removed obsolete functions from lib.distances

[zemanj]

Fixes #2072

Changes made in this Pull Request:

• removed the now obsolete functions calc_distance, calc_angle, and calc_dihedral from lib.distances
• replaced all of their occurrences in the code by suitable calls to calc_bonds, calc_angles, and calc_dihedrals, respectively
• transformed the corresponding tests into tests of calc_bonds, calc_angles, and calc_dihedrals for single coordinate input
• updated the docstrings of calc_bonds, calc_angles, and calc_dihedrals to better reflect the possibility of single coordinate input (also related to issue MDAnalysis.lib.distances needs rework #2046)

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[zemanj]

Regarding my latest commit: The precision used to be 3 decimals in the tests for calc_angle and calc_dihedral. When I applied these tests to calc_angles and calc_dihedrals, I increased the precision to 5 decimals, but that fails in one of the tests for numpy 1.10.4. I therefore decreased the precision again to 4 decimals.
That's in fact pretty inaccurate, and only happens if distances are computed with PBC.
I suspect that is due to the way the minimum image convention is implemented in calc_distances.h, where the inverse box is supplied in single precision.
Changing this to double precision wouldn't really affect performance since it is promoted to double in the calculation anyway.

[zemanj]

Ok this seems good to go.

[richardjgowers]

Cool ty @zemanj

[zemanj]

@richardjgowers The tests are still quite an unstructured mess though...

[zemanj]

@richardjgowers Thanks for reviewing!