Fix issue #201

[gdkwxn]

Issue #201

• Added inner function to 'perform_multiple_alignment' called 'get_gap_letter'
• added more identifiers in gap_letter (a,b..AA, AB..
• Added warning message for when a structure has to get additional identifiers (AA, AB)

[Copilot]

Pull request overview

This PR addresses Issue #201 by extending the residue renumbering “gap identifier” logic in perform_multiple_alignment so alignments with many gaps can continue past the previous single-letter limit, and it adds user-facing warnings when multi-character identifiers are required.

Changes:

• Added a get_gap_letter helper to generate gap identifiers beyond the original single-letter list.
• Introduced tracking (big_structures_warning) to emit a warning when larger gap identifiers are encountered.
• Updated the alignment-to-residue renumbering loop to use generated identifiers instead of a fixed gap_letter list.

Suppressed comments (3)

src/pdbcleanresiduestandardizationutils.py:131

• get_gap_letter hard-codes a 52-character alphabet and uses divmod(..., 52), but Issue #201 requires the single-character space to be A-Z + a-z + 0-9 (62). Also, the current implementation can generate 3+ character identifiers (AAA, ...) without ever emitting the requested "ERROR: Too many gaps, check your alignment!".

        alphabet = string.ascii_uppercase + string.ascii_lowercase

        label = ""
        n += 1
        while n > 0:

src/pdbcleanresiduestandardizationutils.py:244

• The warning trigger uses gap_tracker == 52 (A-Z + a-z), but Issue #201 calls out the single-character space as A-Z + a-z + 0-9 (62). Also, the warning should identify the affected chain(s), not just the structure name, to match the requested "WARNING: Chain xxx contains a lot of gaps. Check alignment!" behavior.

                                if gap_tracker == 52:
                                    big_structures_warning.add(structid_list[I].split("/")[-1])
                                gap_tracker+=1

src/pdbcleanresiduestandardizationutils.py:310

• The final warning text doesn't match the Issue #201 acceptance text and prints a set, which is non-deterministic in order. Consider printing the exact requested per-chain warning(s) and sorting for stable output.

    if len(big_structures_warning) > 0:
        print(f"\nWARNING: The following structures were affected by large gaps in most of the MSA (>62 positions), "
              f"resulting in residue renumbering that requires two-character alternate identifiers. This may lead "
              f"to problems when opening the structure with molecular visualization software. {big_structures_warning}\n")

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