Structure of ModelOrg Class

This class represents a model organism with various attributes related to central model structures, metabolites, reactions, and genes.

Slots

mod_id

A character vector representing the model identifier.

mod_desc

A character vector describing the model.

mod_name

A character vector containing the model name.

mod_compart

A character vector indicating the model compartment.

mod_compart_name

A character vector with the name of the model compartment.

mod_attr

A data frame with additional model attributes.

mod_notes

A character string that can contain an XML block with additional information about the model.

S

A sparse numeric matrix of dgCMatrix-class representing the Stoichiometric matrix.

obj_coef

A numeric vector containing coefficients for the objective function.

obj_dir

Character specifying the objective direction. Either "maximize" or "minimize".

subSys

A sparse Boolean matrix of lgCMatrix-class defining subsystems.

subSys_id

A character vector representing subsystem identifiers.

subSys_name

A character vector containing the subsystem names.

constraints

An object of class Constraints which specifies constraints in a model in addition to stationarity and individual flux bounds.

met_id

A character vector representing metabolite identifiers.

met_name

A character vector with metabolite names.

met_comp

A character vector indicating metabolite compartments.

met_attr

A data.frame that enables the storage of additional data for metabolites. Only specific columns are exported to SBML files. See writeSBMLmod for details.

react_id

A character vector representing reaction identifiers.

react_name

A character vector with reaction names.

react_comp

A character vector indicating reaction compartments.

lowbnd

A character vector containing lower bounds for reactions.

uppbnd

A character vector containing upper bounds for reactions.

react_attr

A data.frame that enables the storage of additional data for reactions. Only specific columns are exported to SBML files. See writeSBMLmod for details.

gprRules

A character vector with Gene-Protein-Reaction association rules (with gene product indices corresponding to the order in slot 'genes').

genes

A list of character vectors. Each vector contains the IDs of gene products associated to the respective reaction.

allGenes

A character vector with all gene identifiers.

genes_attr

A data.frame that enables the storage of additional data (e.g., name and CVTerms) for genes/gene products. Only specific columns are exported to SBML files. See writeSBMLmod for details.