[drroe]

V7.13.0. Add the fixatomnames command.

> help fixatomnames 
  [help fixatomnames]
        { parm <name> | parmindex <#> | crdset <COORDS SET>} [<mask>]
  Attempt to fix duplicated atom names in residues of the specified topology.
WARNING: THIS COMMAND IS STILL EXPERIMENTAL. USE AT YOUR OWN RISK.

This command attempts to fix duplicated atom names in the residues of the specified topology. If no mask is given, all residues will be checked. The algorithm used is extremely simple. When an atom is found with a duplicated name, if it has a digit that digit will be incremented. If multiple digits are present (e.g. H1N1) the right-most digit will be incremented first. If no digits are present one will be appended.

This command was used to fix duplicate atom names in modxna fragments. See: modxna/modxna#20

This PR also makes it so that the molecule and charge type fields of incoming mol2 files are preserved for output mol2 files.

Add 1 test and add a manual entry.