Remove BondType from Bond

All Bond objects are assumed to be covalent bonds
By default, Bonds will now add themselves to their Atoms' bond lists.
For LINK records, work strictly with atoms that aren't alt locs
Use the new bond constructor in PDBFileReader
Add a test making sure ligands get bonds too
Loop through all non-water groups for intra-residue bonds, not just sequence residues
By default, keep the bond arraylist as small as possible
Trim to size all bond arraylists after creating the bonds
Add tests for IDs that make formBonds crash
Bugfix: getAltLocGroup might need to return 'this'
Bugfix: off-by-one error in the SSBOND handler

Oops!
Skip sequence residues that aren't amino acids or are missing atoms for intra-residue bonds
Make more precise error reporting on bond-formation errors
Do not fail "silently" on error while PDB parsing
Add human-friendly toStrings for SSBond and LinkRecord
Added GenbankCookbookTest test case.
Merge pull request #44 from karlnicholas/master

Added GenbankCookbookTest test case.
Merge pull request #39 from ulyssecarion/bond-efficiency

Simplify and optimize bonds for memory usage
Consider Deuterium and Tritium not to be heavy elements by Element#isHeavyAtom

Update the Javadocs and fix a typo as well.
Merge pull request #45 from ulyssecarion/heavy-water

Consider Deuterium and Tritium not to be heavy elements by Element#isHeavyAtom