Net Class Reference

#include <net.h>

Inheritance diagram for Net:

Public Member Functions
	Net ()
	default constructor
	Net (NetStruct &str2)
	new Net with existing NetStruct.
	Net (int32 nr, int32 nc)
	constructor with allocate.
	Net (const Net &net2)
	copy constructor.
	Net (string &st)
	Net (string &st, int32 &pos)
	constructor with string
	~Net ()
	destructor
void	initFromString (string &st, int32 &pos)
void	resize (int32 nr, int32 nc)
	resize all vectors.
int32	numR ()
	number of reactions
int32	numC ()
	number of compounds
int32	at (int32 reaidx, int32 comidx)
	value at position in stoichiometric matrix
int32	addRea (array< int32 > subs, array< int32 > prds, int8 rev=0, array< int32 > subsst=NULL, array< int32 > prdsst=NULL, array< int32 > cat=NULL, array< int32 > inhs=NULL, array< int32 > inhd=NULL, array< int32 > prps=NULL)
	Add reaction to the end of reaction list.
int32	replaceRea (int32 reaidx, array< int32 > subs, array< int32 > prds, int8 rev=0, array< int32 > subsst=NULL, array< int32 > prdsst=NULL, array< int32 > cat=NULL, array< int32 > inhs=NULL, array< int32 > inhd=NULL, array< int32 > prps=NULL)
	Replace reaction at a particular index.
void	delRea (int32 reaidx)
	Delete reaction at a particular index.
void	delRea (array< int8 > *mask)
	Delete reactions at positons determined by mask.
void	delRea (array< int32 > *idxs)
	Delete reactions at positons determined by index list.
int	hasRea (array< int32 > subs, array< int32 > prds, int8 rev=-10, array< int32 > subsst=NULL, array< int32 > prdsst=NULL)
	checks whether a particular reaction already exists
array< int32 > *	neighbors (int32 comidx)
	reaction in which compound comidx takes part
array< int32 > *	succs (int32 comidx)
	successor reactions of compound comidx
array< int32 > *	preds (int32 comidx)
	predecessors reactions of compound comidx
array< int32 > *	metabolites (int32 reaidx)
	substrates and products of reactions
array< int32 > *	substrates (int32 reaidx)
	substrates of reaction reaidx
array< int32 > *	products (int32 reaidx)
	products of reaction reaidx
array< int32 > *	inhibitors (int32 reaidx)
	inhibitors of reaction reaidx
array< int32 > *	inhibited (int32 reaidx)
	inhibited substrates of reaction reaidx
array< int32 > *	catalysts (int32 reaidx)
	catalysts of reaction reaidx
array< int32 > *	propagators (int32 reaidx)
	catalysts of reaction reaidx
array< int32 > *	subs_stoich (int32 reaidx)
	substrate stoichiometries of reaction reaidx
array< int32 > *	prod_stoich (int32 reaidx)
	product stoichiometries of reaction reaidx
int8	rev (int32 reaidx)
	reversibility of the reaction;
int8	enabled (int32 reaidx)
	is reaction enabled
string *	toString ()
	copy network data into a string
void	appendToString (string &st)
	copy network data into a string
string *	printToString ()
	print a summary of network to string
void	print ()
	print a summary of network to stdout
Public Attributes
array< int8 > *	reaMask
	which reactions are enabled in the current network
Protected Attributes
NetStruct *	str
	the network topology

Constructor & Destructor Documentation

Net::Net ( )

default constructor

Net::Net ( NetStruct & str2 )

new Net with existing NetStruct.

Net::Net	(	int32	nr,
		int32	nc
	)

constructor with allocate.

Net::Net ( const Net & net2 )

copy constructor.

Net::Net ( string & st )

Net::Net	(	string &	st,
		int32 &	pos
	)

constructor with string

Net::~Net ( )

destructor

Member Function Documentation

int32 Net::addRea	(	array< int32 > *	subs,
		array< int32 > *	prds,
		int8	rev = `0`,
		array< int32 > *	subsst = `NULL`,
		array< int32 > *	prdsst = `NULL`,
		array< int32 > *	cats = `NULL`,
		array< int32 > *	inhs = `NULL`,
		array< int32 > *	inhd = `NULL`,
		array< int32 > *	prps = `NULL`
	)

Add reaction to the end of reaction list.

add a new reaction to the network.

Parameters:

	subs	array of substrate indices
	prds	array of product indices
	rev	reversibility, 0=reversible, 1=irreversible, -1=irreversible but in prds->subs direction.
	subsst	stoichiometries for the substrates (same order). Omit if all stoich. equal 1
	prdsst	stoichiometries for the products (same order). Omit if all stoich. equal 1
	cats	catalysts of reaction
	inhs	inhibitors of the reaction
	inhd	inhibited substrates of the reaction (competitive)
	prps	depletion propagators of the reactions

places a new reaction at the next position after the lastly added reaction. if a reaction with that index existed it is removed. Note: all inhd's must also be substrates and all prps must also be products. If prps is given, substrate inhibition only occurs if at least one of the propagators is depleted

The content of the arrays is copied. They can be deleted afterwards.

void Net::appendToString ( string & st )

copy network data into a string

int32 Net::at	(	int32	reaidx,
		int32	comidx
	)

value at position in stoichiometric matrix

Parameters:

	reaidx	which reaction
	comidx	which compound

returns the corresponding entry of the stoichiometric matrix

array< int32 > * Net::catalysts ( int32 reaidx ) [inline]

catalysts of reaction reaidx

Parameters:

reaidx

which reaction

Note: this returns the original array from the Net object. Do not delete!

void Net::delRea ( array< int32 > * idxs )

Delete reactions at positons determined by index list.

void Net::delRea ( array< int8 > * mask )

Delete reactions at positons determined by mask.

void Net::delRea ( int32 idx )

Delete reaction at a particular index.

delete reaction at position idx

Parameters:

idx

index of reaction to delete

int8 Net::enabled ( int32 reaidx ) [inline]

is reaction enabled

int Net::hasRea	(	array< int32 > *	subs,
		array< int32 > *	prds,
		int8	rev = `-10`,
		array< int32 > *	subsst = `NULL`,
		array< int32 > *	prdsst = `NULL`
	)

checks whether a particular reaction already exists

array< int32 > * Net::inhibited ( int32 reaidx ) [inline]

inhibited substrates of reaction reaidx

Parameters:

reaidx

which reaction

Note: this returns the original array from the Net object. Do not delete!

array< int32 > * Net::inhibitors ( int32 reaidx ) [inline]

inhibitors of reaction reaidx

Parameters:

reaidx

which reaction

Note: this returns the original array from the Net object. Do not delete!

void Net::initFromString	(	string &	st,
		int32 &	pos
	)

array< int32 > * Net::metabolites ( int32 reaidx )

substrates and products of reactions

Parameters:

reaidx

which compound

Note: this returns a newly generated array. Delete youself!

array< int32 > * Net::neighbors ( int32 comidx )

reaction in which compound comidx takes part

Parameters:

comidx

which compound

Note: this returns a newly generated array. Delete youself!

int32 Net::numC ( ) [inline]

number of compounds

int32 Net::numR ( ) [inline]

number of reactions

array< int32 > * Net::preds ( int32 comidx ) [inline]

predecessors reactions of compound comidx

Parameters:

comidx

which compound

Note: this returns the original array from the Net object. Do not delete!

void Net::print ( )

print a summary of network to stdout

prints the array to stdout

Note: This only works for certain types T

string * Net::printToString ( )

print a summary of network to string

array< int32 > * Net::prod_stoich ( int32 reaidx ) [inline]

product stoichiometries of reaction reaidx

Parameters:

reaidx

which reaction

Note: this returns the original array from the Net object. Do not delete!

array< int32 > * Net::products ( int32 reaidx ) [inline]

products of reaction reaidx

Parameters:

reaidx

which reaction

Note: this returns the original array from the Net object. Do not delete!

array< int32 > * Net::propagators ( int32 reaidx ) [inline]

catalysts of reaction reaidx

Parameters:

reaidx

which reaction

Note: this returns the original array from the Net object. Do not delete!

int32 Net::replaceRea	(	int32	reaidx,
		array< int32 > *	subs,
		array< int32 > *	prds,
		int8	rev = `0`,
		array< int32 > *	subsst = `NULL`,
		array< int32 > *	prdsst = `NULL`,
		array< int32 > *	cats = `NULL`,
		array< int32 > *	inhs = `NULL`,
		array< int32 > *	inhd = `NULL`,
		array< int32 > *	prps = `NULL`
	)

Replace reaction at a particular index.

place a new reaction into the network

Parameters:

	reaidx	position where to place
	subs	array of substrate indices
	prds	array of product indices
	rev	reversibility, 0=reversible, 1=irreversible, -1=irreversible but in prds->subs direction.
	subsst	stoichiometries for the substrates (same order). Omit if all stoich. equal 1
	prdsst	stoichiometries for the products (same order). Omit if all stoich. equal 1
	cats	catalysts of reaction
	inhs	inhibitors of the reaction
	inhd	inhibited substrates of the reaction (competitive)
	prps	depletion propagators of the reactions

places a new reaction at position reaidx. if a reaction with that index existed it is removed. Note: all inhd's must also be substrates and all prps must also be products. If prps is given, substrate inhibition only occurs if at least one of the propagators is depleted

The content of the arrays is copied. They can be deleted afterwards.

void Net::resize	(	int32	nr,
		int32	nc
	)

resize all vectors.

sets the network size.

Parameters:

	nr	number of reactions
	nc	number of compounds

Resizes the underlying array accordingly, thus avoiding continious reallocation if the reactions are added one by one.

int8 Net::rev ( int32 reaidx ) [inline]

reversibility of the reaction;

array< int32 > * Net::subs_stoich ( int32 reaidx ) [inline]

substrate stoichiometries of reaction reaidx

Parameters:

reaidx

which reaction

Note: this returns the original array from the Net object. Do not delete!

array< int32 > * Net::substrates ( int32 reaidx ) [inline]

substrates of reaction reaidx

Parameters:

reaidx

which reaction

Note: this returns the original array from the Net object. Do not delete!

array< int32 > * Net::succs ( int32 comidx ) [inline]

successor reactions of compound comidx

Parameters:

comidx

which compound

Note: this returns the original array from the Net object. Do not delete!

string * Net::toString ( )

copy network data into a string

Member Data Documentation

array<int8>* Net::reaMask

which reactions are enabled in the current network

NetStruct* Net::str [protected]

the network topology

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

src/core/net.h
src/core/net.cc

Net Class Reference

Public Member Functions

Public Attributes

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation