Towards fixing #148, compiles but some tests don't pass yet
- some exception handling fixes #111
- important bug fixed in alt loc handling, the lookup map for atom names wasn't properly reset when adding a new alt loc group
- fixed implementation of StructureTools.getBackboneAtomArray (was including CB atoms, and excluding all GLY groups)
- added some tests for the StructureTools methods
Full fix for #148, all tests pass
- some improvement in exceptions and logging #111 and #155
More #111 and #155
Adding a test for correct writing of atom names in PDB format
Adding some better javadoc to clarify ambiguity in atom names
Merge branch 'josemduarte-master'
manually resolving merge conflict