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name: data-and-outputs description: "Validate OmegaFold FASTA inputs, inspect pseudo-MSA tensors, predict PDB output names, and interpret confidence stored as B-factors." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

OmegaFold Data and Outputs

Use this sub-skill when an agent needs to validate OmegaFold FASTA input, explain how pipeline.fasta2inputs converts sequences into pseudo-MSA cycles, predict output PDB file names, or interpret confidence values stored in PDB B-factor columns.

For end-to-end model inference commands, use inference CLI. For model construction, configs, and OmegaFold.forward, use model API.

Quick Routes

• Inspect FASTA parsing and output names safely with scripts/inspect_fasta_pipeline.py; it imports omegafold.pipeline, runs CPU-only fasta2inputs, and never downloads weights or runs the model.
• Check accepted FASTA syntax, residue normalization, pseudo-MSA tensor keys/shapes, output naming, and PDB confidence semantics in references/data-formats.md.
• Use Python APIs with parameter details, return contracts, examples, and gotchas in references/api-reference.md.
• Debug malformed FASTA, invalid residues, long headers, missing output directories, Biopython/PDB writer problems, empty outputs, and B-factor interpretation with references/troubleshooting.md.

Safe Inspection Pattern

Run the bundled helper before full inference when input/output behavior is unclear:

python sub-skills/data-and-outputs/scripts/inspect_fasta_pipeline.py --write-tiny-pdb

The helper creates a tiny FASTA unless --fasta is provided, prints sequence count, normalized residue indices, p_msa/p_msa_mask shapes for every cycle, predicted PDB paths, and optionally writes a tiny synthetic PDB through pipeline.save_pdb.

Ownership Boundaries

This sub-skill owns FASTA parsing, pseudo-MSA input preparation, output file naming, save_pdb, atom14 writer expectations, and confidence-as-B-factor explanations. It intentionally does not cover weight downloads, accelerator selection, resource flags, or full prediction commands; route those to inference CLI.