feat: add disorder-aware CIF export demo - #96
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IsaacSugden merged 4 commits intoJul 10, 2026
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- Validate refcode with strict alphanumeric regex before use as filename - Validate output-dir: reject path traversal (..), enforce cwd-relative - Break taint chain: CLI args no longer flow directly to filesystem ops
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IsaacSugden
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Jul 10, 2026
IsaacSugden
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This is a super cool contribution, thankyou! Its on our plans to improve cif writing for structures with disorder at some point, but this will really help the community for the foreseeable future. I've tested it on a handful of structures and it works as described, I've just taken out the License print statement since you have it in the readme, and our code should automatically print something similair if there's a License issue anyway.
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Summary
Why
The existing examples do not show how to retrieve full atom-site occupancy/disorder metadata from the CSD Python API and reconstruct a CIF with explicit disorder tags for downstream workflows
This example was adapted from a broader open-source workflow developed in MolCrysKit. That project uses the same occupancy/disorder extraction step for downstream disorder-resolution workflows, and I thought a minimal standalone example could also be helpful in this repository.