RK Class Reference

#include <rk.h>

Public Member Functions
	RK ()
	Default constructor.
	RK (const RK &rk)
	Copy constructor.
	RK (map< int, string > knock_reacs, MetabolicNetwork *metab_network)
	Class constructor.
int	get_avg_path_length ()
int	get_max_path_length ()
int	get_min_path_length ()
string	get_key ()
map< int, string > &	get_knock_reacs ()
vector< long > &	get_uncollapsed_ineff_efm_indices ()
vector< long > &	get_uncollapsed_eff_efm_indices ()
int	add_reac (int reac, long &rank)
int	add_reac_direct (int reac, double &rank)
	Method to add reaction to the current reaction knockout subset and compute the score associated with the added reaction.
int	add_reacs (map< int, string > reacs)
	Append new reactions to the member knock_reacs.
int	test_reac (int reac, long &rank)
int	is_core_collapsed (int &cnt_not_collapsed)
long	test_knock_reacs2 (map< int, string > knock_reacs, vector< double > &min_yields, long &num_eff_efm_rem, long &num_ineff_efm_rem)
Private Attributes
map< int, string >	knock_reacs
string	key
MetabolicNetwork *	metab_network
vector< double >	min_yields
vector< int >	inactive_reacs
vector< long >	uncollapsed_ineff_efm_indices
vector< long >	collapsed_ineff_efm_indices
vector< long >	uncollapsed_eff_efm_indices
int	avg_path_length
int	max_path_length
int	min_path_length
Friends
ostream &	operator<< (ostream &out, const RK &rk)

---

Detailed Description

Reaction knockouts subset class. Contains list of knockout reactions, associated metabolic network, and indices of collapsed growth-efficient and inefficient modes, as well as min/max pathway length in remaining modes, and average pathway length

Definition at line 14 of file rk.h.

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Constructor & Destructor Documentation

RK::RK

(

)

Default constructor.

Definition at line 9 of file rk.cpp.

RK::RK

(

const RK &

rk

)

Copy constructor.

Parameters:

[in]

rk

instance of class RK

Definition at line 18 of file rk.cpp.

RK::RK	(	map< int, string >	knock_reacs,
		MetabolicNetwork *	metab_network
	)

Class constructor.

Parameters:

[in]	knock_reacs	reactions initially knocked out from network (in addition to those passed in options)
[in]	metab_network	pointer to metabolic network object

Definition at line 36 of file rk.cpp.

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Member Function Documentation

int RK::add_reac	(	int	reac,
		long &	rank
	)

Definition at line 233 of file rk.cpp.

int RK::add_reac_direct	(	int	reac,
		double &	rank
	)

Method to add reaction to the current reaction knockout subset and compute the score associated with the added reaction.

Parameters:

[in]	reac	identifier of the new knockout reactin to be added to subset
[out]	rank	list of knockout reactions

Returns:

indicator of success

See also:

EnumEffKnocks::enum_erk_direct()

Definition at line 158 of file rk.cpp.

int RK::add_reacs

(

map< int, string >

reacs

)

Append new reactions to the member knock_reacs.

Update the indices of inefficient and efficient modes which are collapsed/retained after deletion of new reactions.

Parameters:

[in]

reacs

list of knockout reactions

Returns:

indicator of success

Definition at line 72 of file rk.cpp.

int RK::get_avg_path_length

(

)

[inline]

Definition at line 31 of file rk.h.

string RK::get_key

(

)

[inline]

Definition at line 34 of file rk.h.

map<int,string>& RK::get_knock_reacs

(

)

[inline]

Definition at line 35 of file rk.h.

int RK::get_max_path_length

(

)

[inline]

Definition at line 32 of file rk.h.

int RK::get_min_path_length

(

)

[inline]

Definition at line 33 of file rk.h.

vector<long>& RK::get_uncollapsed_eff_efm_indices

(

)

[inline]

Definition at line 37 of file rk.h.

vector<long>& RK::get_uncollapsed_ineff_efm_indices

(

)

[inline]

Definition at line 36 of file rk.h.

int RK::is_core_collapsed

(

int &

cnt_not_collapsed

)

Definition at line 431 of file rk.cpp.

long RK::test_knock_reacs2	(	map< int, string >	knock_reacs,
		vector< double > &	min_yields,
		long &	num_eff_efm_rem,
		long &	num_ineff_efm_rem
	)

Definition at line 339 of file rk.cpp.

int RK::test_reac	(	int	reac,
		long &	rank
	)

Definition at line 298 of file rk.cpp.

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	out,
		const RK &	rk
	)		[friend]

Definition at line 406 of file rk.cpp.

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Field Documentation

int RK::avg_path_length [private]

Definition at line 25 of file rk.h.

vector<long> RK::collapsed_ineff_efm_indices [private]

Definition at line 24 of file rk.h.

vector<int> RK::inactive_reacs [private]

Definition at line 22 of file rk.h.

string RK::key [private]

Definition at line 17 of file rk.h.

map<int,string> RK::knock_reacs [private]

Definition at line 16 of file rk.h.

int RK::max_path_length [private]

Definition at line 25 of file rk.h.

MetabolicNetwork* RK::metab_network [private]

Definition at line 19 of file rk.h.

int RK::min_path_length [private]

Definition at line 25 of file rk.h.

vector<double> RK::min_yields [private]

Definition at line 20 of file rk.h.

vector<long> RK::uncollapsed_eff_efm_indices [private]

Definition at line 24 of file rk.h.

vector<long> RK::uncollapsed_ineff_efm_indices [private]

Definition at line 24 of file rk.h.

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

• rk.h
• rk.cpp