Mustang header length issue in PDB files causing infinite loop

[valentinum]

Issue Description:
When Mustang method processes PDB files without a header file, it automatically adds one , with the first row starting with HEADER and including the protein name derived from the input filename. The PDB format limits lines to 80 characters. If the input filename is long, the HEADER row exceeds this limit. This does not trigger an error but causes Mustang to run indefinitely, never completing the alignment.

Reproduction:
Input: PDB file with no header and a long filename (e.g., very_long_protein_name_1234567890.pdb).
Command: Run Mustang via T-Coffee (t_coffee ... -method mustang_pair ...).
Observation: The process hangs after parsing, with no output or error in logs.

Environment:
T-Coffee: Version 13.46.0.919e8c6b.
OS: Linux (Ubuntu 20.04).
Input: PDB files processed via T-Coffee’s structural alignment pipeline.