Name and suffix do not contribute to output filenames when output.output_filename is not None:mk_prepare_ligand.py outputs (overwrites) prepared covalent ligands at different residues to the same file

[rwxayheee]

This is because the current way to get suffixes (to distinguish output filename) is the length of molsetup. The covalent ligand preparation may yield multiple molsetups, but the suffix can be empty if the length of each molsetup is 1. Therefore, these molsetups of length of 1 will be (over)written to the same output file, even with a table of summary ilke:

Input molecules processed: 77, skipped: 0
PDBQT files written: 77
PDBQT files not written due to error: 0
Input molecules with errors: 0

There is a similar issue when there are multiple binding patterns (tether smarts have multiple matches).

Posting here as a known issue. Will be fixed in PR #277

[rwxayheee]

This is because the suffix tuple does not go to the output filename, if the output filename is not None.

There really isn't a good way to disambiguate covalent outputs without changing the structure of class Output. I will just override the output_filename attribute in the is_covalent routine..