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).
getSBMLSpeciesList(sbmlm)An object of class '>sbmlPtr as returned by
getSBMLmodel. This is basically a pointer to a SBML model.
If the SBML model contains a ListOfSpecies section, a list is
returned:
character vector containing the species id's. If no id is given for a
particular species, the corresponding value is set to "no_id".
character vector containing the species names. If
not available, the value is set to the empty string "".
character vector containing the species compartments. If
not available, the value is set to the empty string "".
integer vector containing the charge of the species. If no charge is given
for a particular species, the corresponding value is set to 0.
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.
Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008) LibSBML: An API Library for SBML. Bioinformatics 24, 880--881.
getSBMLmodel, '>sbmlPtr