pdb_renameatom - Renames atoms.

[joaomcteixeira]

Adds a tool to rename atom names.

Sometimes when exchanging PDBs between programs we find atom names are not compatible. For example, here is a table with the different atom name nomenclatures for some of the most relevant software and databases in the field.

This tool comes also as a request from my colleagues at @formankay lab, yet I trust it will be very helpful for the whole community.

What it does:

Atom names are renamed and formatted according to the element type. In case of missing elements, the atom name will be left-justified to four characters.

@JoaoRodrigues I added only my name in the authors and copyright just because of what we commented in #112. But just add also yours if you feel so, or we can use instead CSB Group, @amjjbonvin

NOTE: add [FEATURE] in the commit message when merging.

[amjjbonvin]

Seems like an interesting tool. I could see more name categories, e.g. HADDOCK - could be the xplor one already matches it - Gromacs, ...

[joaomcteixeira]

The tool now is agnostic, as the user has to provide the original atom name and the target atom name. I haven't built any translation tables inside. Yet, @JoaoRodrigues commented that translation tables might be good. However, having translation tables directly in this tool would make the tools strict and not agnostic. Honestly, I think we should keep the tool agnostic and build the tables a layer above (in some other script or project). What are your thoughts?

[amjjbonvin]

Probably a good strategy, but then we should at least provide a few translation tables, otherwise nobody will use the tool (experienced users will have their own scripts).

[joaomcteixeira]

Okay, so I will make some translation tables and have those as options. Still, I will keep this script somewhere and make a new PR.

[joaomcteixeira]

Because both @JoaoRodrigues and @amjjbonvin agree on going to a conversion table. I am closing this PR and opening a new one for the new tool.