Better specification of single-hydrogen rotator initial rotation

[russell-taylor]

We want the hydrogen to be placed at the same orientation for each run. For Tyrosine, it must be placed opposite the carbon rather than one of the hydrogens. For other cases, it must be placed at the same angle on all instances of the same residue or HET group.

New algorithm:

• Find the list of neighbor-of-neighbor atoms that are not hydrogens.
  • If there are none that are not hydrogens, then place all neighbors in the list.
• Sort this list in increasing order by total atom name.
• Select the lowest-named atom and place opposite it

[russell-taylor]

It turns out that the probe.Helpers.dihedralChoicesForRotatableHydrogens() method is being used to determine which hydrogen and which neighbor-of-neighbors to be used based on the results of calling model.get_riding_h_manager().

The code to determine this is thus inside of CCTBX and is not just randomly selecting one of either of them.