Find ligands by comparing seqResGroups and groups.

If a group is found by the method getAtomGroups() but not by
getSeqResGroups(), then it's a ligand group.
adding new utility method to filter out polymeric and solvent groups
making water names publicly accessible
Merge branch 'master' of https://github.com/ulyssecarion/biojava into
ulyssecarion-master

Conflicts:
	biojava3-structure/src/main/java/org/biojava/bio/structure/StructureTools.java
updating to new location of utility method in StructureTools
updating unit test for 1a4w and new ligand access methods
fixing access to getAtomLigands method
minor update
cleanup
Merge branch 'master' of github.com:biojava/biojava
Merge remote-tracking branch 'upstream/master'