Fix the placed-hydrogen distance behavior

[russell-taylor]

(This will take effect once we try to change the original values of 1.0 for the call to getPhantomHydrogensFor in Probe2. It is already broken in Reduce2.)

The placed HydrogenDistance should be less than 1 for both nuclear and e-cloud; this is the OH bond distance:

• 0.98 and 0.84

The H radius should be 1.00 for neutron or 1.05 for electron cloud

Have a look at the OH_BOND_LENGTH and see how this stuff all fits together

• Three numbers: (1) Distance from water O to H, (2) vdw radius of Hydrogen, and (3) is vdw radius of acceptor
• Rename placedHydrogenDistance, almost certainly should be radius
• https://github.com/cctbx/cctbx_project/blob/molprobity2-debug3/mmtbx/probe/Helpers.py#L652
• https://github.com/cctbx/cctbx_project/blob/molprobity2-debug3/mmtbx/probe/Helpers.py#L697

[russell-taylor]

(done) Fix in both Probe2 and Reduce2. Consider using a Probe Phil parameter for this. (done) Fix the test code.