Beginning in SBML Level 2 Version 2, the "charge" attribute on Species is deprecated and in SBML Level 3 it does not exist at all. Its use strongly discouraged. Its presence is considered a misfeature in earlier definitions of SBML because its implications for the mathematics of a model were never defined, and in any case, no known modeling system ever used it. Instead, models take account of charge values directly in their definitions of species by (for example) having separate species identities for the charged and uncharged versions of the same species. This allows the condition to affect model mathematics directly. LibSBML retains this method for easier compatibility with SBML Level 1.
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