Holding structures in Reactions

[goldmanm]

Reaction objects hold lists of species/objects/indexes depending on where it is in the code. This leads to confusion in what methods accept what types of reactions.

Currently any reaction generated using families estimation is a TemplateReaction stored with molecule objects, created in generateReactions. In makeNewReaction, it converts the molecules into species objects, and then generates resonance isotomers and thermo.

It may be better to always have species objects in reactions, and whenever TemplateReactions are called in family.py, they use the species.molecule[0]. (or add a property called reactantsMol in TemplateReaction)

[github-actions]

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