Code work on thiols and TraPPE torsions.
Changed some logic in Polynomial, PolynomialTorsionType, and CharmmTorsionType to allow for polynomials to be set via the = operator.
Many fixes for Charmm-type torsions.
Formatting to prettify the code
Adding single precision capabilities to c++ side
OptionSectionParser get compiled
xemacs has been drafted to perform our indentation services
merging new_design branch into OOPSE-2.0
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