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AI Fix Prompts for Conformers

Copy any prompt below into Claude, ChatGPT, or your AI coding assistant to automatically fix the issue. Each prompt includes full context, code location, and step-by-step fix instructions.

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MEDIUM ⚒ significant #1

Simplify 5 high-complexity files

complexity refactoring quality
Expected outcome: All listed files reduced to medium or low complexity
Files to modify: pipelines/protenix-avb3-template/scripts/template_self_sampling_workflow.py, pipelines/protenix-a5b1/scripts/merge_staged_tagged_complex.py, pipelines/avb3-conformers/scripts/run_conformer_pipeline.sh, pipelines/protenix-a5b1/scripts/check_tagged_structure_quality.py, pipelines/protenix-a5b1/scripts/run_complete_tagged_until_pass.sh
Prompt (copy this into your AI assistant) 
These files in 'dfu99__conformers' have high cyclomatic complexity:

- **pipelines/protenix-avb3-template/scripts/template_self_sampling_workflow.py**: complexity=95, max nesting=6, longest function=186 lines
- **pipelines/protenix-a5b1/scripts/merge_staged_tagged_complex.py**: complexity=95, max nesting=6, longest function=81 lines
- **pipelines/avb3-conformers/scripts/run_conformer_pipeline.sh**: complexity=66, max nesting=7, longest function=72 lines
- **pipelines/protenix-a5b1/scripts/check_tagged_structure_quality.py**: complexity=65, max nesting=5, longest function=234 lines
- **pipelines/protenix-a5b1/scripts/run_complete_tagged_until_pass.sh**: complexity=44, max nesting=3, longest function=153 lines

For each file:
1. Break large functions into smaller, focused functions
2. Reduce nesting depth (extract early returns, use guard clauses)
3. Simplify conditional logic
4. Extract complex expressions into named variables