SMILES parsing doesn't set atom types

[rajarshi]

Atom types can be perceived using the following code

acm <- J("org.openscience.cdk.tools.manipulator.AtomContainerManipulator")
acm$percieveAtomTypesAndConfigureAtoms(mol)

This does not happen by default when parsing a SMILES or reading an SDF. Either provide this as a function (e..g, set.atom.types) or else include in the molecule parsing/loading function as a optional parameter.

In both cases, should support the possibility of different atom typing schemes

[rajarshi]

There was a function, do.typing that implemented this. Renamed to set.atom.types and updated the code to use J notation. Currently only supports CDK atom types