getSBMLSpeciesList: Get Species List

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

Get Species List

Description

Retrieve list of species 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

  getSBMLSpeciesList(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 ListOfSpecies section, a list is returned:

id	character vector containing the species id's. If no id is given for a particular species, the corresponding value is set to "no_id".
name	character vector containing the species names. If not available, the value is set to the empty string "".
compartment	character vector containing the species compartments. If not available, the value is set to the empty string "".
charge	integer vector containing the charge of the species. If no charge is given for a particular species, the corresponding value is set to 0.
boundaryCondition	logical vector containing the boundaryCondition flag of the species. If no boundaryCondition flag is given for a particular species, the corresponding value is set to FALSE.

All list elements have the same length. If the SBML model does not contain a ListOfSpecies 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.