Bug #117: Adding support for ~ in AtomClass
Expanding ~ in PDBFileReader paths
Merge remote-tracking branch 'emmebi/master'

This adds a fix for #117

Conflicts:
	biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java
Expand ~ in MMCIFFileReader
Merge pull request #218 from sbliven/master

Fix #117: Support ~ in File readers
Better logging in sifts #155
Better logging and some clean up in SeqRes2AtomAligner
Added a couple of methods to classes in contact package
Small bug fix: calling getCompounds explicitly at the end of parsing