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
Revert "Remove @throws from methods no longer throwing StructureExceptions"

This reverts commit fd33bf317af296e1f9402784644970e063416ff4.
Revert "Remove useless StructureExceptions in Calc"

This reverts commit fc8647540fabb2496341e65e8e51e341afe9f228.
Merge pull request #28 from ulyssecarion/master

Overall result: deprecates "skalarProduct" for "scalarProduct".
Add an isWater method to Group; add water names to GroupType

Adds an isWater() method to the Group interface, which is implemented
in HetatomImpl; ChainImpl's static field 'waternames' has been moved to
GroupType.WATERNAMES.

Updates StructureTools, TestAltLocs, and ChainImpl to use the renamed
and relocated field.
Replace all uses of waternames with isWater(); move waternames into HetatomImpl

All uses of waternames were for doing what isWater now does, so
waternames can now be made a private field of ChainImpl.
Have StructureIO set the atom cache of getBioUnitDataProvider

Otherwise, calls to hasBiologicalAssembly or getNrBiologicalAssemblies
ignore the user's cache.
Get rid of a few debugging println calls
Merge pull request #30 from ulyssecarion/non-verbose

Get rid of a few debugging println calls
Merge pull request #29 from ulyssecarion/master

Add an isWater method for Groups
catching NPE
Merge branch 'master' of github.com:biojava/biojava
making sure cache can't be null
adding cleaner logging and new option to disable domain based alignments
Merge branch 'master' of https://github.com/biojava/biojava