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name: inputs-and-formats description: "Prepare and validate ColabFold FASTA, CSV, A3M, AlphaFold3 molecule, and PDB/mmCIF inputs before MSA search or prediction." disable-model-invocation: true metadata: disco-role: operating license: MIT

ColabFold inputs and formats

Use this sub-skill when the task is about making ColabFold input files valid, explaining how get_queries will read them, serializing A3M content, or extracting sequence/template-ready content from PDB/mmCIF files.

Route by task

• FASTA, CSV, TSV, or directory inputs: use data-formats.md to choose file layout, multimer syntax, sorting, and naming behavior.
• AlphaFold3 non-protein components: use data-formats.md for dna|, rna|, ccd|, and smiles| entries, including SMILES semicolon escaping.
• Parser/API behavior: use api-reference.md for parse_fasta, classify_molecules, get_queries, msa_to_str, and pdb_to_string signatures and return shapes.
• Input validation: run scripts/validate_colabfold_input.py before recommending expensive search or prediction.
• Format failures: use troubleshooting.md for optional dependency, backend, data/config, CLI/API, and workflow failures owned by input preparation.

Safe validation commands

python sub-skills/inputs-and-formats/scripts/validate_colabfold_input.py input.fasta
python sub-skills/inputs-and-formats/scripts/validate_colabfold_input.py input.csv --sort none
python sub-skills/inputs-and-formats/scripts/validate_colabfold_input.py msas/ --sort msa_depth --json

The validator only reads local input files, imports lightweight ColabFold parsing helpers when available, and performs no network, database, GPU, prediction, relaxation, or destructive actions.

Boundaries

• For generating/searching MSAs, route to ../msa-search/SKILL.md.
• For colabfold_batch model execution, templates during prediction, and output ranking, route to ../batch-prediction/SKILL.md.
• For Amber relaxation, PDB/mmCIF output inspection after prediction, confidence plots, and citations, route to ../relaxation-and-outputs/SKILL.md.

Do not send future agents back to the source repository for input syntax; this sub-skill distills the needed parser and format behavior into bundled references and scripts.