reactId_Exch-class: Class '"reactId_Exch"'

In sybil: Efficient Constrained Based Modelling

Description

Structure of the class "reactId_Exch". Objects of that class are returned by the function findExchReact.

Objects from the Class

Objects can be created by calls of the form new("reactId_Exch", mod_id, mod_key, rpnt, rid, upt, mpnt, mid, lb, ub).

mod_id:

Object of class "character" containing the model id.

mod_key:

Object of class "character" containing the model key.

rpnt:

Object of class "numeric" containing the column indices in a stoichiometric matrix of the reactions given in rid.

rid:

Object of class "character" containing the reaction id's corresponding to argument rpnt.

upt:

Object of class "logical": upt[j] equals TRUE if reaction j in rid is an uptake reaction (an exchange reaction with a lower bound less than zero).

mpnt:

Object of class "numeric" containing the row indices in a stoichiometric matrix of the metabolites given in mid. The reaction given in rid[j] transports metabolite mid[j] across the system boundary of the model.

mid:

Object of class "character" containing the metabolite id's corresponding to argument mpnt.

lb:

Object of class "numeric" containing the lower bounds of the reactions given in rpnt.

ub:

Object of class "numeric" containing the upper bounds of the reactions given in rpnt.

Slots

uptake:

Object of class "logical" indicating if a certain reaction is an uptake reaction or not.

met_pos:

Object of class "integer" containing the row indices of metabolite id's in the stoichiometric matrix of the metabolic model with id mod_id.

met_id:

Object of class "character" containing the metabolite id's corresponding to the indices given in slot met_pos.

lowbnd:

Object of class "numeric" containing the lower bounds of the reactions given in slot react_pos.

uppbnd:

Object of class "numeric" containing the upper bounds of the reactions given in slot react_pos.

mod_id:

Object of class "character" containing the model id.

mod_key:

Object of class "character" containing the model key of the used model.

react_pos:

Object of class "integer" containing the column indices of reaction id's in the stoichiometric matrix of the metabolic model with id mod_id.

react_id:

Object of class "character" containing the reaction id's corresponding to the indices given in slot react_pos.

react_num:

Object of class "integer" containing the number of reaction id's.

Extends

Class "reactId", directly.

Methods

met_pos

signature(object = "reactId_Exch"): gets the met_pos slot.

met_pos<-

signature(object = "reactId_Exch"): sets the met_pos slot.

met_id

signature(object = "reactId_Exch"): gets the met_id slot.

met_id<-

signature(object = "reactId_Exch"): sets the met_id slot.

react_pos

signature(object = "reactId_Exch"): gets the react_pos slot.

react_pos<-

signature(object = "reactId_Exch"): sets the react_pos slot.

react_id<-:

signature(object = "reactId"): sets the react_id slot.

react_id:

signature(object = "reactId"): gets the react_id slot.

lowbnd

signature(object = "reactId_Exch"): gets the lowbnd slot.

lowbnd<-

signature(object = "reactId_Exch"): sets the lowbnd slot.

uppbnd

signature(object = "reactId_Exch"): gets the uppbnd slot.

uppbnd<-

signature(object = "reactId_Exch"): sets the uppbnd slot.

uptake

signature(object = "reactId_Exch"): gets the uptake slot.

uptake<-

signature(object = "reactId_Exch"): sets the uptake slot.

uptReact

signature(object = "reactId_Exch"): gets the id's of uptake reactions.

uptMet

signature(object = "reactId_Exch"): gets the metabolite id's of metabolites used by uptake reactions.

[:

signature(x = "reactId_Exch"): access like a vector. x[i] returns a new object of class reactId_Exch containing the ith exchange reaction id.

show:

signature(x = "reactId_Exch"): prints a table of all exchange reactions. If an upper or lower bound is equal or greater than abs(SYBIL_SETINGS("MAXIMUM")), it will be shown as Inf or -Inf.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

checkReactId

Examples

  showClass("reactId")

sybil documentation built on May 31, 2021, 5:08 p.m.