Topology attribute handling

As per the discussion started in #942, missing attributes from a topology will be handled according to different categories (a few more categories were added in this page). These are:

Classes

1. Left out of the Topology, with a general AttributeError on accession;
2. Left out of the Topology, but with a specific MDAnalysis.MissingTopologyAttributeError on accession, perhaps suggesting how to set/guess values;
3. Added to the topology, set to a default;
4. Added to the topology, guessed — possibly with a warning that it is guessed. If guess fails, assign some default;
5. Added to the topology, guessed — possibly with a warning that it is guessed. If guess fails, warn and leave unassigned (like category 2 above);
6. Absolutely necessary; abort Topology/Universe loading if absent;
7. Internal: attribute generated internally that does not depend on topology availability or guessing;
8. Attribute that you think should be removed from consideration.

(Thanks to @jbarnoud for suggesting some of the possibilities above)

Poll

We need to decide which attributes go into which category. This will be implemented as part of the topology refactor (#363). Please edit the table below to vote your opinion, and if needed add your justification to #942. Factors you might want to take into account are

• consistency,
• ease for the user in case of missing attributes,
• little boilerplate for the most common cases,
• and backwards compatibility (though this last factor might be of less importance since compatibility will already be broken by the topology refactor).

Attribute	@mnmelo
residues*	3
segments*	3
indices	7
resindices	7
segindices	7
ids	3
names	6
types	1
elements	5
radii	5
chainIDs	1
icodes	1
tempfactors	1
masses	5
charges	2
bfactors	1
occupancies	1
altLocs	1
resids	3
resnames	2
resnums	3
segids	3
bonds	5
angles	5
dihedrals	5
impropers	1
other attrs	1

* While not strictly attributes, Residue/Segment assignment falls pretty much in the same categories, and their handling is relevant for related attributes (resindices, resids, etc.).