Non english months in pdb headers 4449

[exs-gbartlett]

• I hereby agree to dual licence this and any previous contributions under both
  the Biopython License Agreement AND the BSD 3-Clause License.

• I have read the CONTRIBUTING.rst file, have run pre-commit
  locally, and understand that continuous integration checks will be used to
  confirm the Biopython unit tests and style checks pass with these changes.

• [] I have added my name to the alphabetical contributors listings in the files
  NEWS.rst and CONTRIB.rst as part of this pull request, am listed
  already, or do not wish to be listed. (This acknowledgement is optional.)

Closes #4449

Non-recognized months in pdb header no longer raise ValueError but return '0', the same behaviour as a month of 'xxx'. Unit test included.

[peterjc]

Currently this silently ignores the bad month in a PDB file, using zero instead.

Unless our PDB team think otherwise, I would prefer this to consider the permissive/strict mode, and adjust the behavior accordingly.

CC @JoaoRodrigues @etal @jgreener64 (not an exhaustive list)

[jgreener64]

I don't have strong opinions here. On the one hand I don't think returning a zero will cause problems in user code. On the other hand it does say at https://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#HEADER that

The verification program checks that the deposition date is a legitimate date

so I would guess that all PDB entries have a legitimate date (I haven't checked).

[peterjc]

I strongly suspect the test case here is from a third party tool exporting in PDB format, not a file from an official repository/mirror.

[exs-gbartlett]

The test case is from a PDB file generated by a third party tool and is not a public repository file. Does biopython only support PDB files that have been deposited at wwPDB? The month 'xxx' is tolerated in the code without strict/permissive checks.

[peterjc]

We try to parse "unofficial" files, but where they break the specification it is reasonable to give a warning or error.

In this case I personally would not want this to be silently parsed in strict mode.

[exs-gbartlett]

Updated with warning and permissive flag carried through to the _format_date function. Updated unit tests. Hopefully this is an acceptable solution.

[peterjc]

A minor improvement aside (warning message and class), this looks good to me.

[mdehoon]

I still object against warnings, as by default they get printed only once in one Python session.