Add mechanism for indicating user-specified charges should be used

[jchodera]

Perhaps if charges for the provided molecules are provided, we can cache those and use them instead?

How would we mix user and generated charges in the cache?

[jchodera]

Should we just use the charges from the Molecule object if they are non-zero?

[jchodera]

#94 implements a scheme in which user-provided charges are used if the provided Molecule contains non-zero charges.