bfactors and tempfactors

[RMeli]

Expected behavior

I expect attributes representing the same thing to be consistent across file formats.

Actual behavior

For the MMTF format we have the bfactors attribute, while for other formats we have tempfactors (see user guide).

From a quick search within the code, I think bfactors is also used by TPRParser and ParmEdParser.

In topologyattrs.pythere are both class Tempfactors and class Bfactors. Should the two attributes be merged?

[lilyminium]

Yes!

It's especially annoying that the PDB format only uses tempfactors when writing out to PDB, as that's quite a common task to do for e.g. RMSF visualisation.

At least in Oct 2019 TPRParser did not actually have either bfactors or tempfactors. ParmedParser uses Tempfactors despite ParmEd calling them bfactors (as does nglview).

Personally I prefer bfactors > tempfactors, but the latter seems to be the majority attribute.

[RMeli]

I must learn to search for open issues before opening new ones...

[RMeli]

@lilyminium you are right about the TRPParser; it popped up because of a docstring:

mdanalysis/package/MDAnalysis/topology/TPRParser.py

Line 114 in 3e56b70

[residue, segment, radius, bfactor, resnum, moltype]

[orbeckst]

duplicates #1901