SameSelection should have an option for indices

[lilyminium]

Expected behavior

byres and same residue as selects the whole residue for each atom in the subsequent selection, by the canonical and unique resindex. Likewise same segment as uses segindex.

Actual behavior

byres and same residue as use the user-supplied, potentially repeated resid values. same segment as uses segid. This is redundant as you can already use same resid as or same segid as for the same behaviour. This may result in unexpected behaviour with altLocs also.

Code to reproduce the behavior

Leads to problems like in this mailing list issue where selecting "byres resname TIP3" returns various amino acids and ions as well.

>>> import MDAnalysis as mda
>>> u = mda.Universe('a.psf', 'a.dcd')
>>> ag = u.select_atoms('byres resname TIP3')
>>> print(set(ag.resnames))
{'GLN', 'LEU', 'TRP', 'THR', 'LYS', 'GLU', 'POPE', 'ASP', 'TYR', 'VAL', 'ARG', 'PHE', 'MET', 'CYS', 'ILE', 'PRO', 'TIP3', 'ALA', 'SOD', 'CLA', 'SER', 'GLY', 'ASN', 'HSD'}

Current version of MDAnalysis

• Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)") 0.20.1
• Which version of Python (python -V)? 3.7.3
• Which operating system? MacOS

[richardjgowers]

Oops yeah, that's the whole reason we have ix and friends