⚡ Bolt: Optimize Pandas DataFrame iteration

[alinelena]

💡 What: Replaced iterrows() with itertuples(index=False, name=None) or to_dict('records') in Pandas DataFrame iterations.
🎯 Why: iterrows() is slow because it creates a Series object for each row, and it can trigger FutureWarnings when using integer keys for position-based Series access.
📊 Impact: Measurable speedup in DataFrame iteration across bulk crystal, conformer calculations and utility scripts by avoiding row-by-row Series generation.
🔬 Measurement: Observe reduction in benchmark setup and data parsing time.

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PR created automatically by Jules for task 8703084877674280547 started by @alinelena

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