ProDy crashes while reading an mmCIF generated using OpenFold3

[rckormos]

Bug: parseCIF fails on valid mmCIF when _atom_site.auth_seq_id is . for non-polymer atoms

I’m parsing an OpenFold3-generated mmCIF with prody.parseCIF(...), with ProDy v2.6.1 installed via pip with Python 3.12.12, and get:

ValueError: invalid literal for int() with base 10: '.'

The failure occurs in ciffile.py when ProDy reads _atom_site.auth_seq_id and assumes it can always be cast to int.

In the mmCIF file:

• polymer atoms have integer auth_seq_id
• non-polymer ligand atoms (LIG0, chain B) have _atom_site.auth_seq_id = '.'
• the file also contains _pdbx_nonpoly_scheme.auth_seq_num = 1 for that ligand

According to the wwPDB mmCIF dictionary, _atom_site.auth_seq_id is optional and “not necessarily a number,” so this seems to be a parser bug rather than a file-format violation.

Expected behavior:

• ProDy should tolerate missing/non-numeric auth_seq_id values, especially for non-polymers, instead of unconditionally casting them to int.