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
Added a convenience getScop(String) method.
Added getTMScoreAlternate().
Made updateSuperposition() set block rotation matrices and shift
vectors.
Added a demo for using FastaAFPChainConverter for display.
Added an extra CP test, and fixed a test to work with change in
updateSuperposition().
Merge branch 'master' of https://github.com/dmyersturnbull/biojava.git
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 branch 'master' of https://github.com/biojava/biojava
Remove useless StructureExceptions in Calc

None of these methods can actually throw any checked exceptions, so it
makes no sense to force others to catch them.
Deprecate skalarProduct for scalarProduct (fix typo)
Remove @throws from methods no longer throwing StructureExceptions