Merge pull request #68 from RosettaCommons/JWLabonte/Atom_output
This branch has made a number of (I think) improvements to the `show()` methods of several classes. In particular:
- [x] Added `conformation/Atom.cc`.
- [x] Added `conformation::Atom::show()` (and an `operator<<`).
- [x] Renamed `chemical::Atom::print()` to `chemical::Atom::show()`.
- [x] `Residue::show()` now calls `conformation::Atom::show()`.
- [x] Added optional parameters to `Residue::show()` and `ResidueType::show()` to cause the latter to call `chemical::Atom::show()` for each atom.
- [x] Expanded what is output by `chemical::Atom::show()`.
I also cleaned up the Doxygen in the files.
I also added `GasteigerAtomType`s to sugar residues and ouput the results in the carbohydrates integration test to both test these new `show()` modifications and to test Gasteiger typing of sugars.
no unit test changes
Only the carbohydrates integration test changes, as expected.