Fixes

Addressed problem where critical failures are missed in testing (#262). This doesn't represent a change to the (documented) API but will change functionality for external code that isn't ready to handle the raised error.
Fixed calculation of non-integer charge (#264).
Fixed problem with missing RNA phosphate oxygens (#267).
Fixed problem with non-optimal hydrogen bond orientation for non-bonded atoms; mainly affects water orientation. (#9).

Changes

Supressed excessive "Tetrahedral hydrogen reconstruction not available for nucleic acids" warnings (#253).
Increased verbosity of output (warnings and information) for missing and reconstructed atoms.
Standardized testing and output for troubleshooting with non-integer residue charges.
Added HG1 as alternate name for serine hydroxyl hydrogen (#214).
Removed non-functional command line version of psize (#181).
Provided clearer error messages for unsupported MOL2 bond types (#178).
Added --run-long option to tests and cleaned up test warning messages.
Updated list of visualization tools to include NGL Viewer (#38).
Updated documentation to warn users against using more than one ligand in calculations (#23).