Made a general-purpose public method
getAminoAcidSubstitutionMatrix(String).
Ran cleanup on AtomCache.
Merge pull request #36 from dmyersturnbull/master

Small changes
adding support for different types of file access
Merge remote-tracking branch 'andreas/mmcif' into 'andreas/master'

Conflicts:
	biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java
Fixing formatting with biojava lGPL header
Add tests for atom bonds

This tests for intra-residue, peptide, disulfide, and LINK bonds. Tests
are done on PDB ID 1KH9, which has all of those.
Introduce a new Bond class

The previous Bond class was barely used, so this completely replaces it.

Bonds keep track of two atoms, their type (using BondType), and their
order.

Also included are a few utility methods, like those for getting
distances between the two atoms and getting the other atom in a bond,
given the first one.
Add a getBonds() method to Atoms and implement it.
Comment out StructureTools.findBonds

This code relies on an old version of Bonds.
ChempComp and ChemCompConsumer now use ChemCompBonds.
Add a utility method to convert a ChemCompBond's order into an int
Add a utility class to store information stored from LINK records
Add a getAltLocGroup method to Groups, implement it in HetatomImpl
Add bond-parsing to PDBFileParser
Add a createAtomBonds flag to FileParsingParameters
Only form bonds if params has createAtomBonds set to true
Set createAtomBonds to be true in TestBond
Merge pull request #37 from ulyssecarion/peptide-bond-007

Add functionality for Bonds