Tool to convert between atom names conventions

[joaomcteixeira]

Follows discussion on #113

For now, adds two conversion tables between:

• BMRB/PDBv3/Amber
• Old PDB

The input pdb atom name format is guessed on the fly, hence there is a bit of computation penalty.

TODO:

• implement XPLOR
• tests
• improve docs
• N-terminal Hs, also PRO
• histidines
• make trick to implement OT1 like atoms.

What are your thoughts?

Still, I think #113 is a valuable tool.

[amjjbonvin]

Looks good to me. Did not check though against the HADDOCK topologies. The file containing all amino acids topologies in HADDOCK is in the toppar directory and called: protein-allhdg5-4.top

[joaomcteixeira]

I am checking and they are the same as xplor. One difference is that xplor (according to here) has HB2/HB1 swapped with 1HB/2HB with the other nomenclatures. Did you know anything about this for CNS?

Another important change is:

! CNS v1.3 (27-Feb-10): changed OT1, OT2 to O, OXT, respectively. xplor keeps OT1 and OT2.

[joaomcteixeira]

I think this is it. tests okay in py27 and py38. @JoaoRodrigues have your say.

[joaomcteixeira]

A user from the forum is requesting this tool -> https://ask.bioexcel.eu/t/prodigy-fails-to-calculate-binding-energy-of-protein-protein-complex/3420/3

I think is it's a useful tool and we should merge it soon.

[JoaoRodrigues]

I'm gonna go ahead and close this since we discussed online that this falls a little out of the scope of the tools and requires a lot of maintenance (all the conversion schemes, etc need to be maintained).