Merge pull request #32 from biojava/master

Merging master into release for release 3.0.6.
Reverting version in release to 3.0.6.
Reverting version of integrationtest to 3.0.6.
Reverting version of protein-comparison-tool to 3.0.6.
Reverting version of biojav3-modfinder to 3.0.6.
Added caching using soft references in a multiton pattern. Commented.
Added two constructors for non-standard needs, allowing future ASTRAL
sets and parsing of local files.
Merge branch 'master' of https://github.com/dmyersturnbull/biojava.git
Critical null check of soft reference.
Some of the URLs and Ids were swapped; critical fix.
Fixed incorrect URLs and Ids in Astral.
Made a general-purpose public method
getAminoAcidSubstitutionMatrix(String).
Ran cleanup on AtomCache.
Merge branch 'master' of https://github.com/biojava/biojava into release
Merge branch 'master' of https://github.com/dmyersturnbull/biojava into release
Fixed strange merge conflict.
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.