwork()

Definition at line 443 of file metabolicnetwork.cpp.

BitEfm& MetabolicNetwork::get_bit_efm ( ) [inline]

Definition at line 57 of file metabolicnetwork.h.

vector<long>& MetabolicNetwork::get_core_efm_indices ( ) [inline]

Definition at line 75 of file metabolicnetwork.h.

vector< vector<double> >& MetabolicNetwork::get_core_efms ( ) [inline]

Definition at line 70 of file metabolicnetwork.h.

vector<long>& MetabolicNetwork::get_eff_efm_indices ( ) [inline]

Definition at line 73 of file metabolicnetwork.h.

double MetabolicNetwork::get_efm_elem	(	unsigned long	index,
		int	reac
	)

Definition at line 351 of file metabolicnetwork.cpp.

vector< vector<double> >& MetabolicNetwork::get_efm_yields ( ) [inline]

Definition at line 71 of file metabolicnetwork.h.

vector<long>& MetabolicNetwork::get_ineff_efm_indices ( ) [inline]

Definition at line 74 of file metabolicnetwork.h.

map<string,int>& MetabolicNetwork::get_init_knocks_names ( ) [inline]

Definition at line 64 of file metabolicnetwork.h.

vector<long>& MetabolicNetwork::get_knock_cand_reacs ( ) [inline]

Definition at line 76 of file metabolicnetwork.h.

map<string,double>& MetabolicNetwork::get_max_yields ( ) [inline]

Definition at line 67 of file metabolicnetwork.h.

unsigned long MetabolicNetwork::get_num_modes ( )

Definition at line 325 of file metabolicnetwork.cpp.

int MetabolicNetwork::get_num_reacs ( )

Returns number of reactions in the network.

Returns:: number of reactions in the network

Definition at line 322 of file metabolicnetwork.cpp.

Options& MetabolicNetwork::get_options ( ) [inline]

Definition at line 77 of file metabolicnetwork.h.

vector<string>& MetabolicNetwork::get_reacs_names ( ) [inline]

Definition at line 60 of file metabolicnetwork.h.

map<string,int>& MetabolicNetwork::get_substrate_names ( ) [inline]

Definition at line 61 of file metabolicnetwork.h.

map<string,int>& MetabolicNetwork::get_target_names ( ) [inline]

Definition at line 62 of file metabolicnetwork.h.

map<string,int>& MetabolicNetwork::get_transport_names ( ) [inline]

Definition at line 63 of file metabolicnetwork.h.

map<string,double>& MetabolicNetwork::get_yields ( ) [inline]

Definition at line 66 of file metabolicnetwork.h.

int MetabolicNetwork::init_efm_yields ( )

int MetabolicNetwork::init_max_yields ( )

Scan the preloaded array of elementary mode yields in 'efm_yields' and find maximal target reaction yields.

Maximal yields are assigned to member variable 'max_yields'

Returns:: return indicator of success of execution

See also:: MetabolicNetwork()

Definition at line 279 of file metabolicnetwork.cpp.

int MetabolicNetwork::init_yields ( )

Given the name of the file containing precomputed yields of the target reactions for given substrate reactions, load the yield values into the member of the class object 'efm_yields'.

If parallel execution mode is required, the file is loaded by node 0 and then distributed to other nodes.

Returns:: return indicator of success of execution

See also:: MetabolicNetwork()

Definition at line 237 of file metabolicnetwork.cpp.

int MetabolicNetwork::is_core_efms_collapsed	(	map< int, string >	knock_reacs,
		int &	cnt_not_collapsed
	)

Finds out if the set of reaction collapses all the production-efficient modes and how many modes remain.

Parameters:

[in]	knock_reacs	reactions which are knocked out
[out]	cnt_not_collapsed	number of remaining production-efficient modes

Returns:: return indicator of success of execution

Definition at line 414 of file metabolicnetwork.cpp.

int MetabolicNetwork::is_efm_elem_zero	(	unsigned long	efm_index,
		int	reac,
		int &	is_zero
	)

Check if elementary flux mode has zero value for given reaction.

Parameters:

[in]	efm_index	Index of elementary flux mode in the EFM matrix
[in]	reac	index of reaction in the elementary mode
[out]	is_zero	Indicator if the mode has non-zero or zero value for given reaction. 0:non-zero value , 1:zero value