getSBMLReactionsList: Get Reaction List

In SysBioChalmers/sybil-SBML: 'SBML' Integration in Package 'Sybil'

Get Reaction List

Description

Retrieve list of reactions included in a SBML model.

If sybilSBML was built with a libSBML version, that was not including the FBC plugin, FBC constraints are ignored. Please make sure that you build sybilSBML with the libSBML version containing the FBC plugin (check out installation details).

If sybilSBML was built with a libSBML version, that was not including the Groups plugin, Groups are ignored. Please make sure that you build sybilSBML with the libSBML version containing the Groups plugin (check out installation details).

Usage

  getSBMLReactionsList(sbmlm)

Arguments

sbmlm

An object of class sbmlPtr as returned by getSBMLmodel. This is basically a pointer to a SBML model.

Value

If the SBML model contains a ListOfReactions section, a list is returned:

id	character vector containing the reaction id's. If no id is given for a particular reaction, the corresponding value is set to "no_id".
name	character vector containing the reaction names. If not available, the value is set to the empty string "".
reversible	logical vector containing the reversible flag of the reactions. If no reversible flag is given for a particular reaction, the corresponding value is set to FALSE.
notes	character vector containing the note strings. If no note is given for a particular reaction, the corresponding value is set to the empty string "".
annotation	character vector containing the annotation strings. If no annotation is given for a particular reaction, the corresponding value is set to the empty string "".
reactants	a list containing the reactions reactants. id character vector containing the species reference id's involved as reactants. If no id is given for a particular species, the corresponding value is set to "no_id". species character vector containing the species id's involved as reactants. If no id is given for a particular species, the corresponding value is set to "no_species". stoichiometry numeric vector containing the stoichiometry of the species. If no value is given for a particular species, the corresponding value is set to 1. If no reactant is given for a particular reaction, the corresponding value is set to NULL.
products	a list containing the reactions products. id character vector containing the species reference id's involved as products. If no id is given for a particular species, the corresponding value is set to "no_id". species character vector containing the species id's involved as products. If no id is given for a particular species, the corresponding value is set to "no_species". stoichiometry numeric vector containing the stoichiometry of the species. If no value is given for a particular species, the corresponding value is set to 1. If no product is given for a particular reaction, the corresponding value is set to NULL.
kinetic_law	a list containing the reactions parameters. id character vector containing the parameter id's. If no id is given for a particular parameter, the corresponding value is set to "no_id". value numeric vector containing the parameter values. If no value is given for a particular parameter, the corresponding value is set to 0. units character vector containing the parameter units. If no unit is given for a particular parameter, the corresponding value is set to the empty string "". If no parameter is given for a particular reaction, the corresponding value is set to NULL.

All list elements have the same length. If the SBML model does not contain a ListOfReactions section, NULL is returned.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

References

Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008) LibSBML: An API Library for SBML. Bioinformatics 24, 880–881.

See Also

getSBMLmodel, sbmlPtr

SysBioChalmers/sybil-SBML documentation built on Aug. 24, 2023, 1:11 p.m.