Molecule from Schema needs work

[sgoodlett]

There are a few issues I've noticed with how we use QCSchema to read xyz files.

1. In the current workflow, QCSchema will always attempt to apply an Angstrom to Bohr unit conversion. We have circumvented this by telling QCSchema that the units are always in Bohr. This feels kind of hacky and I think needs looking into for a more stable solution.
2. The way we process xyz files actually doesn't allow for properly formatted xyz file reading as we cannot handle when there is an atom number line and a comment line. This needs to be fixed.