style: ruff-format virtual_atoms.py in rfd3 and rfd3na

[daylight-00]

lint_production has been red on production since #377: its ruff format --diff step (ruff 0.8.3, the version pinned in pyproject.toml) flags the same two files on every run and the job stops there, so ruff check is skipped as well.

-                    #... Pad_atoms should never inherit fixed state
+                    # ... Pad_atoms should never inherit fixed state
...
-                        <whitespace only>
+

This applies the formatter to models/rfd3/src/rfd3/transforms/virtual_atoms.py and models/rfd3na/src/rfd3na/transforms/virtual_atoms.py, two lines each.

• Comment and whitespace only: the AST of both files is identical before and after.
• ruff format --diff src models tests now reports 398 files already formatted and ruff check src models tests passes (ruff 0.8.3), so the job should go green.
• Open PRs such as Docs: Add RFOptimization documentation #388 and fix(mpnn): honor parser overrides for AtomArray inputs #389 currently fail on exactly these two files.

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[rclune]

LGTM