An issue with hydrogen bonding groups on the protein being ignored when
the available volume for an interacting molecule near the hydrogen bond group
was less than 100 cubic angstroms has been fixed. Previously, the scoring
function was set up with a protein and box, rather than a receptor object.
Internal refactoring has been added to improve stability.
A bug in the hydrogen bonding geometry perception of primary planar amines with
interaction directions perpendicular to the plane has been fixed.
Under this bug, such an interacting group had a 50% chance of selecting the
wrong perpendicular direction.