optsol_blockedReact-class: Class '"optsol_blockedReact"'

In sybil: Efficient Constrained Based Modelling

Description

Structure of the class "optsol_blockedReact". Objects of that class are returned by the function blockedReact.

Objects from the Class

Objects can be created by calls of the form new("optsol_blockedReact", ...).

Slots

blocked:

Object of class "logical" indicating if a reaction is blocked, or not.

react:

Object of class "reactId" containing the reaction id's of checked reactions.

mod_id:

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

mod_key:

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

solver:

Object of class "character" indicating the used solver.

method:

Object of class "character" indicating the used method.

algorithm:

Object of class "character" containing the name of the algorithm used for optimizations.

num_of_prob:

Object of class "integer" indicating the number of optimization problems.

lp_num_cols:

Object of class "integer" indicating the number of columns.

lp_num_rows:

Object of class "integer" indicating the number of rows.

lp_obj:

Object of class "numeric" containing the optimal values of the objective function after optimization. If no flux distribution is available, slot lp_obj contains the cross-product of the objective coefficients in slot obj_coef and the part of the flux distribution in slot fluxdist containing the values representing fluxes in the entire metabolic network (slot fldind).

lp_ok:

Object of class "integer" containing the exit code of the optimization.

lp_stat:

Object of class "integer" containing the solution status of the optimization.

lp_dir:

Object of class "character" indicating the direction of optimization.

obj_coef:

Object of class "numeric" containing the objective coefficients of the used model (slot obj_coef of an object of class modelorg). These are not necessarily the objective coefficients of the used algorithm.

obj_func:

Object of class "character" containing the objective function of the used model. Usually, it contains the return value of printObjFunc.

fldind:

Object of class "integer" pointers to columns (variables) representing a flux (reaction) in the original network. The variable fldind[i] in the problem object represents reaction i in the original network.

fluxdist:

Object of class "fluxDistribution" containing the solutions flux distributions.

alg_par:

Object of class "list" containing a named list containing algorithm specific parameters.

Extends

Class "optsol", directly.

Methods

blocked:

signature(object = "optsol_blockedReact"): gets the blocked slot.

blocked<-:

signature(object = "optsol_blockedReact") sets the blocked slot.

react:

signature(object = "optsol_blockedReact"): gets the react slot.

react<-:

signature(object = "optsol_blockedReact") sets the react slot.

maxSol:

signature(object = "optsol_blockedReact")(slot): returns the values in the slot given in slot for optimizations in “max” direction.

minSol:

signature(object = "optsol_blockedReact")(slot): returns the values in the slot given in slot for optimizations in “min” direction.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

checkOptSol and optsol

Examples

  showClass("optsol_blockedReact")

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