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name: input-data-and-features description: "Author, validate, and convert Protenix input JSON for proteins, nucleic acids, ligands, ions, paths, bonds, and constraints without running inference." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

Input Data and Features

Use this sub-skill when a task is about preparing Protenix input before prediction: authoring JSON jobs, validating entity blocks, choosing ligand encodings, checking MSA/template path fields, defining covalent bonds or constraints, or planning structure-to-JSON conversion.

Use This For

• Build the top-level list-of-jobs JSON with name, sequences, optional covalent_bonds, optional constraint, and optional modelSeeds.
• Author proteinChain, dnaSequence, rnaSequence, ligand, and ion entries with correct count, optional id, modifications, and sequence alphabets.
• Fill existing pairedMsaPath, unpairedMsaPath, and templatesPath fields without running MSA/template searches.
• Encode ligand CCD_, SMILES, and FILE_ forms, bare-code ions, polymer-ligand bonds, ligand-ligand bonds, contact constraints, and pocket constraints.
• Plan protenix json conversion from PDB/mmCIF/CIF or use conversion API signatures when an installed Protenix environment is available.

Route Elsewhere

• Run prediction, choose model variants, tune inference flags, or interpret output confidence files with ../cli-and-inference/SKILL.md.
• Generate missing protein MSA, template, or RNA MSA files with ../msa-template-and-prep/SKILL.md.
• Prepare training datasets, bioassembly caches, or training-time data schemas with ../training-and-data-pipeline/SKILL.md.

Start Here

1. Read references/input-json-schema.md for accepted job/entity/path/bond/constraint shapes and copyable snippets.
2. Run python scripts/validate_protenix_input_json.py scripts/protenix_minimal_input.json for a validator smoke test.
3. Run python scripts/validate_protenix_input_json.py INPUT.json --check-paths before handing authored JSON to prediction or preprocessing.
4. Read references/conversion-and-features.md for protenix json, cif_to_input_json, and feature-conversion behavior.
5. Read references/troubleshooting.md when JSON is rejected, paths are missing, chemistry parsing fails, or conversion output looks surprising.

Critical Reminders

• The top-level JSON value is always a list, even for one job.
• Entity numbers in bonds and constraints are 1-based positions in sequences, not chain IDs.
• Ligand values use CCD_, FILE_, or SMILES; ion values use bare codes such as MG or ZN.
• pairedMsaPath, unpairedMsaPath, and templatesPath should point to existing files, preferably by absolute path.
• protenix json converts structures to input JSON; it does not run prediction or generate missing MSA/template files.