getSBMLReactionsList: Get Reaction List
In sybilSBML: 'SBML' Integration in Package 'Sybil'

Description Usage Arguments Value Author(s) References See Also

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).

1	getSBMLReactionsList(sbmlm)

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 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`.