This would be my approach:
1) Use seam-gen to generate an app (not using reveng of tables)
2) Translate your schema into JPA/EJB3 entity beans with appropriate annotations
3) Create the relevant framework components (i.e. a entityquery for atoms and compounds,
entityhome for molecule
4) Create a simple CRUD screen using a mixture of h:inputText, h:commandButton
s:selectItems and s:convertEntity
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