The following classes/module/exception are defined in the embedded Ruby interpreter in Molby. The methods defined in the module Kernel can be used as if they are builtin functions, like in the standard Ruby interpreter. All other classes and MolbyError exception are defined under the a module Molby. However, Molby:: prefix is not necessary because include Molby is invoked on startup.
On startup, include Math is also invoked, so that the methods and constants in the Math module can also be used without prefix.
It is recommended for you to read the document of the most important class Molecule. Follow the links as necessary, and you will understand how other classes are defined and used.