What does the -m flag do?

[tuckerburgin]

There appears to be only very scant documentation on what the -m (or --mutation) flag does or how it is used. As far as I can tell it is only documented in the propka3 command's help text, which says:

specifying mutation labels which is used to modify <filename> according to, e.g. N25R/N181D (default: None)

When I read this it sounds to me like propka will apply the indicated mutation(s) to the specified PDB file and then make a pKa prediction on that mutant structure. In practice, however, this option appears to be doing nothing. For example, here I am calling it with the intention to mutate Asn-64 in my file "stability.pdb" to an aspartate residue:

$ propka3 stability.pdb
$ mv stability.pka stability_wt.pka
$ propka3 stability.pdb -m N64D
$ diff stability.pka stability_wt.pka

The above diff produces no output; the files are identical. There's no terminal output from propka either, and I can't identify any other files that have been changed. I've also tried this with various syntax changes and settings for the equally mysterious --mutator and --mutator-option flags, to no avail. So: what does the -m option do, and does propka3 in fact have a built-in protein mutator function that does what I think -m is supposed to do?

Here's the relevant snippet of stability.pdb, for reference:

...
ATOM   1048  C   GLU    63      25.715  34.942  24.698  1.00  0.00           C
ATOM   1049  O   GLU    63      25.005  34.225  23.942  1.00  0.00           O
ATOM   1050  N   ASN    64      25.426  35.095  25.967  1.00  0.00           N
ATOM   1051  H   ASN    64      26.032  35.695  26.508  1.00  0.00           H
ATOM   1052  CA  ASN    64      24.320  34.531  26.702  1.00  0.00           C
ATOM   1053  HA  ASN    64      24.145  33.483  26.460  1.00  0.00           H
ATOM   1054  CB  ASN    64      24.714  34.570  28.223  1.00  0.00           C
ATOM   1055  HB2 ASN    64      25.623  34.016  28.458  1.00  0.00           H
ATOM   1056  HB3 ASN    64      24.964  35.611  28.429  1.00  0.00           H
ATOM   1057  CG  ASN    64      23.606  34.142  29.130  1.00  0.00           C
ATOM   1058  OD1 ASN    64      23.656  33.099  29.793  1.00  0.00           O
ATOM   1059  ND2 ASN    64      22.574  34.967  29.368  1.00  0.00           N
ATOM   1060 HD21 ASN    64      21.896  34.772  30.091  1.00  0.00           H
ATOM   1061 HD22 ASN    64      22.422  35.864  28.929  1.00  0.00           H
ATOM   1062  C   ASN    64      23.018  35.254  26.387  1.00  0.00           C
ATOM   1063  O   ASN    64      21.927  34.661  26.240  1.00  0.00           O
ATOM   1064  N   SER    65      23.061  36.540  26.170  1.00  0.00           N
ATOM   1065  H   SER    65      23.948  36.984  25.980  1.00  0.00           H
...

[speleo3]

I confirm that -m, --mutation, and also --mutator, --mutator-option, -t, --thermophile, -a, --alignment, -r, --reference, -o, --pH, are unused.

[speleo3]

Flag was removed in #187