Update __main__.py

[rolan701]

new pathway for structgen

In general, to fix commented-out code, either (a) fully reinstate it as active code if it is actually needed, or (b) remove it entirely if it is obsolete or intentionally disabled. If the intent is to document example usage, it should be rephrased as a proper comment (possibly with quoting or formatting) rather than raw commented code.

Here, the commented elif branches for 'chainb' and 'autocorr' are clearly non-functional and appear to be obsolete subcommand handlers. Since we should not change existing functionality, the safest choice is to delete these commented-out lines altogether. This maintains current behavior (they were not executed anyway) while resolving the CodeQL warning and improving readability.

Concretely, in molSimplify/__main__.py within the main function’s help-handling block (lines ~505–510), remove the six lines:

        #    elif 'chainb' in args:
        #        parser = argparse.ArgumentParser(description=DescString_chainb)
        #        parseinputs_chainb(parser)
        #    elif 'autocorr' in args:
        #        parser = argparse.ArgumentParser(description=DescString_autocorr)
        #        parseinputs_autocorr(parser)

No new imports, functions, or definitions are required.

[codecov]

Codecov Report

❌ Patch coverage is 9.47867% with 191 lines in your changes missing coverage. Please review.
✅ Project coverage is 40.61%. Comparing base (37bc057) to head (4bb9582).
⚠️ Report is 6 commits behind head on main.

Files with missing lines	Patch %	Lines
molSimplify/__main__.py	9.47%	191 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #523      +/-   ##
==========================================
- Coverage   40.64%   40.61%   -0.03%     
==========================================
  Files          93       93              
  Lines       30015    30024       +9     
==========================================
- Hits        12199    12194       -5     
- Misses      17816    17830      +14     

Flag	Coverage Δ
unittests	40.61% <9.47%> (-0.03%)	⬇️

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