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Added
Batch AF model fast parser: add experimental zsasa batch --af-model-fast for AlphaFold-like mmCIF batches. The fast path preserves multiple chains and atom metadata, and falls back to the generic parser for unsupported layouts.
Batch input I/O selection: add --input-io=auto|mmap|read to compare or select file input strategies where supported.
Batch stage profiling: add --profile-stages with --timing to report aggregate read/parse, classifier, and JSONL write times.
Changed
Batch JSONL streaming: buffer normal-sized JSONL records while streaming large records directly to avoid regressions for PDB batches with large atom-area payloads.